diff --git a/RELEASE_NOTES b/RELEASE_NOTES index b59315652429bc5fb771a924d56aaea83e94a310..13ba90be8d0131e9cc6b19744b60c8b44129d310 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,102 @@ 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 3,689 easyconfig files, for 611 different software packages, -33 different (compiler) toolchains and 8 software bundles. +The latest version of easybuild-easyconfig provides 4,260 easyconfig files, for 692 different software packages, +34 different (compiler) toolchains, 12 software bundles and 1 meta-package. + +v2.3.0 (September 2nd 2015) +--------------------------- + +feature + bugfix release +- added example easyconfig files for 19 new software packages: + ATK (#1780), Atkmm (#1780), cairomm (#1780), GLibmm (#1780), GlobalArrays (#1868), gdk-pixbuf (#1780), + gtk+ (#1780), Gtkmm (#1780), libbeef (#1827), libsigc++ (#1780), libsodium (#1876), MACS (#1869), MCR (#1677), + Molpro (#1880), NFFT (#1921), p7zip (#1931), Pangomm (#1780), pygraphviz (#1861), pycosat (#1859) +- added new easyconfigs for existing toolchains: GNU/4.9.3-2.25 (#1836), foss/2015b (#1695), intel/2015b (#1696) + add easyconfigs using this toolchain for BLAST+ 2.2.31, Boost 1.58.0, CP2K 2.6.1, OpenFOAM 2.3.1, + Perl 5.20.2 + 5.22.0 (bare), Python 2.7.10, R 3.2.1 +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... + including Boost 1.59.0, CP2K 2.6.1, GCC 5.2.0 +- various other enhancements, including: + - enhance texinfo easyconfig w.r.t. texmf, only use it as a build dependency (#1840) + - enable building of ld.gold in binutils 2.25 (#1885) +- various bug fixes, including: + - fix enabling MPI support for h5py 2.5.0 (#1825) + - fix versions of Bioconductor packages + add a couple extra (#1828, #1852, #1895, #1917) + - put dummy values in place for builddir/installdir templates in easyconfigs unit tests (#1835) + - fix easyconfigs unit tests w.r.t. changes made in framework (#1853, #1870, #1874, #1875) + - add GMP as missing dep in Python 2.7.10 easyconfigs, required for pycrypto extension (#1858) + - specify installation prefix for SIP (#1888, #1892) + - add custom sanity check paths in various easyconfigs (#1889, #1894, #1897 - #1909) + - required because of fix in EasyBuild framework, causing default sanity check paths to be considered + for extensions that are installed as a module + - affected easyconfigs include: AnalyzeFMRI, Biggus, bibtexparser, DB_File, DBD-Pg, DBD-SQLite, DBD-mysql, + evmix, fmri, FPM, GraphViz, gsl, GSSAPI, MDP, mpi4py, ncdf, ncdf4, netifaces, NetLibIDN, networkx, + ordereddict, Parallel-ForkManager, paycheck, PyQuante, Pyke, PyQt, r2py, rjags, runjags, scikit-learn, + SOBAcl, vsc-processcontrol, vsc-mympirun-scoop, XML, XML-Dumper, XML-Parser, XML-Twig, YAML-Syck + - don't enable 'static' toolchain option in SuiteSparse 4.4.3 easyconfig (#1911) + - add --exclude unpack options for OpenFOAM 2.3.1 to avoid cyclic symlink causing problems when unpacking (#1925) + +v2.2.0 (July 15th 2015) +----------------------- + +feature + bugfix release +- added example easyconfig files for 62 new software packages: + ADF (#899), AutoDock_Vina (#808), bibtexparser (#1726), Biggus (#1770), Bismark (#990), blasr (#1662), BSMAP (#1171), + Check (#811), Circuitscape (#1222), CONTRAfold (#689), cramtools (#1741), DBD-Pg (#1066), DendroPy (#995), + EMAN2 (#1737), ETSF_IO (#727), eudev (#1578), fastqc (#1636), FDS (#814, #1617, #1625), FPM (#1440), + frealign (#1619), g2log (#1035), GC3Pie (#1692, #1756, #1768), GenotypeHarmonizer (#1672), gensim (#1762), + GraphViz (#1658), hisat (#1674), IDBA-UD (#1045), IMa2 (#828), IMPUTE2 (#824), JUBE (#1396), LAMARC (#760), + libXScrnSaver (#1653), MATIO (#1004), MuTect (#1483), ncdf (#617), NEMO (#1640), ngspice (#1116), + ordereddict (#1774), OSU Micro-Benchmarks (#1777), Parallel-ForkManager (#847), pBWA (#1009), PeakSeq (#1412), + Pillow (#1702), Pindel (#1126), PLUMED (#1596, #1665), PostgreSQL (#1066), PROJ (#1006), PyAMG (#1222), Pyke (#1776), + rpy2 (#1775), Sailfish (#1035), SCANMS (#1386), Seaborn (#1763), snpEff (#1680), SOBAcl (#1658), + SPIDER (#1624, #1723), STAR (#1043, #1676), system GCC (#1778), tabix (#1059), tecplot360ex (#1100), Vampir (#512), + VampirServer (#512), verifyBamID (#1675) +- added easyconfigs for 4 new software bundles: + R-bundle-Bioconductor (#1573, #1795), R-bundle-devtools (#1621, #1759), R-bundle-extra (#1387, #1759), + R-bundle-pbd (#1659) +- added easyconfigs for new GNU toolchain (#1346, #1669) +- added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06 +- added example easyconfig for generating buildenv module (#1503) +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... + including BLAST 2.2.31+, Clang 3.6.1, CUDA 6.x, GCC 4.9.3, GROMACS 5.0.5, HDF5 1.8.15 + 1.8.15-patch1, + Python 2.7.10, R 3.2.0 + 3.2.1, WRF 3.6.1 +- various other enhancements, including: + - update all ncurses easyconfigs to enable ncursesw and use ConfigureMake easyblock (#1337) + - update PDT easyconfigs to use PDT easyblock (#1687) + - add custom sanity_check_paths in libxml2 easyconfigs (#1690) + - enhance unit tests to also cover EasyConfig.dump() method on all easyconfigs (#1761) + - include snappy as dependency in Hadoop easyconfigs (#1758, #1773) + - enable SSL support in CMake v3.2.3 easyconfigs (#1784) + - add additional extensions in R easyconfigs (#1637) +- various bug fixes, including: + - add patch file required for correct CUDA-aware OpenMPI v1.7.3 build (#631) + - fix issue with OpenMPI dependency in ECore easyconfigs (#777) + - don't run the Bloom tests for Jellyfish, they can randomly fail (#1016) + - fix source URLs in BioPerl easyconfigs (#1075) + - patch out svnversion command in Python 2.5.6 to fix build on recent systems (#1576) + - consistently use https for PyPI URLs in homepage/source_urls (#1616, #1722) + - include Tcl and Tk as dependencies in R easyconfig (#1623) + - add patch for installing paycheck as Py3 extension (#1629) + - add Perl dependency in git 2.x easyconfigs (#1631) + - fix easyconfig for GMP 6.0.0, don't use 6.0.0a sources (#1635) + - fix source_urls in QuantumESPRESSO 5.0.2 easyconfigs (#1652) + - include Tk as dependency in Python 2.7.9 easyconfigs (#1654) + - include tk-devel is list of OS deps for Python 2.7.9 Cray easyconfigs, make sure 'import Tkinter' works (#1655) + - drop gpfs versionsuffix and stop using no longer existing --enable-gpfs configopt for recent HDF5 versions (#1657) + - include missing libxml2 dep in GLib easyconfigs (#1666) + - fix source URLs in Qt easyconfigs (#1673) + - fix source URLs for argparse Python extension (#1697) + - fix source URLs for deap Python extension (#1699) + - fix easyconfigs unit tests after making ModulesTool a non-singleton class (#1708) + - fix names for Xmipp easyconfigs and patches (#1719) + - add patch for Qt 4.8.6 to fix build issue on RHEL6 with intel/2015a (#1734) + - add M4 as build dep for GCC 5.1.0 (#1735) + - fix Bioconductor extension versions in R 3.1.3 easyconfigs (#1748) + - remove custom exts_filter definition from Python 3.4.3 easyconfig (#1765) + - fix source_urls in netCDF easyconfigs (#1766) + - fix source_urls in netCDF-C++ and netCDF-Fortran easyconfigs (#1767) v2.1.1 (May 18th 2015) ---------------------- diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a-incl-deps.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a-incl-deps.eb new file mode 100644 index 0000000000000000000000000000000000000000..a8aa4213454f04b7d0ecb32328d04ab22b0b9afb --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a-incl-deps.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '7.10.4' +versionsuffix = '-incl-deps' + +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': '2015a'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bfc76a5f93c3f148c049f57541864e76'] + +configopts = "--with-mpi-prefix=$EBROOTIMPI/intel64 --with-trio-flavor='etsf_io+netcdf' " +configopts += "--with-dft-flavor='atompaw+bigdft+libxc+wannier90' " +configopts += '--with-linalg-flavor=mkl --with-linalg-libs="-L$LAPACK_LIB_DIR $LIBLAPACK" ' +configopts += '--enable-mpi=yes --with-mpi-level=2 --enable-mpi-io=yes ' +configopts += '--with-fft-flavor=fftw3-mkl --with-fft-libs="-L$FFT_LIB_DIR $LIBFFT" ' +configopts += '--with-fft-incs=-I$FFT_INC_DIR/fftw ' +configopts += '--enable-gw-dpc="yes" --enable-64bit-flags="yes" ' + +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-7.10.4-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7561f6f45cc051b43e53ace2de02af23b41a794f --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '7.10.4' + +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': '2015a'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bfc76a5f93c3f148c049f57541864e76'] + +configopts = "--with-mpi-prefix=$EBROOTIMPI/intel64 --with-trio-flavor='etsf_io+netcdf' --with-dft=flavor='libxc' " +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include -I$EBROOTNETCDFMINFORTRAN/include" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff" ' +configopts += '--with-libxc-incs="-I$EBROOTLIBXC/include" --with-libxc-libs="-L$EBROOTLIBXC/lib -lxc" ' + +dependencies = [ + ('libxc', '2.2.2'), + ('netCDF', '4.3.2'), + ('netCDF-Fortran', '4.4.0'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..97bc886c26c88a54f6f93bb0ae7597a9de37b389 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '7.11.6' + +homepage = 'http://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, charge density and + electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional + Theory (DFT), using pseudopotentials and a planewave or wavelet basis.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c8b166ec8e65ad1d795d42b889fd772b'] + +configopts = "--with-mpi-prefix=$EBROOTIMPI/intel64 --with-trio-flavor='etsf_io+netcdf' --with-dft=flavor='libxc' " +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include -I$EBROOTNETCDFMINFORTRAN/include" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff" ' +configopts += '--with-libxc-incs="-I$EBROOTLIBXC/include" --with-libxc-libs="-L$EBROOTLIBXC/lib -lxc" ' + +dependencies = [ + ('libxc', '2.2.2'), + ('netCDF', '4.3.2'), + ('netCDF-Fortran', '4.4.0'), +] + +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-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..4d319523acef9584081e14f56c2b426f7d692824 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb @@ -0,0 +1,40 @@ +## +# 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 = 'ABINIT' +version = '7.4.3' +versionsuffix = '-ETSF_IO-1.0.4' + +homepage = 'http://www.abinit.org/' +description = """Abinit is a plane wave pseudopotential code for doing + condensed phase electronic structure calculations using DFT.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '--enable-mpi --enable-mpi-io --with-mpi-prefix=$EBROOTOPENMPI --enable-fallbacks ' +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff" ' +configopts += '--with-fft-libs="-L$EBROOTFFTW/lib -lfftw3 -lfftw3f" --with-fft-flavor=fftw3 ' +configopts += '--with-trio-flavor="netcdf+etsf_io" --enable-gw-dpc' + +dependencies = [ + ('netCDF', '4.1.3'), + ('ETSF_IO', '1.0.4'), +] + +sanity_check_paths = { + 'files': ["bin/abinit"], + 'dirs': [] +} + +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 new file mode 100644 index 0000000000000000000000000000000000000000..20c30c8e6291466a063743c95a346c88a54af5b8 --- /dev/null +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,41 @@ +## +# 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/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'ABySS' +version = '1.3.7' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.bcgsc.ca/platform/bioinfo/software/abyss' +description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +# eg. http://www.bcgsc.ca/downloads/abyss/abyss-1.3.4.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.bcgsc.ca/downloads/abyss/'] + +dependencies = [ + ('sparsehash', '2.0.2'), + ('Boost', '1.58.0', versionsuffix), +] + +preconfigopts = 'CPPFLAGS=-I$EBROOTSPARSEHASH/include' + +sanity_check_paths = { + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..c055778c8e3e05e3a5576bff202b90062d934395 --- /dev/null +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.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:: Maxime Schmitt , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'ABySS' +version = '1.5.2' + +homepage = 'http://www.bcgsc.ca/platform/bioinfo/software/abyss' +description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] + +dependencies = [('Boost', '1.53.0')] + +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 new file mode 100755 index 0000000000000000000000000000000000000000..6395f17b38d2e35896d2b5a8e14737237cebecd2 --- /dev/null +++ b/easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb @@ -0,0 +1,20 @@ +easyblock = 'Tarball' + +name = "ADF" +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'} + +sources = ['%(namelower)s%(version)s.bin.tgz'] + +dependencies = [('impi', '3.2.2.006')] + +sanity_check_paths = { + 'files': ['bin/adf', 'bin/adf.exe'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb b/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c98e31bbfaef1d9397ee0811dee65fecff6740c6 --- /dev/null +++ b/easybuild/easyconfigs/a/AFNI/AFNI-20150717-intel-2015a.eb @@ -0,0 +1,66 @@ +easyblock = 'ConfigureMake' + +name = 'AFNI' +version = '20150717' + +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': '2015a'} +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 = ['985ce725a68c7b498e3402fd52b41811'] + +patches = ['AFNI-%(version)s_omp-pragma-statement-fix.patch'] + +libx11suff = '-libX11-1.6.3' + +pyver = '2.7.9' +majpyver = '.'.join(pyver.split('.')[:2]) +dependencies = [ + ('tcsh', '6.19.00'), + ('libXp', '1.0.3'), + ('libXt', '1.1.4', libx11suff), + ('libXpm', '3.5.11'), + ('libXmu', '1.1.2', libx11suff), + ('motif', '2.3.4', libx11suff), + ('R', '3.1.2'), + ('PyQt', '4.11.4', '-Python-%s' % pyver), + ('expat', '2.1.0'), + ('libpng', '1.6.16'), + ('libjpeg-turbo', '1.4.0'), + ('GSL', '1.16'), + ('GLib', '2.40.0'), # 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="$EBROOTEXPAT/lib/libexpat.a" LDPYTHON="-lpython%s" ' % majpyver +buildopts += 'CC="${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%s ' % majpyver +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/AFNI/AFNI-20150717_omp-pragma-statement-fix.patch b/easybuild/easyconfigs/a/AFNI/AFNI-20150717_omp-pragma-statement-fix.patch new file mode 100644 index 0000000000000000000000000000000000000000..7f3c8a8c0772026b1e44aa1142fa550e0a7822a1 --- /dev/null +++ b/easybuild/easyconfigs/a/AFNI/AFNI-20150717_omp-pragma-statement-fix.patch @@ -0,0 +1,36 @@ +diff -ru afni_src.orig/thd_dset_to_vectim.c afni_src/thd_dset_to_vectim.c +--- afni_src.orig/thd_dset_to_vectim.c 2015-04-02 02:35:57.000000000 +0200 ++++ afni_src/thd_dset_to_vectim.c 2015-04-03 17:08:33.340433024 +0200 +@@ -74,8 +74,9 @@ + + if( ignore > 0 ){ /* extract 1 at a time, save what we want */ + ++ float *var; + #pragma omp critical (MALLOC) +- float *var = (float *)malloc(sizeof(float)*(nvals+ignore)) ; ++ var = (float *)malloc(sizeof(float)*(nvals+ignore)) ; + for( kk=iv=0 ; iv < nvox ; iv++ ){ + if( mmm[iv] == 0 ) continue ; + (void)THD_extract_array( iv , dset , 0 , var ) ; +@@ -296,8 +297,9 @@ + + if( nvals < DSET_NVALS(dset) ){ /* extract 1 at a time, save what we want */ + ++ float *var; + #pragma omp critical (MALLOC) +- float *var = (float *)malloc(sizeof(float)*(DSET_NVALS(dset))) ; ++ var = (float *)malloc(sizeof(float)*(DSET_NVALS(dset))) ; + for( kk=iv=0 ; iv < nvox ; iv++ ){ + if( mmm[iv] == 0 ) continue ; + (void)THD_extract_array( iv , dset , 0 , var ) ; +@@ -463,8 +465,9 @@ + + if( ignore > 0 ){ /* extract 1 at a time, save what we want */ + ++ float *var; + #pragma omp critical (MALLOC) +- float *var = (float *)malloc(sizeof(float)*(nvals+ignore)) ; ++ var = (float *)malloc(sizeof(float)*(nvals+ignore)) ; + mmmt = mmmv[0]; + for( kk=iv=0 ; iv < nvoxv[0] ; iv++ ){ + if( mmmt[iv] == 0 ) continue ; diff --git a/easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-16.2.eb b/easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-16.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..7497b3bc67cfa74d2d43207e19fc5e65f699b7e9 --- /dev/null +++ b/easybuild/easyconfigs/a/ANSYS_CFD/ANSYS_CFD-16.2.eb @@ -0,0 +1,15 @@ +easyblock = 'EB_FLUENT' + +name = 'ANSYS_CFD' +version = '16.2' + +homepage = 'http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics' +description = """ANSYS computational fluid dynamics (CFD) simulation software allows you to predict, with confidence, + the impact of fluid flows on your product throughout design and manufacturing as well as during end use. + ANSYS renowned CFD analysis tools include the widely used and well-validated ANSYS Fluent and ANSYS CFX.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['FLUIDSTRUCTURES_162_LINX64.tar'] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..b32cf6ce866655f800a12a2ba3b2d6bb3105eca9 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = '2.7.7' + +homepage = "http://www.antlr2.org" +description = """ANother Tool for Language Recognition""" + +toolchain = {'name': 'ictce', 'version': '5.4.0'} + +source_urls = ['http://www.antlr2.org/download'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['ANTLR-%(version)s_cpp-headers.patch'] + +dependencies = [('Java', '1.7.0_60', '', True)] + +configopts = "--disable-examples --disable-csharp" + +sanity_check_paths = { + 'files': ['bin/antlr'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..5cf3b03e646eb9b7cac45584217aef4f95b6069f --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = '2.7.7' + +homepage = "http://www.antlr2.org" +description = """ANother Tool for Language Recognition""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://www.antlr2.org/download'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['ANTLR-%(version)s_cpp-headers.patch'] + +dependencies = [('Java', '1.7.0_60', '', True)] + +configopts = "--disable-examples --disable-csharp" + +sanity_check_paths = { + 'files': ['bin/antlr'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7_cpp-headers.patch b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7_cpp-headers.patch new file mode 100644 index 0000000000000000000000000000000000000000..e10f61e6d6a846cfe16a768bfd053c9c712070b5 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7_cpp-headers.patch @@ -0,0 +1,11 @@ +--- antlr-2.7.7/lib/cpp/antlr/CharScanner.hpp 2006-11-02 10:37:17.000000000 +1300 ++++ antlr-2.7.7/lib/cpp/antlr/CharScanner.hpp 2014-08-25 13:06:46.541050000 +1200 +@@ -10,6 +10,8 @@ + + #include + ++#include ++#include + #include + + #ifdef HAS_NOT_CCTYPE_H diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.5.4-foss-2015a.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.4-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7eb29d95957b950559ef701e4b6e5000c0d67056 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.5.4-foss-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'APR-util' +version = '1.5.4' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('APR', '1.5.2'), + ('SQLite', '3.8.8.1'), + ('expat', '2.1.0'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT " + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.so", "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.5.2-foss-2015a.eb b/easybuild/easyconfigs/a/APR/APR-1.5.2-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..fdaff97c8e7debb3d5dc2488afb870c47278c761 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.5.2-foss-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'APR' +version = '1.5.2' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'foss', 'version': '2015a'} + +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/ATK/ATK-2.16.0-intel-2015a.eb b/easybuild/easyconfigs/a/ATK/ATK-2.16.0-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6fc5e6597fb373e6ff6709fd24632c9e4f3c9df3 --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.16.0-intel-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'ATK' +version = '2.16.0' + +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': '2015a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.41.2'), +] + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/AnalyzeFMRI/AnalyzeFMRI-1.1-15-ictce-4.0.10-R-2.15.2.eb b/easybuild/easyconfigs/a/AnalyzeFMRI/AnalyzeFMRI-1.1-15-ictce-4.0.10-R-2.15.2.eb index cb3b9b70fd7cccc6b3b8b651c910cc73a73ec131..809adaa54bdd2a0192b551bc61b594dabe8b05d4 100644 --- a/easybuild/easyconfigs/a/AnalyzeFMRI/AnalyzeFMRI-1.1-15-ictce-4.0.10-R-2.15.2.eb +++ b/easybuild/easyconfigs/a/AnalyzeFMRI/AnalyzeFMRI-1.1-15-ictce-4.0.10-R-2.15.2.eb @@ -19,9 +19,14 @@ versionsuffix = '-%s-%s' % (r, rver) tcltkver = '8.5.12' dependencies = [ - (r, rver), - ('Tcl', tcltkver), - ('Tk', tcltkver), - ] + (r, rver), + ('Tcl', tcltkver), + ('Tk', tcltkver), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnalyzeFMRI'], +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/AnalyzeFMRI/AnalyzeFMRI-1.1-15-ictce-5.3.0-R-2.15.2.eb b/easybuild/easyconfigs/a/AnalyzeFMRI/AnalyzeFMRI-1.1-15-ictce-5.3.0-R-2.15.2.eb index b66dfc2b4c567e3f0330b6a8afa99a4e956bccb5..530418299d12ced6aa4fe73232096d3a7dfc5b4a 100644 --- a/easybuild/easyconfigs/a/AnalyzeFMRI/AnalyzeFMRI-1.1-15-ictce-5.3.0-R-2.15.2.eb +++ b/easybuild/easyconfigs/a/AnalyzeFMRI/AnalyzeFMRI-1.1-15-ictce-5.3.0-R-2.15.2.eb @@ -20,9 +20,14 @@ versionsuffix = '-%s-%s' % (r, rver) tcltkver = '8.5.12' dependencies = [ - (r, rver), - ('Tcl', tcltkver), - ('Tk', tcltkver), - ] + (r, rver), + ('Tcl', tcltkver), + ('Tk', tcltkver), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnalyzeFMRI'], +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/Aspera-Connect/Aspera-Connect-3.6.1.eb b/easybuild/easyconfigs/a/Aspera-Connect/Aspera-Connect-3.6.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..d5fdd133768be171908002e677cf8bb33e68fef9 --- /dev/null +++ b/easybuild/easyconfigs/a/Aspera-Connect/Aspera-Connect-3.6.1.eb @@ -0,0 +1,24 @@ +easyblock = 'Binary' + +name = 'Aspera-Connect' +version = '3.6.1' + +homepage = 'http://downloads.asperasoft.com/connect2/' +description = """Connect is an install-on-demand Web browser plug-in that facilitates high-speed uploads and + downloads with an Aspera transfer server.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://download.asperasoft.com/download/sw/connect/%(version)s/'] +sources = ['%(namelower)s-%(version)s.110647-linux-64.tar.gz'] + +# install script has ~/.aspera/connect hardcoded, but this can be overridden by redefining $HOME +install_cmd = "tar xfvz %(namelower)s*.tar.gz && HOME=%(builddir)s ./%(namelower)s*.sh && " +install_cmd += "cp -a %(builddir)s/.aspera/connect/* %(installdir)s" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ascp', 'asperaconnect', 'asperaconnect.bin', 'asperacrypt', 'asunprotect']], + 'dirs': ['lib'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/Atkmm/Atkmm-2.22.7-intel-2015a.eb b/easybuild/easyconfigs/a/Atkmm/Atkmm-2.22.7-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..946d69a7a2ec1056e5d382343fae2eff17bd3b87 --- /dev/null +++ b/easybuild/easyconfigs/a/Atkmm/Atkmm-2.22.7-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Atkmm' +version = '2.22.7' + +homepage = 'https://developer.gnome.org/ATK/stable/' +description = """ + Atkmm is the official C++ interface for the ATK accessibility toolkit library. +""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLibmm', '2.41.2'), + ('ATK', '2.16.0'), +] + +sanity_check_paths = { + 'files': ['lib/libatkmm-1.6.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb b/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb new file mode 100644 index 0000000000000000000000000000000000000000..a27cf3bd195f755b9363dd8a834016928b2ac723 --- /dev/null +++ b/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.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 = "Tarball" + +name = 'AutoDock_Vina' +version = '1.1.2' +versionsuffix = '_linux_x86' + +homepage = 'http://vina.scripps.edu/index.html' +description = """ AutoDock Vina is an open-source program for doing molecular docking. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://vina.scripps.edu/download/'] +sources = ['%s_%s%s.tgz' % (name.lower(), version.replace('.','_'), versionsuffix)] + +sanity_check_paths = { + 'files': ["bin/vina_split", "bin/vina"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..90bf6609a6b7cc23d44be5221d05646f3a942981 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-4.9.3-2.25.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': 'GNU', 'version': '4.9.3-2.25'} + +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-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..af0a90aedb78be84b0e1efe9227d06447f610c05 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-5.1.0-2.25.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': 'GNU', 'version': '5.1.0-2.25'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('M4', '1.4.17')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan", + "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..1c089451d832b243a7aeb1334352d199c5b6385e --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.3-2.25.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': 'GNU', 'version': '4.9.3-2.25'} + +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-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..1d63ee839dff2a16ed598b167aadb9cc7255be4b --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-5.1.0-2.25.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': 'GNU', 'version': '5.1.0-2.25'} + +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-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..80fa06d91be10b6a435dc76d31a5eb6f2b253830 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.3-2.25.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': 'GNU', 'version': '4.9.3-2.25'} + +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-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..0d6c26a78c1a07f9750c421fff89738bf6c4a80f --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-5.1.0-2.25.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': 'GNU', 'version': '5.1.0-2.25'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/animation/animation-2.4-intel-2015b-R-3.2.1.eb b/easybuild/easyconfigs/a/animation/animation-2.4-intel-2015b-R-3.2.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..9260cfb55214dcc1475cbf563444566cdfebc519 --- /dev/null +++ b/easybuild/easyconfigs/a/animation/animation-2.4-intel-2015b-R-3.2.1.eb @@ -0,0 +1,32 @@ +easyblock = 'RPackage' + +name = 'animation' +version = '2.4' + +homepage = 'http://cran.r-project.org/web/packages/%(name)s' +description = """animation: A Gallery of Animations in Statistics and Utilities to Create Animations""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [ + 'http://cran.r-project.org/src/contrib/', + 'http://cran.r-project.org/src/contrib/Archive/$(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +r = 'R' +rver = '3.2.1' +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [ + (r, rver), + ('ffmpeg', '2.8'), + ('GraphicsMagick', '1.3.21'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['animation'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..b307dca6af305cabe58479ec0a0208b8304c2cf7 --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-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 +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.1' + +homepage = 'http://www.htslib.org/' +description = """ Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising + SNP and short indel sequence variants """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [('http://sourceforge.net/projects/samtools/files/samtools/%(version)s', 'download')] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +parallel = 1 + +skipsteps = ['configure'] + +installopts = ' prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bcftools", "plot-vcfstats", "vcfutils.pl"]], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..0c511d17e03a4508bcc0a4173ccbf2f508b61b60 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb @@ -0,0 +1,32 @@ +# Author: Maxime Schmitt, University of Luxembourg +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.23.0' + +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': 'goolf', 'version': '1.4.10'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.23.0/bedtools-2.23.0.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-goolf-1.7.20.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..dd1aec5c9264e916e3b02c050fc261913995855e --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-goolf-1.7.20.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': 'goolf', 'version': '1.7.20'} + +# 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/BLAST+/BLAST+-2.2.31-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-foss-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..a64fc6a528073ddaba00106a3b63deff86f0fbe4 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-foss-2015b-Python-2.7.10.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.2.31' +versionsuffix = '-Python-2.7.10' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] + +patches = ['%(name)s-2.2.30_basename-fixes.patch'] + +dependencies = [('Boost', '1.58.0', versionsuffix)] + +configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..e09b9fd29876e76b4e344581f4b17ff4e5b5b387 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015a-Python-2.7.10.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:: 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 = 'ConfigureMake' + +name = 'BLAST+' +version = '2.2.31' +versionsuffix = '-Python-2.7.10' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] + +patches = [ + '%(name)s-2.2.30_ictce-fixes.patch', + '%(name)s-2.2.30_basename-fixes.patch' +] + +dependencies = [('Boost', '1.58.0', versionsuffix)] + +configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..a150b8d6d94ebf2d2d6e3e8bf13806e687c6e290 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015b-Python-2.7.10.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:: 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 = 'ConfigureMake' + +name = 'BLAST+' +version = '2.2.31' +versionsuffix = '-Python-2.7.10' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] + +patches = [ + '%(name)s-2.2.30_ictce-fixes.patch', + '%(name)s-2.2.30_basename-fixes.patch' +] + +dependencies = [('Boost', '1.58.0', versionsuffix)] + +configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..1318374418384cf7a77e6cb10572e1311f0264e2 --- /dev/null +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'BSMAP' +version = '2.74' + +homepage = 'https://code.google.com/p/bsmap/' +description = """BSMAP is a short reads mapping software for bisulfite sequencing reads.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://bsmap.googlecode.com/files/'] +sources = [SOURCELOWER_TGZ] + +skipsteps = ['configure'] + +installopts = "DESTDIR=%(installdir)s" + +patches = [ + 'BSMAP-2.74_makefile-modif.patch', + 'BSMAP-2.74_parameters-cpp.patch', + 'BSMAP-2.74_samtools-deps.patch', +] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.7'), + ('SAMtools', '0.1.18'), +] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bsmap", "methratio.py", "sam2bam.sh"]], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch new file mode 100644 index 0000000000000000000000000000000000000000..daf84a74d5b368a4b53aba678bea4d8fa5ae3fd0 --- /dev/null +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch @@ -0,0 +1,22 @@ +Patch to point to the correct bin directory in the EASYBUILDINSTALLDIR and to +to the correct location of the ZLIB libraries +Thekla Loizou July 2015 +--- bsmap-2.74/makefile.orig 2012-09-20 23:01:57.000000000 +0300 ++++ bsmap-2.74/makefile 2014-12-16 09:24:16.033631393 +0200 +@@ -1,6 +1,6 @@ + CC= g++ + +-BIN = $(DESTDIR)/usr/bin ++BIN = $(DESTDIR)/bin + FLAGS= -DMAXHITS=1000 -DTHREAD -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -m64 + #FLAGS= -DMAXHITS=1000 -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -Wall -Wno-strict-aliasing -m64 + +@@ -16,7 +16,7 @@ + bsmap: $(OBJS1) + (cd samtools; make) + (cd gzstream; make) +- $(CC) $(FLAGS) $^ -o $@ $(THREAD) -lbam -lz -lgzstream ++ $(CC) $(FLAGS) $^ -o $@ $(THREAD) -lbam -L$(EBROOTZLIB)/lib -lz -lgzstream + rm -f *.o + + clean: diff --git a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_parameters-cpp.patch b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_parameters-cpp.patch new file mode 100644 index 0000000000000000000000000000000000000000..21007be7d35fda4929ec5ec8a016d6eea9e4147e --- /dev/null +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_parameters-cpp.patch @@ -0,0 +1,9 @@ +Patch to include unitstd.h in the parameters for cpp +Thekla Loizou July 2015 +--- param.cpp.orig 2014-12-08 22:13:01.439639000 +0200 ++++ param.cpp 2014-12-08 22:14:20.305028000 +0200 +@@ -1,3 +1,4 @@ ++#include + #include "param.h" + #include + diff --git a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_samtools-deps.patch b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_samtools-deps.patch new file mode 100644 index 0000000000000000000000000000000000000000..7475b92e928fc6a7324ae3ee69115797cda880b0 --- /dev/null +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_samtools-deps.patch @@ -0,0 +1,78 @@ +Patch to point to the correct locations of SAMTools dependencies +Thekla Loizou July 2015 +--- bsmap-2.74/samtools/Makefile.orig 2014-12-15 14:42:22.628493847 +0200 ++++ bsmap-2.74/samtools/Makefile 2014-12-15 14:42:51.729602124 +0200 +@@ -10,10 +10,11 @@ + bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \ + cut_target.o phase.o bam2depth.o + PROG= samtools +-INCLUDES= -I. ++INCLUDES= -I$(EBROOTNCURSES)/include -I$(EBROOTZLIB)/include -I. + SUBDIRS= . bcftools misc +-LIBPATH= +-#LIBCURSES= -lcurses # -lXCurses ++LIBPATH= -L$(EBROOTZLIB)/lib ++LIBCURSES= -L$(EBROOTNCURSES)/lib -lcurses -L$(EBROOTZLIB)/lib -lz # -lXCurses ++ + + .SUFFIXES:.c .o + +@@ -44,10 +45,10 @@ + $(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf $(LIBCURSES) -lm -lz + + razip:razip.o razf.o $(KNETFILE_O) +- $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz ++ $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -L$(EBROOTZLIB)/lib -lz + + bgzip:bgzip.o bgzf.o $(KNETFILE_O) +- $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -lz ++ $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -L$(EBROOTZLIB)/lib -lz + + razip.o:razf.h + bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h +@@ -73,10 +74,10 @@ + + + libbam.1.dylib-local:$(LOBJS) +- libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz ++ libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -L$(EBROOTZLIB)/lib -lz + + libbam.so.1-local:$(LOBJS) +- $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz ++ $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -L$(EBROOTZLIB)/lib -lz + + dylib: + @$(MAKE) cleanlocal; \ +--- bsmap-2.74/samtools/misc/Makefile.orig 2012-09-20 23:01:58.000000000 +0300 ++++ bsmap-2.74/samtools/misc/Makefile 2014-12-15 14:40:50.817493925 +0200 +@@ -28,13 +28,13 @@ + lib: + + seqtk:seqtk.o +- $(CC) $(CFLAGS) -o $@ seqtk.o -lm -lz ++ $(CC) $(CFLAGS) -o $@ seqtk.o -lm -L$(EBROOTZLIB)/lib -lz + + wgsim:wgsim.o +- $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz ++ $(CC) $(CFLAGS) -o $@ wgsim.o -lm -L$(EBROOTZLIB)/lib -lz + + md5fa:md5.o md5fa.o md5.h ../kseq.h +- $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz ++ $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -L$(EBROOTZLIB)/lib -lz + + md5sum-lite:md5sum-lite.o + $(CC) $(CFLAGS) -o $@ md5sum-lite.o +@@ -43,10 +43,10 @@ + $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c + + maq2sam-short:maq2sam.c +- $(CC) $(CFLAGS) -o $@ maq2sam.c -lz +- ++ $(CC) $(CFLAGS) -o $@ maq2sam.c -L$(EBROOTZLIB)/lib -lz ++ + maq2sam-long:maq2sam.c +- $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz ++ $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -L$(EBROOTZLIB)/lib -lz + + md5fa.o:md5.h md5fa.c + $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c diff --git a/easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..c3067d56444875e7ecc35b8af1027c50ade0746e --- /dev/null +++ b/easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,26 @@ +easyblock = "PythonPackage" + +name = 'Biggus' +version = '0.11.0' + +homepage = 'https://github.com/SciTools/biggus' +description = """Virtual large arrays and lazy evaluation.""" + +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)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s.egg' % (pyshortver, pyshortver)], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/Biggus/Biggus-0.5.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biggus/Biggus-0.5.0-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..c1cac11dccc977a6bb2a4beb5701a182e1739250 --- /dev/null +++ b/easybuild/easyconfigs/b/Biggus/Biggus-0.5.0-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,26 @@ +easyblock = "PythonPackage" + +name = 'Biggus' +version = '0.5.0' + +homepage = 'https://github.com/SciTools/biggus' +description = """Virtual large arrays and lazy evaluation.""" + +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)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/biggus' % pyshortver], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-goolf-1.4.10-Perl-5.16.3.eb index 35b31e9ad8b4f6ad8b5dbb2940125a24ad74b0e6..2de3974d8c3a969dfb258f37364ab8ae92dcd321 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-goolf-1.4.10-Perl-5.16.3.eb @@ -9,8 +9,8 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['bioperl-release-%s.tar.gz' % version.replace('.', '-')] perl = 'Perl' perlver = '5.16.3' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-4.1.13-Perl-5.16.3.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-4.1.13-Perl-5.16.3.eb index f16cc0e7a36d5844995a0593589f563e53e878ca..9d9654707f97c139be72a51bd97eb26150ece427 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-4.1.13-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-4.1.13-Perl-5.16.3.eb @@ -9,8 +9,8 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['http://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['bioperl-release-%s.tar.gz' % version.replace('.', '-')] perl = 'Perl' perlver = '5.16.3' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-5.3.0-Perl-5.16.3.eb index f989bdd896cb105756ad78d1e2f7b9bf35eae543..47381bc735760d2ba814389661af2ee683f6e0f2 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-5.3.0-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-5.3.0-Perl-5.16.3.eb @@ -9,8 +9,8 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['bioperl-release-%s.tar.gz' % version.replace('.', '-')] perl = 'Perl' perlver = '5.16.3' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-ictce-5.5.0-Perl-5.18.2.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-ictce-5.5.0-Perl-5.18.2.eb index b2c6b6f6298df908842ad858b9bac0831eca1a33..5954f543932b69c0cd8091683fb51238fd73cd43 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-ictce-5.5.0-Perl-5.18.2.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-ictce-5.5.0-Perl-5.18.2.eb @@ -9,8 +9,8 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ['http://www.cpan.org/modules/by-module/Bio/CJFIELDS/'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['release-%s.tar.gz' % version.replace('.', '-')] perl = 'Perl' perlver = '5.18.2' diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..337980614fbfd664844ef62098e2f683b84c0ed5 --- /dev/null +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb @@ -0,0 +1,31 @@ +## +# 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 = "Tarball" + +name = 'Bismark' +version = '0.10.1' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/bismark/' +description = """A tool to map bisulfite converted sequence reads and +determine cytosine methylation states""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ["http://www.bioinformatics.babraham.ac.uk/projects/bismark/"] +sources = ['%s_v%s.tar.gz' % (name.lower(), version) ] + +dependencies = [('Bowtie2', '2.0.2')] + +sanity_check_paths = { + 'files': ["bismark", "bismark2bedGraph", "bismark2report", "bismark_genome_preparation", + "bismark_methylation_extractor", "coverage2cytosine", "deduplicate_bismark"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..1fffb8736fc675f4f7b1cd3d40a6305c54f3cb07 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-5.4.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '2.7' + +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': 'ictce', 'version': '5.4.0'} + +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-2.7-ictce-6.1.5.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-6.1.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..deba4d2a79e3b05a8453b3cca08ca00976d45ba9 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-6.1.5.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '2.7' + +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': 'ictce', 'version': '6.1.5'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.16')] + +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-2.7-intel-2015a.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..48aa608e0d36475fea8d1e26b3928135a3726552 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '2.7' + +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': 'intel', 'version': '2015a'} + +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-3.0.2-foss-2014b.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..821e3cc963d55bbd146a32ebcbaf0ee0149e0e7a --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2014b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +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': 'foss', 'version': '2014b'} + +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-3.0.2-foss-2015a.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0b270e9381ff0a5d78465bfb4d59e94fb039abfb --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +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': 'foss', 'version': '2015a'} + +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-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2-binutils-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..41f43d9b034f0a08c57c7ac4e910d1d3a11c9c79 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.2-binutils-2.25.eb @@ -0,0 +1,26 @@ +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': '4.9.2-binutils-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + # use same binutils version that was used when building GCC 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-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..333050d11401954d56196fa35b2ce38cbd2ca114 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-4.9.3-binutils-2.25.eb @@ -0,0 +1,26 @@ +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-binutils-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + # use same binutils version that was used when building GCC 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-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-5.1.0-binutils-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..128617a43cc6ea7600e8cd7ec76fc032f4013572 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCC-5.1.0-binutils-2.25.eb @@ -0,0 +1,26 @@ +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': '5.1.0-binutils-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + # use same binutils version that was used when building GCC 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-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..22f9944d4d63fdacbc1e5130650db25e6ac25fde --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GNU-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': 'GNU', '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.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..7828372bd5e8e43a10b89961feea512d48c486df --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4.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': 'dummy', 'version': ''} + +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/Boost/Boost-1.55.0-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..8d26308267b848adc9509a6c86f27f2bf4ffe236 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2014b-Python-2.7.8.eb @@ -0,0 +1,26 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2014b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.8' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +osdependencies = ['zlib-devel'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..88a81a73e9b2486a7faef4d0ec8caad67229c1f4 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.55.0' + +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} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..644fd26b387107095983d8147dfeaacff0c6f555 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb @@ -0,0 +1,22 @@ +name = 'Boost' +version = '1.55.0' + +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} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = [SOURCEFORGE_SOURCE] + +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-foss-2015.05-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..24316a807ffee348d2e01f96a48b68baea3c3e6a --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..76622b0263731200d662f710e3a71d10d735c034 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.10.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +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} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.10' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..d4ec7f6e792823f85d4b3951c6b13896f7b6877d --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015b-Python-2.7.10.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.10' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..dba26f94f440c308d3b0d6e63e5957ce65c9c5b0 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20-Python-2.7.10.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +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} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = [SOURCEFORGE_SOURCE] + +pythonversion = '2.7.10' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..bee3eb38e4f0257abd6366b81280cde8cc99f98a --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.58.0' + +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} + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +source_urls = [SOURCEFORGE_SOURCE] + +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-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..d48f0872ddcc24a13d88d152bc431050aa8c328f --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.10' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..b3c4d08fadae83ea7f701f259d92801fe20afa0b --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.10' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..bdadbc8ed1231b7863b16da73f701b51d69669c5 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.59.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.10' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..d65dc97c6cd2e289478bfed6cbb17f4063f701dd --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.59.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.10' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..0240ff0e2c2cedef6f93bbf1400c72e9a3b3152b --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb @@ -0,0 +1,19 @@ +#Modified from existing version by: +#Robert Schmidt +#Ottawa Hospital Research Institute - Bioinformatics Team + +name = 'Bowtie' +version = '1.1.1' + +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': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, '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/Bowtie/Bowtie-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c3c415f11f0f8e3a050d0fc0c17b64f8f91b698d --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb @@ -0,0 +1,32 @@ +#Modified from existing version by: +#Robert Schmidt +#Ottawa Hospital Research Institute - Bioinformatics Team +easyblock = 'MakeCp' + +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': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://download.sourceforge.net/bowtie-bio/'] + +patches = ['int64typedef.patch'] + +buildopts = 'CC="$CC" CXX="$CXX" CPP="$CXX"' + +files_to_copy = [(['bowtie', 'bowtie-build', 'bowtie-inspect'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/bowtie', 'bin/bowtie-inspect'], + 'dirs': [], +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..30dfc1896056ea87807b8d7ae8625639c77340b0 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb @@ -0,0 +1,38 @@ +# 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 + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.5' + +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/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..cc4bd53b3af195625813f229498639fa5e1f0202 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb @@ -0,0 +1,38 @@ +# 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 + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.5' + +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': 'intel', 'version': '2015a'} + +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/bc/bc-1.06.95-GCC-4.8.2.eb b/easybuild/easyconfigs/b/bc/bc-1.06.95-GCC-4.8.2.eb index d9c14913b31a4c843abf80d2a0e18bb5b0b065fa..1d80e71daeeb30231fadbcdd9164da0eeed98815 100644 --- a/easybuild/easyconfigs/b/bc/bc-1.06.95-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/b/bc/bc-1.06.95-GCC-4.8.2.eb @@ -20,6 +20,8 @@ dependencies = [ ('libreadline','6.3'), ('flex','2.5.38'), ('Bison','3.0.2'), +] +builddependencies = [ ('texinfo','5.2'), ] diff --git a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..2ec986e1f9d7089c3d8582a765cc3509b4d362d5 --- /dev/null +++ b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'bibtexparser' +version = '0.5' + +homepage = 'https://github.com/sciunto-org/python-bibtexparser' +description = """Bibtex parser in Python 2.7 and 3.x""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/bibtexparser' % pyshortver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..43af690ca6d32b8bb427effca2aa225fe6372655 --- /dev/null +++ b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'bibtexparser' +version = '0.5' + +homepage = 'https://github.com/sciunto-org/python-bibtexparser' +description = """Bibtex parser in Python 2.7 and 3.x""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/bibtexparser' % pyshortver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..0473d2694fe1cbd3ff8a9bddbed62f2603c2da4e --- /dev/null +++ b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'bibtexparser' +version = '0.6.0' + +homepage = 'https://github.com/sciunto-org/python-bibtexparser' +description = """Bibtex parser in Python 2.7 and 3.x""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/bibtexparser' % pyshortver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..0cf333f02ab64a4a58ec3320b113fd0ffddf5819 --- /dev/null +++ b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'bibtexparser' +version = '0.6.0' + +homepage = 'https://github.com/sciunto-org/python-bibtexparser' +description = """Bibtex parser in Python 2.7 and 3.x""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/bibtexparser' % pyshortver], +} + +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 new file mode 100644 index 0000000000000000000000000000000000000000..1922cb5d1278e46e29a3390b39777eff79f9b58f --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb @@ -0,0 +1,35 @@ +## +# 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_07-02.html +## + +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.22' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils-2.22: GNU binary utilities" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +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-2.25-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 cb9289d4bea11666dbef657dc7c6d827ea9d1c64..82d314f4eb38810cd6a9e50c014c74ba6cc2ed8f 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 @@ -12,7 +12,11 @@ sources = [SOURCE_TAR_GZ] 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', '1.2.8'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils ('binutils', version, '', True) ] @@ -20,10 +24,11 @@ builddependencies = [ preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' -# make sure that system libraries are also considered by ld -configopts = '--with-sysroot=/' +# 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', 'nm', +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] sanity_check_paths = { 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 8aefcfeeee238bf5d4d0fbbd261313843d0a4ff9..5e6cdd80344d2e168c79830e0ca1eef4ca0f2a15 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 @@ -11,16 +11,23 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -builddependencies = [('zlib', '1.2.8')] +# 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', '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 -configopts = '--with-sysroot=/' +# 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', 'nm', +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'ld.gold', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] sanity_check_paths = { 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 new file mode 100644 index 0000000000000000000000000000000000000000..2df030c2398493e9329d8fc9eda40a989fe9e152 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.25' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCC', 'version': '4.9.3-binutils-%(version)s'} + +sources = [SOURCE_TAR_GZ] +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', '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' + +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-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..25962accc29521de0ab123087f3bdbb851dc4cbd --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.25' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCC', 'version': '5.1.0-binutils-%(version)s'} + +sources = [SOURCE_TAR_GZ] +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', '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' + +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 3c7395c4a929e6c669fca21a282481269ba267d3..b2c4f75fab2f87eca47960d96fbf30d8e70b9046 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -11,18 +11,23 @@ toolchain = {'name': 'dummy', 'version': ''} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -builddependencies = [('zlib', '1.2.8')] +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, 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 -configopts = '--with-sysroot=/' +# 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', 'nm', +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']], diff --git a/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..d339980b4f223943993e48e3ed58a9a18184a859 --- /dev/null +++ b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb @@ -0,0 +1,46 @@ +# With <3 for EasyBuild +# +# EasyConfig for BLASR: +# ---------------------------------------------------------------------------- +# Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Petar Forai +# ---------------------------------------------------------------------------- + +easyblock = 'MakeCp' + +name = 'blasr' +version = 'smrtanalysis-2.1' + +homepage = 'https://github.com/PacificBiosciences/blasr' +description = """BLASR (Basic Local Alignment with Successive Refinement) rapidly maps reads to genomes by finding the + highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio's + extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/PacificBiosciences/blasr/archive/'] + +patches = ['blasr-%(version)s_non-static.patch'] + +dependencies = [('HDF5', '1.8.9')] + +buildopts = 'HDF5INCLUDEDIR=${EBROOTHDF5}/include HDF5LIBDIR=${EBROOTHDF5}/lib' + +binaries = [ + 'wordCounter', 'printReadWordCount', 'blasr', 'sdpMatcher', 'swMatcher', 'kbandMatcher', 'sawriter', + 'saquery', 'samodify', 'printTupleCountTable', 'malign', 'cmpPrintTupleCountTable', 'removeAdapters', + 'tabulateAlignment', 'samatcher', 'sals', 'saprinter', 'buildQualityValueProfile', 'extendAlign', + 'guidedalign', 'pbmask', +] + +files_to_copy = [(['alignment/bin/%s' % x for x in binaries], 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binaries], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1_non-static.patch b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1_non-static.patch new file mode 100644 index 0000000000000000000000000000000000000000..03b7b3f2bbe519356f5a1674f87719487bddc34c --- /dev/null +++ b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1_non-static.patch @@ -0,0 +1,13 @@ +--- common.mk.orig 2013-11-08 15:19:36.848815000 +0100 ++++ common.mk 2013-11-08 15:19:54.854217000 +0100 +@@ -24,6 +24,7 @@ + ifeq ($(shell $(CC) -dumpversion | awk -F '.' '$$1*100+$$2>404{print "yes"}'),yes) + CPPOPTS += -fpermissive + endif +-ifneq ($(shell uname -s),Darwin) +- STATIC = -static +-endif ++# Why oh why ... ++#ifneq ($(shell uname -s),Darwin) ++# STATIC = -static ++#endif diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2015a.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0321acfcc558113ac0bb2f652de5ae87c9d60bd1 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2015a.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'intel', 'version': '2015a'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..ee1013b662110f74d64b4b16d06ac2d78ec5e04c --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GNU-4.9.3-2.25.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': 'GNU', 'version': '4.9.3-2.25'} +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-foss-2015.05.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..1c3c8d1851862117494715ee2a9c067517f8456f --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.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': 'foss', 'version': '2015.05'} +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-foss-2015b.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..1e97fbfcefae061fcc3c345c131aecf238a793e1 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015b.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': 'foss', 'version': '2015b'} +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-1.7.20.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..718daa2bc0c40a5dc9c35935e193c46b395e7922 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.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': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.bzip.org/%(version)s/'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2015b.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..b45764711d249f4b521fa08212c2b784f456fee0 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2015b.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': '2015b'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..624902da11d8e7357b4d943b4a89cf4bb0c87644 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.10.eb @@ -0,0 +1,28 @@ +name = 'CGAL' +version = '4.6' + +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': '2015a'} +toolchainopts = {'strict': True} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['https://gforge.inria.fr/frs/download.php/file/34150/'] + +pythonversion = '2.7.10' +versionsuffix = "-Python-%s" % pythonversion + +dependencies = [ + ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), + ('Boost', '1.58.0', versionsuffix), + ('MPFR', '3.1.2', '-GMP-6.0.0a'), + ('Qt', '4.8.6', '-GLib-2.44.0'), +] + +builddependencies = [ + ('CMake', '3.1.3'), +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..9226ece655f6704687dc8a22825d1f70d4f3bcac --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,28 @@ +name = 'CGAL' +version = '4.6' + +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': '2015a'} +toolchainopts = {'strict': True} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['https://gforge.inria.fr/frs/download.php/file/34150/'] + +pythonversion = '2.7.9' +versionsuffix = "-Python-%s" % pythonversion + +dependencies = [ + ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), + ('Boost', '1.58.0', versionsuffix), + ('MPFR', '3.1.2', '-GMP-6.0.0a'), + ('Qt', '4.8.6', '-GLib-2.44.0'), +] + +builddependencies = [ + ('CMake', '3.1.3'), +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..e6ea4f81d287da245aaa0491e8a9798f777beb95 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,29 @@ +name = 'CGAL' +version = '4.6' + +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': '2015a'} +toolchainopts = {'strict': True} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['https://gforge.inria.fr/frs/download.php/file/34150/'] + +pythonversion = '2.7.10' +versionsuffix = "-Python-%s" % pythonversion + +dependencies = [ +#GMP does not compile correctly with ICC on Haswell architecture + ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), + ('Boost', '1.58.0', versionsuffix), + ('MPFR', '3.1.2', '-GMP-6.0.0a'), + ('Qt', '4.8.6', '-GLib-2.44.0'), +] + +builddependencies = [ + ('CMake', '3.1.3'), +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..adb6a381670c335166942c009166527e061a339b --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.6-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,29 @@ +name = 'CGAL' +version = '4.6' + +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': '2015a'} +toolchainopts = {'strict': True} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['https://gforge.inria.fr/frs/download.php/file/34150/'] + +pythonversion = '2.7.9' +versionsuffix = "-Python-%s" % pythonversion + +dependencies = [ +#GMP does not compile correctly with ICC on Haswell architecture + ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), + ('Boost', '1.58.0', versionsuffix), + ('MPFR', '3.1.2', '-GMP-6.0.0a'), + ('Qt', '4.8.6', '-GLib-2.44.0'), +] + +builddependencies = [ + ('CMake', '3.1.3'), +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..155eb5a8aee415696369bf728fba55305175dfd7 --- /dev/null +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb @@ -0,0 +1,28 @@ +# Authors:: Ward Poelmans + +name = "CHARMM" +version = "37b2" + +homepage = "http://www.charmm.org" +description = """CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile +and widely used molecular simulation program with broad application to many-particle systems.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = ["c%(version)s.tar.gz"] + +patches = [ + "qmmm-pme-%(version)s.patch", + "use-xhost-%(version)s.patch", + "main-case-fix-%(version)s.patch", + 'CHARMM-37b2_fix-qgas-double-declared.patch', +] + +# MKL activated automatically when the ictce toolchain is used +build_options = "FULL COLFFT PIPF" + +# Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce +system_size = "medium" + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015b.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..417f7a87856a0351912c83ceb53806f1a5fc0a43 --- /dev/null +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015b.eb @@ -0,0 +1,28 @@ +# Authors:: Ward Poelmans + +name = 'CHARMM' +version = '37b2' + +homepage = "http://www.charmm.org" +description = """CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile +and widely used molecular simulation program with broad application to many-particle systems.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = ["c%(version)s.tar.gz"] + +patches = [ + "qmmm-pme-%(version)s.patch", + "use-xhost-%(version)s.patch", + "main-case-fix-%(version)s.patch", + 'CHARMM-37b2_fix-qgas-double-declared.patch', +] + +# MKL activated automatically when the ictce toolchain is used +build_options = "FULL COLFFT PIPF" + +# Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce +system_size = "medium" + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch new file mode 100644 index 0000000000000000000000000000000000000000..2c8d36a45f335744b44f9e69a330cabc63111b5b --- /dev/null +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch @@ -0,0 +1,53 @@ +reproduction of CHARMM SVN revision 272 (Check-in: http:/charmm.hanyang.ac.kr/6187) +renamed qgas variable in pbeq to qgas1 and updated references in energy +diff -ru c37b2.orig/source/energy/energy.src c37b2/source/energy/energy.src +--- c37b2.orig/source/energy/energy.src 2012-09-29 08:01:42.000000000 +0200 ++++ c37b2/source/energy/energy.src 2015-05-21 16:57:43.951197202 +0200 +@@ -266,7 +266,7 @@ + use param + use pathm + use mpathint, only: qpint, epint !##PATHINT +- use pbeq, only: qpbeq,qpbf,npbeq,qgsbp,pbforce,gsbp0,qgas,qsmbp,smbp0 !##PBEQ ++ use pbeq, only: qpbeq,qpbf,npbeq,qgsbp,pbforce,gsbp0,qgas1,qsmbp,smbp0 !##PBEQ + use pbound + use pert + use polarm, only: qpolar, polar1 !##POLAR +@@ -3203,7 +3203,7 @@ + + CALL PBFORCE(NATOM,X,Y,Z,CG,ETERM(PBELEC),ETERM(PBNP), & + DX,DY,DZ,NPBEQ,ecalls,.false. & +- ,QETERM(QMEL),ETERM(QMEL),QGAS & !##SCCDFTB ++ ,QETERM(QMEL),ETERM(QMEL),QGAS1 & !##SCCDFTB + ) + IF (TIMER.GT.1) & + CALL WRTTIM('Poisson Boltzmann Solvation energy times:') +diff -ru c37b2.orig/source/misc/pbeq.src c37b2/source/misc/pbeq.src +--- c37b2.orig/source/misc/pbeq.src 2012-08-08 20:08:30.000000000 +0200 ++++ c37b2/source/misc/pbeq.src 2015-05-21 16:55:47.871787533 +0200 +@@ -19,7 +19,7 @@ + !public :: pbeq0,pbforce,gsbp0,srdist + !QC: export more + public :: pbeq0,pbforce,gsbp0,srdist,m3,dm3,rpowerl2,cosmphi2,sinmphi2,& +- alpol2,dalpol2,lpol2,dlpol2,pbeq1,oldpbeq1,mayer,pbeq2,qgas, & ++ alpol2,dalpol2,lpol2,dlpol2,pbeq1,oldpbeq1,mayer,pbeq2,qgas1, & + pbeq_iniall,smbp0 + + !variables +@@ -115,7 +115,7 @@ + + ! The following is related to QM/MM implementation of gsbp and pb + ! Xiao_QC_UW0609 +- LOGICAL QPSC,QGAS ++ LOGICAL QPSC,QGAS1 + ##IF SCCDFTB + ! + ! COEFX -----> heap index for COEFX(NTPOL) +@@ -2734,7 +2734,7 @@ + ! XIAO_QC_UW0609 keyword for SCC/PB + MXTPSC = GTRMI(COMLYN,COMLEN,'MXPS',5000) + PSCTOL = GTRMF(COMLYN,COMLEN,'PSTL',1.0D-2) +- QGAS = INDXA(COMLYN,COMLEN,'IGAS').GT.0 ++ QGAS1 = INDXA(COMLYN,COMLEN,'IGAS').GT.0 + ! XIAO_QC_UW0609 add charge dependant radii + QCHDRAD = INDXA(COMLYN,COMLEN,'CHDR').GT.0 + IF (QCHDRAD) THEN 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 new file mode 100644 index 0000000000000000000000000000000000000000..9408c50361728c93b17344d0b374918fddb26230 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.2.0.5' + +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': '2015a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] + +builddependencies = [('CMake', '3.2.2')] + +separate_build_dir = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..08b9903802b50b1c48d02f63c0f8fda070122374 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.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': 'foss', 'version': '2014b'} + +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-3.0.0-foss-2014b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..872f8b4d7dab341b5923730930c018f6e49ac459 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.0.0' + +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': '2014b'} + +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-3.0.0-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c55a48656c2b7eba2de2ad9c1dc465c5857ab755 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.0.0' + +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': '2015a'} + +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-3.2.1-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.1-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..966a727842db8f89dfb08ee97ed8eef41e032975 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.1-GNU-4.9.3-2.25.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.1' + +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': 'GNU', 'version': '4.9.3-2.25'} + +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-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e6f905f4098a3847b4fe46f1617f55ba6220dd3c --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.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': 'foss', 'version': '2015a'} + +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-3.2.3-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5e1447f0f0fab7b743fad920befa5282f21791e7 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.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': 'intel', 'version': '2015a'} + +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-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b8e7064fcc563ab912f7b9fe48def82c5ae4b35d --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.1-intel-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.3.1' + +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': '2015a'} + +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-3.3.1.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..3107e6dbdffd82b11b418d575929710f4dbb7086 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.1.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.3.1' + +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': 'dummy', 'version': 'dummy'} + +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-3.3.2-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..86f4ad56814d99e8a4e1ede147df5cbb9f619847 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-GNU-4.9.3-2.25.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.3.2' + +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': 'GNU', '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', '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-3.3.2-intel-2015b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ba3ca2e1aa50f78fceb673090cf9999dfb8779e8 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.3.2-intel-2015b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.3.2' + +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': '2015b'} + +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/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..f772aaa29cdaed52dd453f8867154cee139cd1ad --- /dev/null +++ b/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-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 +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'CONTRAfold' +version = '2.02' + +homepage = 'http://contra.stanford.edu/contrafold/' +description = ''' CONditional TRAining for RNA Secondary Structure Prediction ''' + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [homepage] +sources = ['%s_v%s.tar.gz' % (name.lower(),version.replace('.','_'))] + +patches = ['contrafold-gcc47.patch'] + +start_dir = 'src' + +files_to_copy = [(['score_prediction', 'contrafold', 'score_directory.pl',\ + 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] + +sanity_check_paths = { + 'files': ['bin/score_prediction', 'bin/contrafold'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CONTRAfold/contrafold-gcc47.patch b/easybuild/easyconfigs/c/CONTRAfold/contrafold-gcc47.patch new file mode 100644 index 0000000000000000000000000000000000000000..d484c76bfdbecf7fd1479723f76090af68e69030 --- /dev/null +++ b/easybuild/easyconfigs/c/CONTRAfold/contrafold-gcc47.patch @@ -0,0 +1,20 @@ +--- contrafold.orig/src/Makefile 2008-08-14 02:08:30.000000000 +0200 ++++ contrafold/src/Makefile 2014-02-04 13:51:29.041589171 +0100 +@@ -1,6 +1,6 @@ + CXX = g++ + +-CXXFLAGS = -O3 -DNDEBUG -W -pipe -Wundef -Winline --param large-function-growth=100000 -Wall ++CXXFLAGS = -O3 -DNDEBUG -W -pipe -Wundef -Winline --param large-function-growth=100000 -Wall -fpermissive + LINKFLAGS = -lm + GDLINKFLAGS = -lgd -lpng + +--- contrafold.orig/src/Utilities.cpp 2008-08-14 02:08:31.000000000 +0200 ++++ contrafold/src/Utilities.cpp 2014-02-04 14:09:09.082650184 +0100 +@@ -2,6 +2,7 @@ + // Utilities.cpp + ////////////////////////////////////////////////////////////////////// + ++#include + #include "Utilities.hpp" + + bool toggle_error = false; diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-foss-2015b.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..9aa1e31e3dbeb72e03caf4b328cfeb6d0d65ffe7 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-foss-2015b.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.1' + +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': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.2'), +] + +builddependencies = [ + ('flex', '2.5.39', '', ('GNU', '4.9.3-2.25')), + ('Bison', '3.0.4', '', ('GNU', '4.9.3-2.25')), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-intel-2015b.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ec3d535442673108e3df63aea12b41f11f2040f8 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.1-intel-2015b.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.1' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.2'), +] + +builddependencies = [ + ('flex', '2.5.39', '', ('GNU', '4.9.3-2.25')), + ('Bison', '3.0.4', '', ('GNU', '4.9.3-2.25')), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20130228-intel-2015a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20130228-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..fd8d96a13d0cc18b5c58e4ae858a7e8bafbbc5cc --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20130228-intel-2015a.eb @@ -0,0 +1,36 @@ +name = 'CP2K' +version = '20130228' + +homepage = 'http://cp2k.berlios.de/index.html' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular +simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different +methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and +classical pair and many-body potentials. """ + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = ['CP2K-%(version)s.tar.gz'] + +patches = [ + 'CP2K-2013_fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch', +] + +dependencies = [ + ('FFTW', '3.3.3'), + ('Libint', '1.1.4'), +] + +builddependencies = [ + ('flex', '2.5.37'), + ('Bison', '2.7'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2013_fix_compile_date_lastcvs.patch b/easybuild/easyconfigs/c/CP2K/CP2K-2013_fix_compile_date_lastcvs.patch new file mode 100644 index 0000000000000000000000000000000000000000..7533a553087cd6b3bc47065640e9197379b3e7e7 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2013_fix_compile_date_lastcvs.patch @@ -0,0 +1,11 @@ +--- cp2k/makefiles/Makefile.orig 2013-02-04 17:55:57.000000000 +0100 ++++ cp2k/makefiles/Makefile 2013-02-05 17:55:06.811020304 +0100 +@@ -200,7 +200,7 @@ + # + ifeq ($(CPPSHELL),) + CPPSHELL := -D__COMPILE_ARCH="\"$(ARCH)\""\ +- -D__COMPILE_DATE="\"$(shell date)\""\ ++ -D__COMPILE_DATE="\"$(shell date | sed 's/ /_/g'))\""\ + -D__COMPILE_HOST="\"$(shell hostname)\""\ + -D__COMPILE_REVISION="\"$(strip $(REVISION))\"" + endif diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20150904-ifort-compiler-bug-fix.patch b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-ifort-compiler-bug-fix.patch new file mode 100644 index 0000000000000000000000000000000000000000..42ccd853c4a6962ad46c55bbaff650bebbc85812 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-ifort-compiler-bug-fix.patch @@ -0,0 +1,13 @@ +# workaround for ifort bug +# https://groups.google.com/forum/#!topic/cp2k/LorI2Z4pQgc +diff -ur cp2k-68331ef35b7890a8b05b9111660f57863af14df0.orig/cp2k/src/dbcsr/error/dbcsr_error_handling.F cp2k-68331ef35b7890a8b05b9111660f57863af14df0/cp2k/src/dbcsr/error/dbcsr_error_handling.F +--- cp2k-68331ef35b7890a8b05b9111660f57863af14df0.orig/cp2k/src/dbcsr/error/dbcsr_error_handling.F 2015-09-04 15:29:57.000000000 +0200 ++++ cp2k-68331ef35b7890a8b05b9111660f57863af14df0/cp2k/src/dbcsr/error/dbcsr_error_handling.F 2015-09-04 17:37:48.000000000 +0200 +@@ -20,7 +20,6 @@ + !$ USE OMP_LIB, ONLY: omp_get_max_threads, omp_get_thread_num, omp_get_num_threads + + IMPLICIT NONE +- PRIVATE + + ! procedures + PUBLIC :: dbcsr_error_set, dbcsr_error_stop diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..1e3ba56c1e0471293f0a9af95ce731ac7843bfd9 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20150904-intel-2015a-PLUMED-2.1.3.eb @@ -0,0 +1,42 @@ +name = 'CP2K' +version = '20150904' +versionsuffix = '-PLUMED-2.1.3' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +# we use the git mirror: this is r15816 or 68331ef35b7 +sources = ['68331ef35b7.zip'] +source_urls = ['https://github.com/cp2k/cp2k/archive/'] + +patches = [ + 'CP2K-%(version)s-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +# use short directory names to avoid 'argument list is too long' in build process +unpack_options = ' && mv cp2k-68331* cp2k' + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.1'), + ('PLUMED', '2.1.3'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +plumed = True + +# regression test reports failures +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb b/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb new file mode 100644 index 0000000000000000000000000000000000000000..76cb0b94f93ad8e194242f21948db74ec1df4039 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb @@ -0,0 +1,29 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University +# Authors:: George Tsouloupas , Fotis Georgatos , 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_2012-99.html +## + +name = 'CUDA' +version = '6.0.37' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# http://developer.download.nvidia.com/compute/cuda/6_0/rel/installers/cuda_6.0.37_linux_64.run +source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major)s_%(version_minor)s/rel/installers/'] +sources = ['%(namelower)s_%(version)s_linux_64.run'] +checksums = ['22f50793b6704fe987983302fa7d1707'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb b/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..920ee4c4faaaa53963d81d4c5260c23ffd8767c1 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB, Ghent University +# Authors:: George Tsouloupas , Fotis Georgatos , 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_2012-99.html +## + +name = 'CUDA' +version = '6.5.14' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# eg. http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/cuda_6.5.14_linux_64.run +source_urls = ['http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/'] + +sources = ['%(namelower)s_%(version)s_linux_64.run'] +checksums = [('md5', '90b1b8f77313600cc294d9271741f4da')] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..665f1371cbdbf2eb8f7a0f9eb1815a7e6f00286b --- /dev/null +++ b/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb @@ -0,0 +1,23 @@ +# 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 = "Check" +version = "0.9.12" + +homepage = 'http://check.sourceforge.net' +description = """ Check is a unit testing framework for C. It features a simple interface + for defining unit tests, putting little in the way of the developer. Tests are run in a + separate address space, so both assertion failures and code errors that cause segmentation + faults or other signals can be caught. Test results are reportable in the following: + Subunit, TAP, XML, and a generic logging format.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..b2653a86750e60470f7c77bf9ed51b0d0f3af423 --- /dev/null +++ b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'Circuitscape' +version = '4.0.5' + +homepage = 'http://www.circuitscape.org/' +description = """Circuitscape is a free, open-source program which borrows algorithms + from electronic circuit theory to predict patterns of movement, gene flow, + and genetic differentiation among plant and animal populations in + heterogeneous landscapes. Circuit theory complements least-cost path + approaches because it considers effects of all possible pathways + across a landscape simultaneously.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.8' +pyshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), + ('PyAMG', '2.2.1', versionsuffix), +] + +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/%%(namelower)s/__init__.py' % pyshortver] + + ['bin/cs%s.py' % x for x in ['run', 'verify']], + 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pyshortver], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb index 445ace09850d17b8c0ac28919c403350b3ac5424..40f0a86d6f88f57be99c3c2828537ba9a17af9c6 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb @@ -30,7 +30,7 @@ sources = [ ] dependencies = [ - ('GMP', '6.0.0'), + ('GMP', '6.0.0a'), ('ISL', '0.14'), ] diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..966759d71cd17ea26dc4cf0cbe3336c20850e610 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = "Clang" +version = "3.6.1" + +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': '4.9.2'} +# 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", +] + +dependencies = [ + ('GMP', '6.0.0a'), + ('ISL', '0.14'), +] + +builddependencies = [ + ('CMake', '3.2.1'), + ('Python', '2.7.9', '-bare'), + ('libxml2', '2.9.2'), +] + +assertions = True + +usepolly = True + +build_targets = ['X86'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb index b1b5830754fac02a2f1b9ab65cc20b25ffb53be4..94eaf15f8dd907b211f15c47454a24c5c574e60d 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb @@ -1,11 +1,15 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## + easyblock = 'ConfigureMake' name = "Cube" @@ -20,9 +24,12 @@ description = """Cube, which is used as performance report explorer for Scalasca toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -# http://apps.fz-juelich.de/scalasca/releases/cube/3.4/dist/cube-3.4.3.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/3.4/dist'] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] + +checksums = [ + '703d4681851a5abf50946868f05e8f9e', # cube-3.4.3.tar.gz +] dependencies = [('Qt', '4.8.4')] diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb index 941a048ad17e912df1e610ffec5ac60f70d84a66..7159c84d00340784eaee2a3197754cf914269110 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb @@ -1,12 +1,15 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# Authors:: Markus Geimer -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## + easyblock = 'EB_Score_minus_P' name = "Cube" @@ -30,16 +33,22 @@ patches = [ 'Cube-4.2_fix-with-qt-check.patch', ] +checksums = [ + 'aa1b1594bacddd3a1931f9a9dea23ce8', # cube-4.2.tar.gz + 'da69fe49d347dc7722c30bb785106d96', # Cube-4.2_fix-Qt-version-check.patch + '5a746d4f6f4eb5eb8b464ca355b46891', # Cube-4.2_fix-with-qt-check.patch +] + dependencies = [('Qt', '4.8.4')] # The Cube Java reader is currently only used by TAU, which ships it's own # copy as a jar file. If you really want to enable it, make sure to set -# 'maxparallel=1', as automake's Java support is has difficulties handling +# 'maxparallel=1', as automake's Java support has difficulties handling # parallel builds. configopts = "--without-java-reader" sanity_check_paths = { - 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.so", "lib64/libcube4.so")], 'dirs': ["include/cube", "include/cubew"], } diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..7bda257ed231f7102fd0103e87be93c729b84284 --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb @@ -0,0 +1,41 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Authors:: Jordi Blasco +# License:: New BSD +# +## + +easyblock = 'EB_Score_minus_P' + +name = "Cube" +version = "4.2.3" + +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': 'goolf', 'version': '1.5.14'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] + +checksums = [ + '8f95b9531f5a8f8134f279c2767c9b20', # cube-4.2.3.tar.gz +] + +dependencies = [('Qt', '4.8.4')] + +# The Cube Java reader is currently only used by TAU, which ships it's own +# copy as a jar file. If you really want to enable it, make sure to set +# 'maxparallel=1', as automake's Java support has difficulties handling +# parallel builds. +configopts = "--without-java-reader" + +sanity_check_paths = { + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.so", "lib64/libcube4.so")], + 'dirs': ["include/cube", "include/cubew"], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..01eebc5f7e4e2b066bf6550339be1282e465b6a3 --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb @@ -0,0 +1,47 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 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" + +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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] + +checksums = [ + 'ed4d6f3647eefa65fc194b5d1a5f4ffe', # cube-4.3.tar.gz +] + +dependencies = [('Qt', '4.8.6')] + +# The Cube Java reader is currently only used by TAU, which ships it's own +# copy as a jar file. If you really want to enable it, make sure to set +# 'maxparallel=1', as automake's Java support has difficulties handling +# parallel builds. +configopts = "--without-java-reader" + +sanity_check_paths = { + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.so", "lib64/libcube4.so")], + 'dirs': ["include/cube", "include/cubew"], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb index 0a2aec777e38ca0ffbffb2845bb586c634974568..560d4ea5c5f8d46862c8791dac23921bc8db5a36 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb @@ -1,12 +1,15 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# # Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# Authors:: Markus Geimer -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## + easyblock = 'EB_Score_minus_P' name = "Cube" @@ -24,16 +27,20 @@ toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +checksums = [ + 'ed4d6f3647eefa65fc194b5d1a5f4ffe', # cube-4.3.tar.gz +] + dependencies = [('Qt', '4.8.4')] # The Cube Java reader is currently only used by TAU, which ships it's own # copy as a jar file. If you really want to enable it, make sure to set -# 'maxparallel=1', as automake's Java support is has difficulties handling +# 'maxparallel=1', as automake's Java support has difficulties handling # parallel builds. configopts = "--without-java-reader" sanity_check_paths = { - 'files': ["bin/cube", "lib/libcube4.a", "lib/libcube4.so"], + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.so", "lib64/libcube4.so")], 'dirs': ["include/cube", "include/cubew"], } diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b12da485bc27115bfdf88a5ff755a1ec5abae1e0 --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb @@ -0,0 +1,41 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 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 = "4.3.2" + +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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] + +checksums = [ + 'a9119524df5a39e7a5bf6dee4de62e30', # cube-4.3.2.tar.gz +] + +dependencies = [('Qt', '4.8.6')] + +sanity_check_paths = { + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.so", "lib64/libcube4.so")], + '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 new file mode 100644 index 0000000000000000000000000000000000000000..96199f4bf20a56fe1a8489a05a3637e5502822dc --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb @@ -0,0 +1,45 @@ +## +# 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 +## + +name = 'Cufflinks' +version = "1.3.0" + +homepage = 'http://cufflinks.cbcb.umd.edu/' +description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] + +dependencies = [ + ('Boost', '1.51.0', '-Python-2.7.3'), + ('SAMtools', '0.1.18'), + ('Eigen', '3.1.1'), + ('zlib', '1.2.7'), +] + +patches = [ + 'Cufflinks_GCC-4.7.patch', + 'cufflinks-1.x-ldflags.patch' +] + +preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' + +sanity_check_paths = { + 'files': ['bin/cufflinks'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d0372e6f7036ef03b18931e96882e5a5a80096ed --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb @@ -0,0 +1,29 @@ +name = 'Cufflinks' +version = '2.2.1' + +homepage = 'http://cole-trapnell-lab.github.io/cufflinks/' +description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] + +dependencies = [ + # issues with boost > 1.55, see https://github.com/cole-trapnell-lab/cufflinks/issues/3 + ('Boost', '1.55.0', '-Python-2.7.9'), + ('SAMtools', '0.1.19'), + ('Eigen', '3.2.3'), + ('zlib', '1.2.8'), +] + +preconfigopts = 'CPPFLAGS=-I$EBROOTEIGEN/include' +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' + +sanity_check_paths = { + 'files': ['bin/cufflinks'], + 'dirs': [] +} + +moduleclass = 'bio' 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 new file mode 100644 index 0000000000000000000000000000000000000000..3fdf2a09230495578758559129e37683df9a0ac1 --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb @@ -0,0 +1,28 @@ +name = 'Cufflinks' +version = '2.2.1' + +homepage = 'http://cufflinks.cbcb.umd.edu/' +description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['cufflinks-%(version)s.tar.gz'] +source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] + +dependencies = [ + ('Boost', '1.51.0', '-Python-2.7.3'), + ('SAMtools', '0.1.19'), + ('Eigen', '3.1.1'), + ('zlib', '1.2.7'), +] + +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' +preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' + +sanity_check_paths = { + 'files': ['bin/cufflinks'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Cufflinks/cufflinks-1.x-ldflags.patch b/easybuild/easyconfigs/c/Cufflinks/cufflinks-1.x-ldflags.patch new file mode 100644 index 0000000000000000000000000000000000000000..9c2bd9e9a203b4bd2a2b0fe6f1ce7ee4ca186a59 --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/cufflinks-1.x-ldflags.patch @@ -0,0 +1,45 @@ +diff -ru cufflinks-1.3.0/configure cufflinks-1.3.0_patched/configure +--- cufflinks-1.3.0/configure 2012-01-02 13:36:44.000000000 +0000 ++++ cufflinks-1.3.0_patched/configure 2015-01-27 18:32:24.810282390 +0000 +@@ -6386,7 +6386,8 @@ + CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}" + CXXFLAGS="$CFLAGS" + CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS" +-LDFLAGS="$ext_LDFLAGS" ++user_LDFLAGS="$LDFLAGS" ++LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}" + + # Checks for structures/functions that can be used to determine system memory + echo "$as_me:$LINENO: checking for struct sysinfo.totalram" >&5 +diff -ru cufflinks-1.3.0/src/Makefile.in cufflinks-1.3.0_patched/src/Makefile.in +--- cufflinks-1.3.0/src/Makefile.in 2012-01-02 13:36:43.000000000 +0000 ++++ cufflinks-1.3.0_patched/src/Makefile.in 2015-01-27 18:20:02.944386541 +0000 +@@ -438,24 +438,24 @@ + # (echo '#!$(PYTHON)'; sed '/^#!/d' $<) > $@ + cufflinks_SOURCES = cufflinks.cpp + cufflinks_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) +-cufflinks_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) #$(ZLIB_LDFLAGS) ++cufflinks_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) #$(ZLIB_LDFLAGS) + cuffcompare_SOURCES = cuffcompare.cpp + cuffcompare_LDADD = libgc.a + gffread_SOURCES = gffread.cpp + gffread_LDADD = libgc.a + cuffdiff_SOURCES = cuffdiff.cpp + cuffdiff_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) +-cuffdiff_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++cuffdiff_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + gtf_to_sam_SOURCES = gtf_to_sam.cpp + gtf_to_sam_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) +-gtf_to_sam_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++gtf_to_sam_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + + #cuffcluster_SOURCES = cuffcluster.cpp + #cuffcluster_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) + #cuffcluster_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + compress_gtf_SOURCES = compress_gtf.cpp + compress_gtf_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) +-compress_gtf_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++compress_gtf_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + all: all-am + + .SUFFIXES: diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..5b829d6a73d164579c66f55718c674d93f99d091 --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'Cython' +version = '0.22' + +homepage = 'https://pypi.python.org/pypi/Cython/' +description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. +Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonver = '2.7.3' +versionsuffix = '-%s-%s' % (python, pythonver) +pyshortver = '.'.join(pythonver.split('.')[0:2]) +cythonlibdir = 'lib/python' + pyshortver + '/site-packages/Cython-%(version)s-py' + pyshortver + '-linux-x86_64.egg' + +dependencies = [(python, pythonver)] + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % cythonlibdir], + 'dirs': ['%s/%%(name)s' % cythonlibdir], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2014b.eb b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..00fec4f4d114791d69d862e922f383318da66298 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2014b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.37.1' + +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': '2014b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +#dependencies = [('OpenSSL', '1.0.1i')] # OS dependency should be preferred for security reasons +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0ba45ba9e526d5225207c829ef7370ea107cc2fe --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.37.1' + +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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +#dependencies = [('OpenSSL', '1.0.1i')] # OS dependency should be preferred for security reasons +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4e2d371a7115bb7b09002e94202bb5e4b25b5d83 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.41.0' + +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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1m')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-foss-2015b.eb b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..00dbb79c54a156842fd56050e9f241b6149484ca --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-foss-2015b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.43.0' + +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': '2015b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..f234e4353beecca8317a4b449ac9acf73058faa0 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.43.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..2dbc140a53cfcaf4bd3a95d2086a8db91ac8c739 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.43.0' + +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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015b.eb b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..853014d95e13db0bbb18c3aa49ef28d86eae9bf4 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.43.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.44.0-foss-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.44.0-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..19e23c5058fef104d68809ba6b6bd80c6a7086ee --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.44.0-foss-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.44.0' + +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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.44.0-goolf-1.7.20.eb b/easybuild/easyconfigs/c/cURL/cURL-7.44.0-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..22021b62b570cbc306a2197f8fb73ee55c1806ff --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.44.0-goolf-1.7.20.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.44.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.44.0-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.44.0-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4957904abe55186754cbeea4423fe5d53ece532b --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.44.0-intel-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.44.0' + +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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..3638dbedbc6ba26e35130cd96f8b9e614c918257 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = "cairo" +version = '1.12.18' + +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': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.12'), + ('freetype', '2.5.3'), + ('pixman', '0.32.6'), + ('fontconfig', '2.11.1'), + ('expat', '2.1.0'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no" + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c4afd6154b57cd027c512280708af02ddf4cdeb7 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = "cairo" +version = '1.12.18' + +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': '2015a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('libpng', '1.6.16'), + ('freetype', '2.5.5'), + ('zlib', '1.2.8'), + ('pixman', '0.32.6'), + ('fontconfig', '2.11.1'), + ('expat', '2.1.0'), + ('bzip2', '1.0.6'), +] + +builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] + +patches = ['cairo-1.12.18-pthread-check.patch'] + +preconfigopts = " autoconf configure.ac > configure && " + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no" + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch new file mode 100644 index 0000000000000000000000000000000000000000..9019afb9464eaeda9491f22a79efca74d95839f3 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch @@ -0,0 +1,17 @@ +# Make sure the configure script doesn't fail over a 'no version information available' warning +# by wpoely86@gmail.com +diff -ur cairo-1.12.18.orig/build/aclocal.cairo.m4 cairo-1.12.18/build/aclocal.cairo.m4 +--- cairo-1.12.18.orig/build/aclocal.cairo.m4 2013-03-15 21:29:27.000000000 +0100 ++++ cairo-1.12.18/build/aclocal.cairo.m4 2015-01-14 14:08:01.000000000 +0100 +@@ -101,9 +101,9 @@ + $1 + AC_LINK_IFELSE( + [AC_LANG_SOURCE([$_compile_program])], +- [cairo_cc_stderr=`test -f conftest.err && cat conftest.err` ++ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err | grep -v 'no version information available' ` + cairo_cc_flag=yes], +- [cairo_cc_stderr=`test -f conftest.err && cat conftest.err` ++ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err | grep -v 'no version information available' ` + cairo_cc_flag=no]) + + if test "x$cairo_cc_stderr" != "x"; then diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.2-goolf-1.7.20.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.2-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..63d09e359a4f0f219d6eacc7c1f1b312ffbf985b --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.2-goolf-1.7.20.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = "cairo" +version = '1.14.2' + +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': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.17'), + ('freetype', '2.6'), + ('pixman', '0.32.6'), + ('fontconfig', '2.11.94'), + ('expat', '2.1.0'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no" + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.2-intel-2015a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..357e47a331cef056f0b6efe471e73389a6dd7d35 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.2-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = "cairo" +version = '1.14.2' + +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': '2015a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.17'), + ('freetype', '2.6'), + ('pixman', '0.32.6'), + ('fontconfig', '2.11.94'), + ('expat', '2.1.0'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no" + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cairomm/cairomm-1.10.0-intel-2015a.eb b/easybuild/easyconfigs/c/cairomm/cairomm-1.10.0-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5aa8ded5d683cedf7e9f7f35b12bc63892986735 --- /dev/null +++ b/easybuild/easyconfigs/c/cairomm/cairomm-1.10.0-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = "cairomm" +version = '1.10.0' + +homepage = 'http://cairographics.org' +description = """ + The Cairomm package provides a C++ interface to Cairo. +""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('cairo', '1.14.2'), + ('libsigc++', '2.4.1'), +] + +sanity_check_paths = { + 'files': ['lib/libcairomm-1.0.so'], + 'dirs': [], +} + +moduleclass = 'vis' 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 new file mode 100644 index 0000000000000000000000000000000000000000..928b078aac4b112449fc8c1ceaa5be6863568b3d --- /dev/null +++ b/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb @@ -0,0 +1,29 @@ +easyblock = 'Tarball' + +name = 'cramtools' +version = '2.0' + +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': 'dummy'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/enasequence/%(name)s/archive/'] + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +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/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..1d7c0f2ab8d3bf4b71f27c9b706800278c6d7b73 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-goolf-1.4.10-Python-2.7.10.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.5' + +homepage = 'http://code.google.com/p/cutadapt/' +description = """ cutadapt removes adapter sequences + from high-throughput sequencing data. This is usually + necessary when the read length of the sequencing machine + is longer than the molecule that is sequenced, for + example when sequencing microRNAs. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://cutadapt.googlecode.com/files/'] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/cutadapt/_align.so' % pyshortver], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..55ffd3cd6a1a22860e3bd48c41feb311eeda93e7 --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'DBD-Pg' +version = '3.4.1' + +homepage = 'http://search.cpan.org/~turnstep/DBD-Pg-3.4.1/' +description = """Perl binding for PostgreSQL""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://cpan.metacpan.org/authors/id/T/TU/TURNSTEP/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.20.0' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ("PostgreSQL", "9.3.5") +] + +options = {'modulename': 'DBD::Pg'} + +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DBD/Pg.pm' % (perlmajver, perlver)], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/DBD-SQLite/DBD-SQLite-1.42-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DBD-SQLite/DBD-SQLite-1.42-intel-2014b-Perl-5.20.0.eb index 318f3d639e57bb6c47142b11c6b5c0d64a84dae1..c8b287035b510d93a72afcfb7079b5efe2371226 100644 --- a/easybuild/easyconfigs/d/DBD-SQLite/DBD-SQLite-1.42-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/d/DBD-SQLite/DBD-SQLite-1.42-intel-2014b-Perl-5.20.0.eb @@ -23,4 +23,10 @@ dependencies = [ options = {'modulename': 'DBD::SQLite'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DBD/SQLite.pm' % (perlmajver, perlver)], + 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DBD/SQLite' % (perlmajver, perlver)], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.028-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.028-intel-2014b-Perl-5.20.0.eb index 2bcf9d9a0e32612b85e7acc0539f55194dba74f3..b518ac35ed2646703b27926392bffc73b309d675 100644 --- a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.028-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.028-intel-2014b-Perl-5.20.0.eb @@ -22,4 +22,10 @@ dependencies = [ options = {'modulename': 'DBD::mysql'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DBD/mysql.pm' % (perlmajver, perlver)], + 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DBD/mysql' % (perlmajver, perlver)], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2015b-Perl-5.20.3.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2015b-Perl-5.20.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..0496e7650c89eaaf557ece97b0462d62aa7ccb69 --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2015b-Perl-5.20.3.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'DBD-mysql' +version = '4.032' + +homepage = 'http://search.cpan.org/~capttofu/DBD-mysql-%(version)s/' +description = """Perl binding for MySQL""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['http://cpan.metacpan.org/authors/id/C/CA/CAPTTOFU/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.20.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ('MySQL', '5.6.26', '-clientonly', ('GNU', '4.9.3-2.25')), +] + +options = {'modulename': 'DBD::mysql'} + +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DBD/mysql.pm' % (perlmajver, perlver)], + 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DBD/mysql' % (perlmajver, perlver)], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb index 3aa72fb22ae0741c84227fed652066e607ed9638..bdcb00e69d1f7d3d754727227733019e25c1498f 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.18.2.eb @@ -21,4 +21,10 @@ dependencies = [ (perl, perlver), ] +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DB_File.pm' % (perlmajver, perlver)], + 'dirs': [], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb index 3636f4ea5c1a6f02d1dc9427e229dc5b3e68d23b..831d1e849462cc3bbfc6e0863e1192a0b1882286 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.831-ictce-5.5.0-Perl-5.20.0.eb @@ -21,4 +21,10 @@ dependencies = [ (perl, perlver), ] +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/DB_File.pm' % (perlmajver, perlver)], + 'dirs': [], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/DISCOVARdenovo/DISCOVARdenovo-52488-foss-2015a.eb b/easybuild/easyconfigs/d/DISCOVARdenovo/DISCOVARdenovo-52488-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5f9ea822ee521a3cd7f95683950fdf08a2d934af --- /dev/null +++ b/easybuild/easyconfigs/d/DISCOVARdenovo/DISCOVARdenovo-52488-foss-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'DISCOVARdenovo' +version = '52488' + +homepage = 'http://www.broadinstitute.org/software/discovar/blog/' +description = """DISCOVAR de novo can generate de novo assemblies for both large and small genomes. + It currently does not call variants.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['ftp://ftp.broadinstitute.org/pub/crd/DiscovarDeNovo/latest_source_code'] + +dependencies = [ + ('GMP', '6.0.0a'), + ('jemalloc', '3.6.0'), +] + +sanity_check_paths = { + 'files': ["bin/AffineAlign"], + 'dirs': ["bin","share"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..2734b69ecf14a796ce307f7e71c28e2dbc4109a0 --- /dev/null +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,39 @@ +## +#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 +# $Id$ +# +## +easyblock = "PythonPackage" + +name = 'DendroPy' +version = '3.12.0' + +homepage = 'https://pypi.python.org/pypi/DendroPy/' +description = """A Python library for phylogenetics and phylogenetic computing: +reading, writing, simulation, processing and manipulation of phylogenetic trees +(phylogenies) and characters.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://pypi.python.org/packages/source/D/DendroPy/'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.3' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [(python, pythonversion)] + +sanity_check_paths = { + 'files': ['bin/cattrees.py','bin/long_branch_symmdiff.py','bin/sumlabels.py', + 'bin/sumtrees.py','bin/strict_consensus_merge.py'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-5.4.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..76e4e4d410a270759624548a4bb729cecabf846c --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-5.4.0.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.3.1' + +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': 'ictce', 'version': '5.4.0'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('flex', '2.5.37'), + ('Bison', '2.7'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-6.1.5.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-6.1.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..2f5d07d58fd5609038288cf391cba9d8fd36edb1 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-6.1.5.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.3.1' + +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': 'ictce', 'version': '6.1.5'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +dependencies = [ + ('flex', '2.5.37'), + ('Bison', '2.7'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2014b.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..9604d1fe3e7a01a257c59b907f5fd5cd842ba276 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2014b.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.7' + +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': '2014b'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2015a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6fae2382dd0225658c93c6920012b285f0908c98 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2015a.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.7' + +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': '2015a'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-clusterapps.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb similarity index 67% rename from easybuild/easyconfigs/e/ECore/ECore-1.5.2-clusterapps.eb rename to easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb index 526f2442cdd7e8c8e56f0b317332f460a831e895..ca072da66b97cf40efb62307a4a5ff7187e826b3 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-clusterapps.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb @@ -5,20 +5,21 @@ version = '1.5.2' versionsuffix = '-clusterapps' homepage = 'http://www.numericalrocks.com/index.php?option=com_content&task=blogcategory&id=25&Itemid=25' -description = """The e-Core technology simulates the natural processes of sedimentary rock formation; i.e. sedimentation, compaction and diagenesis.""" +description = """The e-Core technology simulates the natural processes of sedimentary rock formation; i.e. + sedimentation, compaction and diagenesis.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'ictce', 'version': '5.5.0'} -sources = ['%s-%s%s.tgz' % (name.lower(), version, versionsuffix)] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tgz'] patches = ['ecore-license-var.patch'] -comp = ('GCC', '4.6.3') -dependencies = [('OpenMPI', '1.4.5', '-no-OFED', comp)] +# needs to be 1.4.x, because it's linked with the libmpi_cxx.so.0 +dependencies = [('OpenMPI', '1.4.5')] sanity_check_paths = { 'files': ['arch/linux-rh5-x86_64/bin/%s' % x for x in ['absperm', 'FormationFactor', 'nmr', - 'orterun', 'packer', 'randomwalkffmpi', + 'orterun', 'packer', 'randomwalkffmpi', 'unpacker']] + \ ['absperm.sh', 'formationfactor.sh', 'nmr.sh', 'rw_formationfactor.sh'], 'dirs': [], diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0.eb similarity index 74% rename from easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb rename to easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0.eb index 382a1b327eb8c0d8c21a38ba201628f3b7f84b64..7c028041b8bfab81c7c099d20a5f69dee694a615 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0.eb @@ -4,16 +4,16 @@ name = 'ECore' version = '1.5.2' homepage = 'http://www.numericalrocks.com/index.php?option=com_content&task=blogcategory&id=25&Itemid=25' -description = """The e-Core technology simulates the natural processes of sedimentary rock formation; i.e. sedimentation, compaction and diagenesis.""" +description = """The e-Core technology simulates the natural processes of sedimentary rock formation; i.e. + sedimentation, compaction and diagenesis.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = [SOURCELOWER_TGZ] patches = ['ecore-license-var.patch'] -comp = ('GCC', '4.6.3') -dependencies = [('OpenMPI', '1.4.5', '-no-OFED', comp)] +dependencies = [('OpenMPI', '1.4.5')] sanity_check_paths = { 'files': ["ecore.sh", 'noarch/launch.sh'] + \ diff --git a/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..e763143dc4fa3f42339d698e9eb9e3ef598014a8 --- /dev/null +++ b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'EMAN2' +version = '2.11' + +homepage = 'http://blake.bcm.edu/emanwiki/EMAN2' +description = """EMAN2 is the successor to EMAN1. It is a broadly based greyscale scientific image processing suite + with a primary focus on processing data from transmission electron microscopes. """ + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://ncmi.bcm.edu/ncmi/software/counter_222/software_130/'] +sources = ['eman%(version)s.source.tar.gz'] + +pyver = '2.7.9' +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + # FFTW provided via toolchain + ('GSL', '1.16'), + ('Python', pyver), # also provides numpy + ('Boost', '1.58.0', versionsuffix), + ('IPython', '3.2.0', versionsuffix), + ('HDF5', '1.8.15-patch1'), + ('freetype', '2.6'), + # optional + ('PyQt', '4.11.4', versionsuffix), + ('LibTIFF', '4.0.4'), + ('libpng', '1.6.17'), +] +builddependencies = [('CMake', '3.2.3')] + +start_dir = 'eman2' +separate_build_dir = True + +configopts = "-DEMAN_INSTALL_PREFIX=%(installdir)s -DENABLE_FTGL=OFF" + +sanity_check_paths = { + 'files': ['bin/e2proc2d.py', 'bin/e2proc3d.py', 'bin/e2bdb.py', 'bin/e2iminfo.py', 'bin/e2display.py', + 'bin/e2filtertool.py'], + 'dirs': ['examples', 'include', 'lib', 'test/rt'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..82523c603be6ea880d88a59c94742006333ca6f8 --- /dev/null +++ b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'EMAN2' +version = '2.11' + +homepage = 'http://blake.bcm.edu/emanwiki/EMAN2' +description = """EMAN2 is the successor to EMAN1. It is a broadly based greyscale scientific image processing suite + with a primary focus on processing data from transmission electron microscopes. """ + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ncmi.bcm.edu/ncmi/software/counter_222/software_130/'] +sources = ['eman%(version)s.source.tar.gz'] + +pyver = '2.7.9' +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('FFTW', '3.3.4'), + ('GSL', '1.16'), + ('Python', pyver), # also provides numpy + ('Boost', '1.58.0', versionsuffix), + ('IPython', '3.2.0', versionsuffix), + ('HDF5', '1.8.15-patch1'), + ('freetype', '2.6'), + # optional + ('PyQt', '4.11.4', versionsuffix), + ('LibTIFF', '4.0.4'), + ('libpng', '1.6.17'), +] +builddependencies = [('CMake', '3.2.3')] + +start_dir = 'eman2' +separate_build_dir = True + +configopts = "-DEMAN_INSTALL_PREFIX=%(installdir)s -DENABLE_FTGL=OFF" + +sanity_check_paths = { + 'files': ['bin/e2proc2d.py', 'bin/e2proc3d.py', 'bin/e2bdb.py', 'bin/e2iminfo.py', 'bin/e2display.py', + 'bin/e2filtertool.py'], + 'dirs': ['examples', 'include', 'lib', 'test/rt'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..f270612d5f3fb42b24c61890c2353e5d5d0ea9f4 --- /dev/null +++ b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb @@ -0,0 +1,34 @@ +## +# 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': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://www.etsf.eu/system/files'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-netcdf-prefix=$EBROOTNETCDF " +configopts += "--with-netcdf-libs='-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff' " +configopts += " --with-netcdf-incs='-I$EBROOTNETCDF/include'" + +dependencies = [ ('netCDF', '4.1.3') ] + +sanity_check_paths = { + 'files': ["bin/etsf_io"], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..116950af4bdc21e32a31a82db11b1fd43995a663 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.2.0' + +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-2.2.3.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-2.3.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..6080ef8f0cee6ad26266040bdc8c4cca3c29e891 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.3.0' + +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-2.2.4.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-3.2.3-foss-2015a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9cca953ebc6cc2b9652bb63d0d44c727845fc488 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb @@ -0,0 +1,14 @@ +name = 'Eigen' +version = '3.2.3' + +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': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [BITBUCKET_SOURCE] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..a1c5928f0bf84c89e93acc15c41b9a4bad728227 --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'eudev' +version = '3.0' + +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': 'intel', 'version': '2014b'} +toolchainopts = {'cstd': 'c99'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://dev.gentoo.org/~blueness/%(name)s/'] +patches = ['%(name)s-%(version)s_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-3.0-intel-2015a.eb b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5108981bdd56eec3bf4f1e4f0863d1da9041657c --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'eudev' +version = '3.0' + +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': 'intel', 'version': '2015a'} +toolchainopts = {'cstd': 'c99'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://dev.gentoo.org/~blueness/%(name)s/'] +patches = ['%(name)s-%(version)s_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-3.0_pre-2.6.34_kernel.patch b/easybuild/easyconfigs/e/eudev/eudev-3.0_pre-2.6.34_kernel.patch new file mode 100644 index 0000000000000000000000000000000000000000..7fb7da7902ec1055cf43563c81cd494c99146393 --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.0_pre-2.6.34_kernel.patch @@ -0,0 +1,16 @@ +#inspiration from http://repository.timesys.com/buildsources/u/udev/udev-181/udev-181-define-trigger-happy.patch +#BTN_TRIGGER_HAPPY is not defined in /usr/include/linux/input.h for pre 2.6.34 kernels +# B. Hajgato April 30 2015 +--- eudev-3.0/src/udev/udev-builtin-input_id.c.org 2015-04-30 09:11:07.990269206 +0200 ++++ eudev-3.0/src/udev/udev-builtin-input_id.c 2015-04-30 09:12:19.407272116 +0200 +@@ -33,6 +33,10 @@ + #include "udev.h" + #include "util.h" + ++#ifndef BTN_TRIGGER_HAPPY ++#define BTN_TRIGGER_HAPPY 0x2c0 ++#endif ++ + /* we must use this kernel-compatible implementation */ + #define BITS_PER_LONG (sizeof(unsigned long) * 8) + #define NBITS(x) ((((x)-1)/BITS_PER_LONG)+1) diff --git a/easybuild/easyconfigs/e/evmix/evmix-2.1-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/e/evmix/evmix-2.1-intel-2014b-R-3.1.1.eb index ffb121f54612ab3ad498fe72cefe713817fbc84f..2b79d60ce92b118172c66e9a1bc87595c9533e9f 100644 --- a/easybuild/easyconfigs/e/evmix/evmix-2.1-intel-2014b-R-3.1.1.eb +++ b/easybuild/easyconfigs/e/evmix/evmix-2.1-intel-2014b-R-3.1.1.eb @@ -24,4 +24,9 @@ dependencies = [ ('gsl', '1.9-10', versionsuffix), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['evmix'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/evmix/evmix-2.3-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/e/evmix/evmix-2.3-intel-2014b-R-3.1.1.eb index ee1750e53d0456918ad49524a6bb2cf7e6b2a238..b3a13971b307e333a4d8d89f396d4f95bcd51db9 100644 --- a/easybuild/easyconfigs/e/evmix/evmix-2.3-intel-2014b-R-3.1.1.eb +++ b/easybuild/easyconfigs/e/evmix/evmix-2.3-intel-2014b-R-3.1.1.eb @@ -24,4 +24,9 @@ dependencies = [ ('gsl', '1.9-10', versionsuffix), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['evmix'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.7.20.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..721806cde96cd288552e64da1d3717bcdcccf91d --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.7.20.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': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..4ed019fad23f13fddd6179b37d7526fb5576cbd2 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.4.0.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': 'ictce', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..13d9d1cb72c6032c4494d7b048c85486eb2bd9a8 --- /dev/null +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb @@ -0,0 +1,45 @@ +## +# 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': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +altname = name.lower().replace('-','_') +source_urls = ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'] +sources = ['%s-%%(version)s.tar.bz2' % altname] + +dependencies = [('libgtextutils', '0.6.1')]; + +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-r18915-intel-2015a.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..3826bdc12482a1e939e42c42afa839b0c96ddd33 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = 'r18915' + +homepage = 'https://code.google.com/p/fds-smv/' +description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, + with an emphasis on smoke and heat transport from fires.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCE_TAR_GZ] +patches = ['FDS-%(version)s_makefile.patch'] + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +modextrapaths = {'PATH': 'FDS_Source'} + +sanity_check_paths = { + 'files': ['FDS_Source/fds'], + 'dirs': [], +} +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-intel-2015a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..10fd990805ef6562229d1fc20f1bfeff124997cb --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-intel-2015a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.3' + +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': '2015a'} +toolchainopts = {'optarch': True, '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-gompi-2015b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..c048de7a215721f7214746df14f0c81ae6584324 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015b.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': '2015b'} +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/FPM/FPM-1.3.3-Ruby-2.1.6.eb b/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb index b6d3efe3ac3d447eda5e4587ff5973b4a2de8cb1..52783b2be4136aaee4c2dc47b10e7501ee7839f8 100644 --- a/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb +++ b/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb @@ -17,4 +17,9 @@ sources = ['%(namelower)s-%(version)s.gem'] dependencies = [('Ruby', rubyver)] +sanity_check_paths = { + 'files': ['bin/fpm'], + 'dirs': ['gems/%(namelower)s-%(version)s'], +} + moduleclass = 'tools' 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-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..41209b695a0bdca4bf6e37e27f3b06957650cd3d --- /dev/null +++ b/easybuild/easyconfigs/f/FastQC/FastQC-0.10.1-goolf-1.4.10.eb @@ -0,0 +1,38 @@ +## +# 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 +# License:: MIT/GPL +# +## +easyblock = "PackedBinary" + +name = 'FastQC' +version = '0.10.1' + +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': 'goolf', 'version': '1.4.10'} + +sources = ['%(namelower)s_v%(version)s.zip'] +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] + +java = 'Java' +javaver = '1.7.0_80' + +dependencies = [('Java', '1.7.0_80', '', True)] + +install_cmd = "cp -a FastQC/* %(installdir)s && 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"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb index 0e1e6d0fb4fe43ac53cf331f2e704ec5bdc69794..3352880d36fb48f6bf034e271a0500ab613fe922 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb @@ -16,7 +16,7 @@ sources = ['%(name)s-%(version)s.c'] skipsteps = ['source'] -cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %(source)s -o FastTree')] +cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] files_to_copy = [(['FastTree'], 'bin')] diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb index 5fb2a1352d9bc24c3bc7e77016715e76a7452f74..7447f915f3260de2e39da4bfefab028e20b8f80e 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb @@ -16,7 +16,7 @@ sources = ['%(name)s-%(version)s.c'] skipsteps = ['source'] -cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %(source)s -o FastTree')] +cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] files_to_copy = [(['FastTree'], 'bin')] diff --git a/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.1.eb b/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..264a1ea82dd02e610cd016b9755b2aaf72c93e6e --- /dev/null +++ b/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.1.eb @@ -0,0 +1,22 @@ +name = 'FoldX' +version = '3.0-beta6.1' + +homepage = 'http://foldx.crg.es/' +description = """FoldX is used to provide a fast and quantitative estimation of the importance of the interactions + contributing to the stability of proteins and protein complexes.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# no source URLs because registration is required to obtain sources +# same name as zip file for 3.0 beta 6 >_< +sources = ['%(name)s_30b6_linux64.zip'] +checksums = ['4b95ea518415d0d3be020f5f75c14e82'] + +start_dir = 'FoldX_30b6_linux64' + +sanity_check_paths = { + 'files': ["bin/foldx3b6", "rotabase.txt"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.eb b/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.eb index 7585ccc7fcef4c0df578f5f8550538d78530352e..4eedd88eaa6918fb861fa2997e66d0426f021866 100644 --- a/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.eb +++ b/easybuild/easyconfigs/f/FoldX/FoldX-3.0-beta6.eb @@ -8,7 +8,9 @@ description = """FoldX is used to provide a fast and quantitative estimation of toolchain = {'name': 'dummy', 'version': 'dummy'} # no source URLs because registration is required to obtain sources +# same name as zip file for 3.0 beta 6.1 >_< sources = ['%(name)s_30b6_linux64.zip'] +checksums = ['d3264460a4fe08b57553ebcdaad2dcad'] sanity_check_paths = { 'files': ["bin/%(namelower)s64Linux", "rotabase.txt"], diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..9ff730ebeda8b1096f7e370f983285c321dcc2c4 --- /dev/null +++ b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb @@ -0,0 +1,27 @@ +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 new file mode 100644 index 0000000000000000000000000000000000000000..c5f20b91654926eb90d7d61fbb9671bdbc67d835 --- /dev/null +++ b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb @@ -0,0 +1,27 @@ +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/fastqz/fastqz-1.5-GCC-4.8.2.eb b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb index 50633eb59802cbdefbad3fbe6707ec1448ce49c2..902b240c0498d9a384a1f761f30e94e85f6be9c1 100644 --- a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb @@ -30,7 +30,7 @@ dependencies = [('ZPAQ', '7.00')] skipsteps = ['source'] cmds_map = [ - ('fastqz%s.cpp' % minver, '$CXX $CFLAGS -lpthread %(source)s $EBROOTZPAQ/include/libzpaq.cpp -o fastqz'), + ('fastqz%s.cpp' % minver, '$CXX $CFLAGS -lpthread %%(source)s $EBROOTZPAQ/include/libzpaq.cpp -o %(name)s'), ('fapack.cpp', '$CXX $CFLAGS -s %(source)s -o %(target)s') ] diff --git a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.8-intel-2015b.eb b/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.8-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..84c4dd1f59087b5693fcf4b27b92d5e209656630 --- /dev/null +++ b/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.8-intel-2015b.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'ffmpeg' +version = '2.8' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX"' + +dependencies = [ + ('NASM', '2.11.08'), + ('zlib', '1.2.8'), +] + +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/flex/flex-2.5.37-ictce-5.4.0.eb b/easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..bf5ece9d3c34903a165e6a83d8f3ae7b3004f210 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-5.4.0.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.37' + +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': 'ictce', 'version': '5.4.0'} +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-2.5.37-ictce-6.1.5.eb b/easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-6.1.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..15e30d50fbf4ec3af759be277af207e5faace014 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-6.1.5.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.37' + +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': 'ictce', 'version': '6.1.5'} +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-2.5.37-intel-2015a.eb b/easybuild/easyconfigs/f/flex/flex-2.5.37-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..086db50be89e50c7884e0598c0629094dc4cfe04 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.37-intel-2015a.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.37' + +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': '2015a'} +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-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..55d2930dcc34a5adb9aae19ef18f51b5eae20753 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.2-binutils-2.25.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +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': 'GCC', 'version': '4.9.2-binutils-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.25', '', True)] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..1d773d362f673d72cd7dc3bf21fd5bb0fc09b54b --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-4.9.3-binutils-2.25.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +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': 'GCC', 'version': '4.9.3-binutils-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.25', '', True)] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..b6406b3fee3e4248c7dc45bd1ed5628d8a758725 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GCC-5.1.0-binutils-2.25.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +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': 'GCC', 'version': '5.1.0-binutils-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.25', '', True)] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..7c5e4528e08f09aacf2307715227d82f66ec7da5 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-GNU-4.9.3-2.25.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +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': 'GNU', 'version': '4.9.3-2.25'} + +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-foss-2014b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..6a24b017aa79cbb8a179bb5730ccdb950543b29b --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2014b.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': 'foss', 'version': '2014b'} +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-foss-2015.05.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..208a02e5403e45baf0640fa33ec53981b1c802b5 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.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': 'foss', 'version': '2015.05'} +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-foss-2015a.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f9226ff5f3631f67338c0176482e53e3ed58e4e3 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.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': 'foss', 'version': '2015a'} +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-foss-2015b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..40befb9e4a6c8fb35ce9eded5398b2f5d0a6366b --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015b.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': 'foss', 'version': '2015b'} +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-intel-2015b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..159eef32748c5e16b8928678a2ff6c851f0bb487 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-intel-2015b.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': '2015b'} +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 new file mode 100644 index 0000000000000000000000000000000000000000..53eb8f6c785226d322419e2e7a2711bce275b9a1 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39.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': 'dummy', 'version': 'dummy'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-4.0.10-R-2.15.2.eb b/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-4.0.10-R-2.15.2.eb index 4cec82a9a57d2f0caff7df89545a60b4daa5256d..af9a94344b87cb6324a7695ac53b3c8c76bf773c 100644 --- a/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-4.0.10-R-2.15.2.eb +++ b/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-4.0.10-R-2.15.2.eb @@ -21,9 +21,14 @@ versionsuffix = '-%s-%s' % (r, rver) tcltkver = '8.5.12' dependencies = [ - (r, rver), - ('Tcl', tcltkver), - ('Tk', tcltkver), - ] + (r, rver), + ('Tcl', tcltkver), + ('Tk', tcltkver), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['fmri'], +} moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-5.3.0-R-2.15.2.eb b/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-5.3.0-R-2.15.2.eb index 6d1befc47f0bca47c7bd68f9d19da4d46ed7be7d..ebe8dc05d0ee6e4aad9df1ec217563e72fe66594 100644 --- a/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-5.3.0-R-2.15.2.eb +++ b/easybuild/easyconfigs/f/fmri/fmri-1.4-8-ictce-5.3.0-R-2.15.2.eb @@ -21,9 +21,14 @@ versionsuffix = '-%s-%s' % (r, rver) tcltkver = '8.5.12' dependencies = [ - (r, rver), - ('Tcl', tcltkver), - ('Tk', tcltkver), - ] + (r, rver), + ('Tcl', tcltkver), + ('Tk', tcltkver), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['fmri'], +} moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/fmri/fmri-1.5-0-ictce-5.3.0-R-2.15.3.eb b/easybuild/easyconfigs/f/fmri/fmri-1.5-0-ictce-5.3.0-R-2.15.3.eb index dacaf55d84346ce2243f20340f895ccc2b29bc7e..b6097690db00b30b868939137e9185df518361cc 100644 --- a/easybuild/easyconfigs/f/fmri/fmri-1.5-0-ictce-5.3.0-R-2.15.3.eb +++ b/easybuild/easyconfigs/f/fmri/fmri-1.5-0-ictce-5.3.0-R-2.15.3.eb @@ -26,4 +26,9 @@ dependencies = [ ('Tk', tcltkver), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['fmri'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..e77da2e1fe8e9bdc91c4533bcc71cddafbadac5e --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = "fontconfig" +version = '2.11.1' + +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': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype','2.5.3'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..54455c5111b2db7d9079598f1df06f44467dbeef --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = "fontconfig" +version = '2.11.1' + +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': '2015a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype', '2.5.5'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2015a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..77235f32a1aa63f8dfb6d9b9ada8d93ede3786fa --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = "fontconfig" +version = '2.11.93' + +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': '2015a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype', '2.5.5'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-goolf-1.7.20.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..8fdfa9a81b7a10270fc68987042f97919f5b5cbb --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-goolf-1.7.20.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': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype','2.6'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-intel-2015a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..df68da2489b8c1a93ee0866afaf1ff9a84e1821c --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.94-intel-2015a.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': 'intel', 'version': '2015a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype', '2.6'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' 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 new file mode 100644 index 0000000000000000000000000000000000000000..7e4853de2ffee65d77d188c357e45632056be381 --- /dev/null +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2015a.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': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files' : [], + 'dirs' : ['include/X11/fonts'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/foss/foss-2015b.eb b/easybuild/easyconfigs/f/foss/foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..b30caf2279ee1de19039c5fbd9fe18c7b1b5f819 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2015b.eb @@ -0,0 +1,39 @@ +easyblock = "Toolchain" + +name = 'foss' +version = '2015b' + +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 = '4.9.3' +binutilsver = '2.25' +tcver = '%s-binutils-%s' % (gccver, binutilsver) + +blaslib = 'OpenBLAS' +blasver = '0.2.14' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.5.0' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc_ver = "%s" % version +comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) + +# 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, '-binutils-%s' % binutilsver), + ('binutils', binutilsver, '', ('GCC', tcver)), + ('OpenMPI', '1.8.8', '', ('GNU', '%s-%s' % (gccver, binutilsver))), + (blaslib, blasver, blassuff, ('GNU', '%s-%s' % (gccver, binutilsver))), + ('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/freetype/freetype-2.5.3-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..c5fb92d43c4f151bdbf760adc52541f881e8a87a --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.5.3' + +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': 'goolf', 'version': '1.7.20'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.12')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..baf0037fb6bd05c168d9b9fd174eda5df34882e4 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.5-intel-2015b.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.5.5' + +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': '2015b'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.16')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..3678616622f855c37aeabec97a8ae35f4c8ce5fe --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.6' + +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': '2015a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.17')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..484ef7705acac9012be473c86b0798b3c5a9105d --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-goolf-1.7.20.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.6' + +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': 'goolf', 'version': '1.7.20'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.17')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6a1b7e739c956a04be39b4b3c1439138e742eece --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.6' + +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': '2015a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.17')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' 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 new file mode 100644 index 0000000000000000000000000000000000000000..13de380c1b550861e16910f07b1fcfe65ac645ae --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 Cyprus Institute +# Authors:: Thekla Loizou +# 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 = '3.0-0' + +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': 'dummy'} + +# download manually from http://www.broadinstitute.org/gatk/download +sources = ['%s-%s.tar.bz2' % ("GenomeAnalysisTK", version)] + +java = 'Java' +javaver = '1.7.0_10' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': ["GenomeAnalysisTK.jar"], + 'dirs': ["resources"], +} + +moduleclass = 'bio' 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 new file mode 100644 index 0000000000000000000000000000000000000000..f53b54862bc930abd62012dac47fed1012790893 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-3.3-0-Java-1.7.0_80.eb @@ -0,0 +1,42 @@ +## +# 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 = '3.3-0' + +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': 'dummy'} + +# download manually from http://www.broadinstitute.org/gatk/download +sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +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 new file mode 100644 index 0000000000000000000000000000000000000000..8bb06bd90a35aaeb7a12ba19b72e6356cbf63681 --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb @@ -0,0 +1,109 @@ +easyblock = 'Bundle' + +name = 'GC3Pie' +version = '2.2.3' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +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)] + +exts_list = [ + ('setuptools', '17.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + # required for paramiko + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + # required for paramiko + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'modulename': 'Crypto', + }), + ('paramiko', '1.13.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('PrettyTable', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PrettyTable/'], + 'source_tmpl': 'prettytable-%(version)s.tar.gz', + }), + ('pyCLI', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], + 'modulename': 'cli', + }), + ('SQLAlchemy', '0.7.9', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('parsedatetime', '0.8.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], + }), + ('boto', '2.9.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/boto/'], + }), + # required for pbr + ('pip', '7.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + # required for python-novaclient + ('pbr', '0.11.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + # required for python-novaclient + ('Babel', '1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + # required for python-novaclient + ('simplejson', '3.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + # required for python-novaclient + ('requests', '2.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + # required for python-novaclient + ('iso8601', '0.1.10', { + 'source_urls': ['https://pypi.python.org/packages/source/i/iso8601/'], + }), + # required for python-novaclient + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + # required for python-novaclient + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('python-novaclient', '2.15.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-novaclient/'], + 'modulename': 'novaclient', + }), + (name.lower(), version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], + 'modulename': 'gc3libs', + }), +] + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +# on RHEL-based systems, some extensions get installed to lib, some to lib64 +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver, 'lib64/python%s/site-packages' % pyshortver]} + +# 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/gc3utils'], + 'dirs': ['lib/python%(pyver)s/site-packages/gc3pie-%%(version)s-py%(pyver)s.egg/gc3libs' % {'pyver': pyshortver}], +} + +sanity_check_commands = [('gc3utils', 'info --version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..6fee6c35e89d1154273ceb311f5dbea15c59d1a6 --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb @@ -0,0 +1,111 @@ +easyblock = 'Bundle' + +name = 'GC3Pie' +version = '2.3' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +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)] + +exts_list = [ + ('setuptools', '18.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + # required for paramiko + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + # required for paramiko + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'modulename': 'Crypto', + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('PrettyTable', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PrettyTable/'], + 'source_tmpl': 'prettytable-%(version)s.tar.gz', + }), + ('pyCLI', 'devel', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], + 'modulename': 'cli', + }), + ('SQLAlchemy', '1.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('parsedatetime', '1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], + }), + ('boto', '2.38.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/boto/'], + }), + # required for pbr + ('pip', '7.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + # required for python-novaclient + ('pbr', '1.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + # required for python-novaclient + ('Babel', '1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + # required for python-novaclient + ('simplejson', '3.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + # required for python-novaclient + ('requests', '2.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + # required for python-novaclient + ('iso8601', '0.1.10', { + 'source_urls': ['https://pypi.python.org/packages/source/i/iso8601/'], + }), + # required for python-novaclient + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + # required for python-novaclient + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('python-novaclient', '2.26.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-novaclient/'], + 'modulename': 'novaclient', + }), + (name.lower(), version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], + 'modulename': 'gc3libs', + }), +] + +pyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +# on RHEL-based systems, some extensions get installed to lib, some to lib64 +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver]} + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver +sanity_check_paths = { + 'files': ['bin/gc3utils', + ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + 'dirs': [], +} + +sanity_check_commands = [('gc3utils', 'info --version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..8a1d9386f8ef8d4d2d480e4fec0bd2bcf8149847 --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb @@ -0,0 +1,111 @@ +easyblock = 'Bundle' + +name = 'GC3Pie' +version = '2.4.0' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +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)] + +exts_list = [ + ('setuptools', '18.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + # required for paramiko + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + # required for paramiko + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'modulename': 'Crypto', + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('PrettyTable', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PrettyTable/'], + 'source_tmpl': 'prettytable-%(version)s.tar.gz', + }), + ('pyCLI', 'devel', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], + 'modulename': 'cli', + }), + ('SQLAlchemy', '1.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('parsedatetime', '1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], + }), + ('boto', '2.38.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/boto/'], + }), + # required for pbr + ('pip', '7.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + # required for python-novaclient + ('pbr', '1.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + # required for python-novaclient + ('Babel', '1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + # required for python-novaclient + ('simplejson', '3.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + # required for python-novaclient + ('requests', '2.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + # required for python-novaclient + ('iso8601', '0.1.10', { + 'source_urls': ['https://pypi.python.org/packages/source/i/iso8601/'], + }), + # required for python-novaclient + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + # required for python-novaclient + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('python-novaclient', '2.26.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-novaclient/'], + 'modulename': 'novaclient', + }), + (name.lower(), version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], + 'modulename': 'gc3libs', + }), +] + +pyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +# on RHEL-based systems, some extensions get installed to lib, some to lib64 +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver]} + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver +sanity_check_paths = { + 'files': ['bin/gc3utils', + ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + 'dirs': [], +} + +sanity_check_commands = [('gc3utils', 'info --version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..b62aa2387d6f8806ade0be67e3e1375fbc1476a4 --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb @@ -0,0 +1,111 @@ +easyblock = 'Bundle' + +name = 'GC3Pie' +version = '2.4.1' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +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)] + +exts_list = [ + ('setuptools', '18.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + # required for paramiko + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + # required for paramiko + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'modulename': 'Crypto', + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('PrettyTable', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PrettyTable/'], + 'source_tmpl': 'prettytable-%(version)s.tar.gz', + }), + ('pyCLI', 'devel', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], + 'modulename': 'cli', + }), + ('SQLAlchemy', '1.0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('parsedatetime', '1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], + }), + ('boto', '2.38.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/boto/'], + }), + # required for pbr + ('pip', '7.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + # required for python-novaclient + ('pbr', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + # required for python-novaclient + ('Babel', '2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + # required for python-novaclient + ('simplejson', '3.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + # required for python-novaclient + ('requests', '2.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + # required for python-novaclient + ('iso8601', '0.1.10', { + 'source_urls': ['https://pypi.python.org/packages/source/i/iso8601/'], + }), + # required for python-novaclient + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + # required for python-novaclient + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('python-novaclient', '2.23.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-novaclient/'], + 'modulename': 'novaclient', + }), + (name.lower(), version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], + 'modulename': 'gc3libs', + }), +] + +pyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +# on RHEL-based systems, some extensions get installed to lib, some to lib64 +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver]} + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver +sanity_check_paths = { + 'files': ['bin/gc3utils', + ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + 'dirs': [], +} + +sanity_check_commands = [('gc3utils', 'info --version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..e73e2257cc55e8b263e900b27ee5702259fc5d32 --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb @@ -0,0 +1,111 @@ +easyblock = 'Bundle' + +name = 'GC3Pie' +version = '2.4.2' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +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)] + +exts_list = [ + ('setuptools', '18.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + # required for paramiko + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + # required for paramiko + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'modulename': 'Crypto', + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('PrettyTable', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PrettyTable/'], + 'source_tmpl': 'prettytable-%(version)s.tar.gz', + }), + ('pyCLI', 'devel', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], + 'modulename': 'cli', + }), + ('SQLAlchemy', '1.0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('parsedatetime', '1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], + }), + ('boto', '2.38.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/boto/'], + }), + # required for pbr + ('pip', '7.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + # required for python-novaclient + ('pbr', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + # required for python-novaclient + ('Babel', '2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + # required for python-novaclient + ('simplejson', '3.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + # required for python-novaclient + ('requests', '2.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + # required for python-novaclient + ('iso8601', '0.1.10', { + 'source_urls': ['https://pypi.python.org/packages/source/i/iso8601/'], + }), + # required for python-novaclient + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + # required for python-novaclient + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('python-novaclient', '2.23.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-novaclient/'], + 'modulename': 'novaclient', + }), + (name.lower(), version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], + 'modulename': 'gc3libs', + }), +] + +pyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +# on RHEL-based systems, some extensions get installed to lib, some to lib64 +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver]} + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver +sanity_check_paths = { + 'files': ['bin/gc3utils', + ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + 'dirs': [], +} + +sanity_check_commands = [('gc3utils', 'info --version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..719bc6f3153e1237155c22ecca4522fd903e8d62 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb @@ -0,0 +1,37 @@ +name = "GCC" +version = '4.5.2' + +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': 'dummy'} + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(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 +] +sources = [ + SOURCELOWER_TAR_GZ, + 'gmp-5.0.2.tar.gz', + 'mpfr-3.0.1.tar.gz', + 'mpc-0.8.2.tar.gz', +] + +checksums = [ + 'e31fe695d7235f11fb5a63eafdfbfe88', # gcc-4.5.2.tar.gz + '87e73447afdc2ca5cefd987da865da51', # gmp-5.0.2.tar.gz + 'e9c191fc46a4f5741f8a0a11ab33b8bf', # mpfr-3.0.1.tar.gz + 'e98267ebd5648a39f881d66797122fb6', # mpc-0.8.2.tar.gz +] + +languages = ['c', 'c++', 'fortran'] + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +withlto = False + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb b/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..f310421ff2f2ab48f7d4c21d5a216e75c9f73ce4 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb @@ -0,0 +1,35 @@ +name = "GCC" +version = '4.6.0' + +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': 'dummy'} + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(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 +] +sources = [ + SOURCELOWER_TAR_GZ, + 'gmp-5.0.4.tar.bz2', + 'mpfr-3.0.1.tar.gz', + 'mpc-0.9.tar.gz', +] + +checksums = [ + '009f59ee0f9c8100c12939140698cf33', # gcc-4.6.0.tar.gz + '50c3edcb7c9438e04377ee9a1a061b79', # gmp-5.0.4.tar.bz2 + 'e9c191fc46a4f5741f8a0a11ab33b8bf', # mpfr-3.0.1.tar.gz + '0d6acab8d214bd7d1fbbc593e83dd00d', # mpc-0.9.tar.gz +] + +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/GCC/GCC-4.8.5.eb b/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..861866153237fa8bb6e7c9ada3237e0589fe83ad --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb @@ -0,0 +1,35 @@ +name = "GCC" +version = '4.8.5' + +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': 'dummy'} + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(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 +] +sources = [ + SOURCELOWER_TAR_GZ, + 'gmp-5.1.3.tar.bz2', + 'mpfr-3.1.2.tar.gz', + 'mpc-1.0.1.tar.gz', +] + +checksums = [ + 'bfe56e74d31d25009c8fb55fd3ca7e01', # gcc-4.8.5.tar.gz + 'a082867cbca5e898371a97bb27b31fea', # gmp-5.1.3.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz +] + +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/GCC/GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..d762426d0618730787e39f334cdde95902342b52 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.3-binutils-2.25.eb @@ -0,0 +1,45 @@ +name = "GCC" +version = '4.9.3' + +binutilsver = '2.25' +versionsuffix = '-binutils-%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': ''} + +mpfr_version = '3.1.2' + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(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 +] +sources = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.2.tar.gz', +] + +builddependencies = [('binutils', binutilsver)] + +patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + '6f831b4d251872736e8e9cc09746f327', # gcc-4.9.3.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/GCC/GCC-4.9.3.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..759f134bcc6554ea09caed6b0eb0282658430714 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb @@ -0,0 +1,40 @@ +name = "GCC" +version = '4.9.3' + +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': 'dummy'} + +mpfr_version = '3.1.2' + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(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 +] +sources = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.2.tar.gz', +] + +patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + '6f831b4d251872736e8e9cc09746f327', # gcc-4.9.3.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/GCC/GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..8bbf0ea88e7755cbc48981ead7cadf5f0b405f6b --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb @@ -0,0 +1,55 @@ +name = "GCC" +version = '5.1.0' + +binutilsver = '2.25' +versionsuffix = '-binutils-%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': ''} + +mpfr_version = '3.1.2' + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(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 = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.14.tar.bz2', +] + +builddependencies = [ + ('M4', '1.4.17'), + ('binutils', binutilsver), +] + +patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + 'd5525b1127d07d215960e6051c5da35e', # gcc-5.1.0.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'acd347243fca5609e3df37dba47fd0bb', # isl-0.14.tar.bz2 + '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.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/GCC/GCC-5.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb index 4968008ae895325e7b17c19fb5d8c5e1bb307a77..a69c58da2c59ea2dbfd2013b502eab93a8e43b60 100644 --- a/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb @@ -5,7 +5,7 @@ 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': 'dummy'} +toolchain = {'name': 'dummy', 'version': ''} mpfr_version = '3.1.2' @@ -28,6 +28,8 @@ sources = [ patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] +builddependencies = [('M4', '1.4.17')] + checksums = [ 'd5525b1127d07d215960e6051c5da35e', # gcc-5.1.0.tar.bz2 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb b/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..c25b63f7b1fd3d926eda88ef886de6f153214890 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb @@ -0,0 +1,49 @@ +name = 'GCC' +version = '5.2.0' + +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/%(namelower)s/%(namelower)s-%(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 = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.14.tar.bz2', +] + +patches = [('mpfr-%s-allpatches-20150717.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +builddependencies = [('M4', '1.4.17')] + +checksums = [ + 'a51bcfeb3da7dd4c623e27207ed43467', # gcc-5.2.0.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '7b650781f0a7c4a62e9bc8bdaaa0018b', # mpfr-3.1.l.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'acd347243fca5609e3df37dba47fd0bb', # isl-0.14.tar.bz2 + 'e502185ebb22b41c528f183bb22a7569', # mpfr-3.1.3-allpatches-20150717.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/GCC/GCC-system.eb b/easybuild/easyconfigs/g/GCC/GCC-system.eb new file mode 100644 index 0000000000000000000000000000000000000000..b24177d7132df72b011aaebf4e731d9047544eae --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-system.eb @@ -0,0 +1,23 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2015 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: 3-clause BSD +## + +easyblock = 'SystemCompiler' + +name = 'GCC' +# using 'system' as a version instructs the SystemCompiler easyblock to derive the actual compiler version, +# and define $EBVERSION* accordingly (yet generate a module named GCC/system); +# if an actual version is specified here, it will be checked against the version of the system compiler that was found +version = 'system' + +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': 'dummy'} + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/mpfr-3.1.3-allpatches-20150717.patch b/easybuild/easyconfigs/g/GCC/mpfr-3.1.3-allpatches-20150717.patch new file mode 100644 index 0000000000000000000000000000000000000000..779331605245842dba3b0acb4ba6535d88a2c3a9 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/mpfr-3.1.3-allpatches-20150717.patch @@ -0,0 +1,1699 @@ +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 (", 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 = '5.0.5' +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': '2015a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.2.2'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.58.0', '-Python-2.7.9')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GSSAPI/GSSAPI-0.28-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/g/GSSAPI/GSSAPI-0.28-intel-2014b-Perl-5.20.0.eb index fc5eb6da7baf8cd9ee8e2c19390f0cb8b4e05ef2..96fa7554f48868a220e1b02cff38fcc997e2c8a1 100644 --- a/easybuild/easyconfigs/g/GSSAPI/GSSAPI-0.28-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/g/GSSAPI/GSSAPI-0.28-intel-2014b-Perl-5.20.0.eb @@ -23,4 +23,10 @@ dependencies = [ options = {'modulename': 'GSSAPI'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/GSSAPI.pm' % (perlmajver, perlver)], + 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/GSSAPI' % (perlmajver, perlver)], +} + moduleclass = 'system' diff --git a/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a-GLib-2.44.1.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a-GLib-2.44.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..959c6d7b2b0fb2f636d5b2d9bb8e232962424da7 --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2015a-GLib-2.44.1.eb @@ -0,0 +1,29 @@ +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': '2015a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +glib = 'GLib' +glibver = '2.44.1' +versionsuffix = '-%s-%s' % (glib, glibver) + +dependencies = [ + (glib, glibver), +] + +sanity_check_paths = { + 'files': ['lib/libgts.so', 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [] +} + +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 new file mode 100644 index 0000000000000000000000000000000000000000..412c19225c040f5f5683c04e7a060fc2f3994e44 --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb @@ -0,0 +1,24 @@ +name = 'Geant4' +version = '10.01.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': '2015a'} + +source_urls = ['http://geant4.cern.ch/support/source'] +sources = ['%(namelower)s.%(version)s.tar.gz'] + +dependencies = [ + ('expat', '2.1.0'), + ('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" + +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 new file mode 100644 index 0000000000000000000000000000000000000000..0fa0ab2a82059ddfd643b9cd7fadd2967e62876a --- /dev/null +++ b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb @@ -0,0 +1,27 @@ +easyblock = 'PackedBinary' + +name = 'GenotypeHarmonizer' +version = '1.4.14' + +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'} + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +source_urls = ['http://www.molgenis.org/downloads/GenotypeHarmonizer/'] +sources = ['GenotypeHarmonizer-%(version)s-dist.tar.gz' ] + +checksums = ['0a7b041efdd7a5d7ced0ae48eb4a9e06'] + +sanity_check_paths = { + 'files': ['GenotypeHarmonizer.jar', 'GenotypeHarmonizer.sh'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..41de713278c1e3b91f359ce115801eb709adf51b --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-goolf-1.7.20.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '9.16' + +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': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = ["http://downloads.ghostscript.com/public/"] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['829319325bbdb83f5c81379a8f86f38f'] + +dependencies = [ + ('zlib', '1.2.8'), + ('libpng', '1.6.17'), + ('freetype', '2.6'), + ('fontconfig', '2.11.94'), + ('GLib', '2.44.1'), + ('libjpeg-turbo', '1.3.1'), # note: libjpeg-turbo 1.4.[01] doesn't work + ('expat', '2.1.0'), + ('cairo', '1.14.2'), + ('LibTIFF', '4.0.4'), +] + +configopts = "--with-system-libtiff --enable-dynamic" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-intel-2015a.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..691a90006b03337bbf9d6ec36b65ee8166d8125b --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.16-intel-2015a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '9.16' + +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': '2015a'} +# lowopt (-O1) is used to avoid internal compiler error that is hit when -O2 is used +toolchainopts = {'pic': True, 'lowopt': True} + +source_urls = ["http://downloads.ghostscript.com/public/"] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['829319325bbdb83f5c81379a8f86f38f'] + +dependencies = [ + ('zlib', '1.2.8'), + ('libpng', '1.6.17'), + ('freetype', '2.6'), + ('fontconfig', '2.11.94'), + ('GLib', '2.44.1'), + ('libjpeg-turbo', '1.3.1'), # note: libjpeg-turbo 1.4.[01] doesn't work + ('expat', '2.1.0'), + ('cairo', '1.14.2'), + ('LibTIFF', '4.0.4'), +] + +configopts = "--with-system-libtiff --enable-dynamic" + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.3-intel-2015a-openib.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.3-intel-2015a-openib.eb new file mode 100644 index 0000000000000000000000000000000000000000..160dbeb127845925db0e4bf223255a050ae82dbd --- /dev/null +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.3-intel-2015a-openib.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'GlobalArrays' +version = '5.3' +versionsuffix = '-openib' + +homepage = 'http://hpc.pnl.gov/globalarrays' +description = "Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://hpc.pnl.gov/globalarrays/download/'] +sources = ['ga-%(version_major)s-%(version_minor)s.tgz'] + +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +configopts = '--with-openib' +configopts += ' --with-blas8="-L$BLAS_LIB_DIR $LIBBLAS" --with-lapack="-L$LAPACK_LIB_DIR $LIBLAPACK"' +configopts += ' --with-scalapack8="-L$SCALAPACK_LIB_DIR $LIBSCALAPACK"' + +sanity_check_paths = { + 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', 'lib/libga.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/Go/Go-1.4.2-GCC-4.8.4.eb b/easybuild/easyconfigs/g/Go/Go-1.4.2-GCC-4.8.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..ef95adc2ea4c64ceafda9c35d8dc89b4a1c52645 --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.4.2-GCC-4.8.4.eb @@ -0,0 +1,21 @@ +# Author: Carlos Fenoy +# F. Hoffmann - La Roche + +name = 'Go' +version = '1.4.2' + +homepage = 'http://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +sources = ['%(namelower)s%(version)s.src.tar.gz'] +source_urls = ['https://storage.googleapis.com/golang/'] + +sanity_check_paths = { + 'files': ['bin/go', 'bin/gofmt'], + 'dirs': ['api', 'doc', 'include', 'pkg'], +} + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/Go/Go-1.5-GCC-4.8.4.eb b/easybuild/easyconfigs/g/Go/Go-1.5-GCC-4.8.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..a5378d6f2f089df0e26d5d47a5777edf63d1be0c --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.5-GCC-4.8.4.eb @@ -0,0 +1,23 @@ +# Author: Carlos Fenoy +# F. Hoffmann - La Roche + +name = 'Go' +version = '1.5' + +homepage = 'http://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +sources = ['%(namelower)s%(version)s.src.tar.gz'] +source_urls = ['https://storage.googleapis.com/golang/'] + +builddependencies = [('Go', '1.4.2')] + +sanity_check_paths = { + 'files': ['bin/go', 'bin/gofmt'], + 'dirs': ['api', 'doc', 'lib', 'pkg'], +} + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..4dc6df74624d5a9cd89b64a10a71ad2908c6a6c8 --- /dev/null +++ b/easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PerlModule' + +name = 'GraphViz' +version = '2.18' + +homepage = 'https://metacpan.org/pod/GraphViz' +description = """This module provides a Perl interface to the amazing Graphviz, +an open source graph visualization tool from AT&T.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE/'] +sources = [SOURCE_TGZ] + +perl = 'Perl' +perlver = '5.20.0' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ("Graphviz", "2.38.0"), +] + +options = {'modulename': 'GraphViz'} + +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/GraphViz.pm' % (perlmajver, perlver)], + 'dirs': ['lib/perl%s/site_perl/%s/GraphViz' % (perlmajver, perlver)], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GraphViz2/GraphViz2-2.33-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/g/GraphViz2/GraphViz2-2.33-intel-2014b-Perl-5.20.0.eb index 0165dca50950de26ca91c482892090abd079f677..aa178c12fe9484f5b143166b034a35afecd9581e 100644 --- a/easybuild/easyconfigs/g/GraphViz2/GraphViz2-2.33-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/g/GraphViz2/GraphViz2-2.33-intel-2014b-Perl-5.20.0.eb @@ -21,7 +21,12 @@ dependencies = [ ("Graphviz", "2.38.0"), ] - options = {'modulename': 'GraphViz2'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/GraphViz2.pm' % (perlmajver, perlver)], + 'dirs': ['lib/perl%s/site_perl/%s/GraphViz2' % (perlmajver, perlver)], +} + moduleclass = 'vis' 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 new file mode 100644 index 0000000000000000000000000000000000000000..513feabb7e000a7b4a2b1d5a84bf57b59f9c77c2 --- /dev/null +++ b/easybuild/easyconfigs/g/GraphicsMagick/GraphicsMagick-1.3.21-intel-2015b.eb @@ -0,0 +1,17 @@ +easyblock = 'ConfigureMake' + +name = 'GraphicsMagick' +version = '1.3.21' + +homepage = 'http://www.graphicsmagick.org/' +description = """GraphicsMagick is the swiss army knife of image processing.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [ + 'ftp://ftp.graphicsmagick.org/pub/GraphicsMagick/%(version_major_minor)s/', + SOURCEFORGE_SOURCE, +] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..c5e6a0512b1c00cafee989adddf11438caecbbd4 --- /dev/null +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-2.38.0-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,69 @@ +easyblock = 'ConfigureMake' + +name = 'Graphviz' +version = '2.38.0' + +homepage = 'http://www.graphviz.org/' +description = """Graphviz is open source graph visualization software. Graph visualization + is a way of representing structural information as diagrams of + abstract graphs and networks. It has important applications in networking, + bioinformatics, software engineering, database and web design, machine learning, + and in visual interfaces for other technical domains.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.graphviz.org/pub/graphviz/stable/SOURCES/'] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +glibsuff = '-GLib-2.44.1' + +dependencies = [ + ('cairo', '1.14.2'), + ('expat', '2.1.0'), + ('freetype', '2.6'), + ('fontconfig', '2.11.94'), + ('Ghostscript', '9.16'), + ('GTS', '0.7.6', glibsuff), + ('Java', '1.7.0_80', '', True), + ('libpng', '1.6.17'), + ('Pango', '1.37.2'), + ('Perl', '5.20.0'), + (python, pyver), + ('Qt', '4.8.6', glibsuff), + ('SWIG', '3.0.7', versionsuffix), + ('Tcl', '8.6.4'), + ('zlib', '1.2.8'), +] + +builddependencies = [ + ('M4', '1.4.17'), +] + +patches = [ + 'Graphviz-2.38.0_icc_vmalloc.patch', + 'Graphviz-2.38.0_icc_sfio.patch', +] + +configopts = '--enable-guile=no --enable-lua=no --enable-ocaml=no ' +configopts += '--enable-r=no --enable-ruby=no ' + +prebuildopts = 'qmake -o cmd/gvedit/qMakefile cmd/gvedit/gvedit.pro && ' + +sanity_check_paths = { + 'files': ['bin/cluster', 'bin/dot', 'bin/gvmap', + 'lib/libcdt.so', 'lib/libgvc.so', 'lib/libxdot.so'], + 'dirs': ['include'] +} + +modextrapaths = { + 'PYTHONPATH': 'lib/graphviz/python', + 'CLASSPATH': 'lib/graphviz/java/org/graphviz', + 'LD_LIBRARY_PATH': 'lib/graphviz/java', + 'TCLLIBPATH': 'lib/graphviz/tcl', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb b/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8e1cb764c0a1ba19d3813fbe54457af48da7a4fb --- /dev/null +++ b/easybuild/easyconfigs/g/Gtkmm/Gtkmm-2.24.4-intel-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Gtkmm' +version = '2.24.4' + +homepage = 'https://developer.gnome.org/gtk+/stable/' +description = """ + The Gtkmm package provides a C++ interface to GTK+ 2. +""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('Atkmm', '2.22.7'), + ('gtk+', '2.24.28'), + ('Pangomm', '2.36.0'), +] + +sanity_check_paths = { + 'files': ['lib/libgtkmm-2.4.so.1'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb b/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..342cbc03cbd9888948dd832ac52cc340ea4f3483 --- /dev/null +++ b/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb @@ -0,0 +1,28 @@ +name = 'g2log' +version = '1.0' +easyblock = 'CMakeMake' + +homepage = 'https://sites.google.com/site/kjellhedstrom2//g2log-efficient-background-io-processign-with-c11' +description = """g2log, efficient asynchronous logger using C++11""" + +toolchain = {'name': 'foss', 'version': '2014b'} + +source_urls = ['https://bitbucket.org/KjellKod/g2log/get/'] +sources = ['version-%(version)s.tar.gz'] + +preconfigopts = 'unzip ../3rdParty/gtest/gtest-1.6.0__stripped.zip -d ../3rdParty/gtest/ &&' +preinstallopts = 'mkdir %(installdir)s/lib && cp lib*.a %(installdir)s/lib ||' + +builddependencies = [ + ('CMake', '3.0.0'), +] + +start_dir = 'g2log' +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/liblib_g2logger.a', 'lib/liblib_activeobject.a'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/g2log/g2log-1.0-intel-2015b.eb b/easybuild/easyconfigs/g/g2log/g2log-1.0-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..882630ea2083be8896ae41e682274c54cf493143 --- /dev/null +++ b/easybuild/easyconfigs/g/g2log/g2log-1.0-intel-2015b.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'g2log' +version = '1.0' + +homepage = 'https://sites.google.com/site/kjellhedstrom2//g2log-efficient-background-io-processign-with-c11' +description = """g2log, efficient asynchronous logger using C++11""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['https://bitbucket.org/KjellKod/g2log/get/'] +sources = ['version-%(version)s.tar.gz'] + +preconfigopts = 'unzip ../3rdParty/gtest/gtest-1.6.0__stripped.zip -d ../3rdParty/gtest/ &&' +preinstallopts = 'mkdir %(installdir)s/lib && cp lib*.a %(installdir)s/lib ||' + +builddependencies = [ + ('CMake', '3.3.2', '', ('GNU', '4.9.3-2.25')), +] + +start_dir = 'g2log' +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/liblib_g2logger.a', 'lib/liblib_activeobject.a'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb b/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5cb8ff5f1fc6ff2e43b97646fe1d47dd3c04bdf0 --- /dev/null +++ b/easybuild/easyconfigs/g/gdk-pixbuf/gdk-pixbuf-2.31.4-intel-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'gdk-pixbuf' +version = '2.31.4' + +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': '2015a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.41.2'), + ('libjpeg-turbo', '1.4.0'), + ('libpng', '1.6.17'), + ('LibTIFF', '4.0.3'), + +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gensim/gensim-0.11.1-1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/g/gensim/gensim-0.11.1-1-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..f497f885414f3605533ae38350e095ce8f31f5fe --- /dev/null +++ b/easybuild/easyconfigs/g/gensim/gensim-0.11.1-1-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'gensim' +version = '0.11.1-1' + +homepage = 'https://pypi.python.org/pypi/gensim' +description = """Gensim is a Python library for topic modelling, document indexing and similarity retrieval with + large corpora.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.10' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..b9b28dda44512de1295192445b2a890d43073bb4 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.2' + +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': 'goolf', 'version': '1.7.20'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..51c244d3eff5c7d5b62da4103211813b817abde1 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.4' + +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': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2015a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0dbf6fce3a8884073753360e0c6aab83b9d26e95 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-intel-2015a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.4' + +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': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' 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 48bda49ebe43fce3f118dbe803b088fc00933a2a..6a03e95dbafbc41d59d61b0dbcd5508c4488d4e6 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 @@ -25,18 +25,19 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/git/git/archive'] -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 = "--enable-pthreads='-lpthread'" - dependencies = [ ('cURL', '7.40.0'), ('expat', '2.1.0'), ('gettext', '0.19.4'), + ('Perl', '5.20.1', '-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=${EBPERLROOT} --enable-pthreads='-lpthread'" + sanity_check_paths = { 'files': ['bin/git'], 'dirs': [], diff --git a/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..ec7ac4488bbd61fefb6b589c0f6a1b799a480feb --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb @@ -0,0 +1,46 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# Authors:: Dmitri Gribenko +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.4.1' + +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': 'GCC', 'version': '4.9.2'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/git/git/archive'] + +dependencies = [ + ('cURL', '7.40.0'), + ('expat', '2.1.0'), + ('gettext', '0.19.4'), + ('Perl', '5.20.1', '-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-1.4.17-intel-2015a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e6478944220aff106ad7a49015f88255bc326e02 --- /dev/null +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2015a.eb @@ -0,0 +1,21 @@ +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': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +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/gnuplot/gnuplot-5.0.0-intel-2014b.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..e30d4a22d3964442fee4dead1790dd0cf9d8e671 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2014b.eb @@ -0,0 +1,35 @@ +## +# 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 = '5.0.0' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] + +dependencies = [ + ('cairo', '1.12.18'), + ('libjpeg-turbo', '1.3.1'), +] + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8f7d80279e437e7a1061d89c9f493698a37a23b3 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb @@ -0,0 +1,35 @@ +## +# 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 = '5.0.0' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] + +dependencies = [ + ('cairo', '1.12.18'), + ('libjpeg-turbo', '1.4.0'), +] + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2015b.eb b/easybuild/easyconfigs/g/gompi/gompi-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..dd242ab25460a3de3c52dfacb747ef68fb71c783 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2015b.eb @@ -0,0 +1,23 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '2015b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '4.9.3' +binutilsver = '2.25' +tcver = '%s-binutils-%s' % (gccver, binutilsver) + +# compiler toolchain dependencies +dependencies = [ + ('GCC', gccver, '-binutils-%s' % binutilsver), + ('binutils', binutilsver, '', ('GCC', tcver)), + ('OpenMPI', '1.8.8', '', ('GNU', '%s-%s' % (gccver, binutilsver))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..d44084ea5c696190de421111735b187edcc519a4 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.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': 'intel', 'version': '2014b'} + +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-intel-2015a.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..03d48cbdf1cf69f7f17b3ff896b85515b8f3e7c8 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2015a.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': 'intel', 'version': '2015a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.4-foss-2015a.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.4-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..49065c9ee91121f9ba3694533f15218c045c207f --- /dev/null +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.4-foss-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = "gperftools" +version = "2.4" + +homepage = 'http://github.com/gperftools/gperftools' +description = """gperftools are for use by developers so that they can create more robust applications. + Especially of use to those developing multi-threaded applications in C++ with templates. + Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/gperftools/gperftools/releases/download/%(namelower)s-%(version)s'] + +builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] +dependencies = [('libunwind', '1.1')] + +sanity_check_paths = { + 'files': ["bin/pprof"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gsl/gsl-1.9-10-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/g/gsl/gsl-1.9-10-intel-2014b-R-3.1.1.eb index 616d9c30208019514b75e6d985a3814768dc38ca..36d3ba68631d49bf1c732dba61e9bd0955eb20cd 100644 --- a/easybuild/easyconfigs/g/gsl/gsl-1.9-10-intel-2014b-R-3.1.1.eb +++ b/easybuild/easyconfigs/g/gsl/gsl-1.9-10-intel-2014b-R-3.1.1.eb @@ -21,4 +21,9 @@ dependencies = [ ('GSL', '1.16'), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['gsl'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015a.eb b/easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..289385029dcddb633dbe20464e5a546e496c3e09 --- /dev/null +++ b/easybuild/easyconfigs/g/gtk+/gtk+-2.24.28-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'gtk+' +version = '2.24.28' + +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': '2015a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('ATK', '2.16.0'), + ('gdk-pixbuf', '2.31.4'), + ('Pango', '1.37.1'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb b/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..aeb9e7c8b09993a26717028cbcf8c09e9382df56 --- /dev/null +++ b/easybuild/easyconfigs/h/HBase/HBase-1.0.2.eb @@ -0,0 +1,25 @@ +easyblock = 'PackedBinary' + +name = 'HBase' +version = '1.0.2' + +homepage = 'http://hbase.apache.org/' +description = """Apache HBase. is the Hadoop database, a distributed, scalable, big data store. """ + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s-bin.tar.gz'] +source_urls = ['http://www.us.apache.org/dist/hbase/hbase-%(version)s/'] + +dependencies = [('Java', '1.7.0_80')] + +parallel = 1 + +sanity_check_paths = { + 'files': ["bin/hbase"], + 'dirs': ["conf", "docs", "hbase-webapps", "lib"] +} + +modextravars = {'HBASE_HOME': '%(installdir)s'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb index 5cdf92f035541cfe3317133e862ce009ca817810..fa154ada7f7a483362f151230d9465406a9b1432 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb index 49d7098c878710ad31eacf34082f1ecc8471bef2..558ae70b7fead833a82eff5cee73a0dea7c48c41 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb index 6de0d3d8d3aa53bd540fda7d95c5c72477842d89..0464a3968b9daadd5fce2e177691289c0a8dca31 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb index 46c998562cdf1cbeb1ca1f786e6891ca86f453f4..c9298da39e098f68203b0399ec5b37e8d4571972 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb index b955c4abf7a5b35cd2dcf579c2cda40df6723523..8d4de54b7a9cc467b0c988b9426d0e7b12dea352 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb index c9f730872f6f4006d0b4d05cb59a1318add4d337..fa2a08d015f88a23d2d45730b000606a4e9d4f28 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb @@ -18,7 +18,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb index 6866cddf63e8649a6b3e3d333e96f67e9fdc88d9..fa449b6641226d1b6bcc631c9c99d29cad57952d 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb new file mode 100755 index 0000000000000000000000000000000000000000..1b265145240d6ea7e0f89738ff56a01b6db7755e --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb @@ -0,0 +1,31 @@ +name = 'HDF5' +version = '1.8.10' +versionsuffix = "-gpfs" + +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': 'ictce', 'version': '5.3.0'} +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 = [ + 'HDF5_%(version)s_configure_ictce.patch', + 'HDF5-%(version)s_mpi-includes_order_fix.patch' +] + +zlib = 'zlib' +zlibver = '1.2.5' +versionsuffix += '-%s-%s' % (zlib, zlibver) + +dependencies = [ + (zlib, zlibver), + ('Szip', '2.1'), +] + +configopts = "--enable-gpfs" + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.4.0-gpfs.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.4.0-gpfs.eb new file mode 100644 index 0000000000000000000000000000000000000000..126e4735841547a9bd4289b7e921d2b25f887cd8 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.4.0-gpfs.eb @@ -0,0 +1,27 @@ +name = 'HDF5' +version = '1.8.10' +versionsuffix = "-gpfs" + +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': 'ictce', 'version': '5.4.0'} +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 = [ + 'HDF5_%(version)s_configure_ictce.patch', + 'HDF5-%(version)s_mpi-includes_order_fix.patch' +] + +dependencies = [ + ('zlib', '1.2.7'), + ('Szip', '2.1'), +] + +configopts = "--enable-gpfs" + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-6.1.5-gpfs.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-6.1.5-gpfs.eb new file mode 100644 index 0000000000000000000000000000000000000000..caf75ce765720f6717d7c9c969ed3dca67c459c6 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-6.1.5-gpfs.eb @@ -0,0 +1,27 @@ +name = 'HDF5' +version = '1.8.10' +versionsuffix = "-gpfs" + +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': 'ictce', 'version': '6.1.5'} +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 = [ + 'HDF5_%(version)s_configure_ictce.patch', + 'HDF5-%(version)s_mpi-includes_order_fix.patch' +] + +dependencies = [ + ('zlib', '1.2.7'), + ('Szip', '2.1'), +] + +configopts = "--enable-gpfs" + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2014b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..2af8e449bf044a78d309b97dc0aef326b903e3d6 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2014b.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.8.13' + +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': '2014b'} +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 = ['configure_libtool.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f79d365b61b675b858b3a5ff607c123d7ae398ce --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb @@ -0,0 +1,25 @@ +name = 'HDF5' +version = '1.8.13' + +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': '2015a'} +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 = [ + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..35077bfe35b1c7586ed630324ffed3b37be0a40b --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb @@ -0,0 +1,26 @@ +# Built with EasyBuild version 2.2.0dev on 2015-06-16_11-02-41 +name = 'HDF5' +version = "1.8.14" + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a-gpfs.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb similarity index 92% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a-gpfs.eb rename to easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb index 081c94297ddd33ad48811872beb4006d5af52e9b..2b7af38374dd2b305c787158d6b82bcd54e5aaa6 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a-gpfs.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb @@ -1,6 +1,5 @@ name = 'HDF5' version = '1.8.14' -versionsuffix = '-gpfs' homepage = 'http://www.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of @@ -17,7 +16,6 @@ patches = [ 'configure_libtool.patch', ] -configopts = "--enable-gpfs" buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' dependencies = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..ef7549e98750a39c283e048d38a0641d2b1e02c7 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb @@ -0,0 +1,23 @@ +name = 'HDF5' +version = '1.8.15' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9b028b25b80993ead6d4eed8d6aeb7b7a0e9f432 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.15' + +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': '2015a'} +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-%(version)s_configure_intel.patch', + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a9ec210198beb82aa7b7f62a359dbeb28d19e940 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb @@ -0,0 +1,23 @@ +name = 'HDF5' +version = '1.8.15-patch1' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..ec9b5d3a8a312b650c67e1dbcbf0e7e6d5698017 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.15-patch1' + +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': '2015a'} +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="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15_configure_intel.patch b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15_configure_intel.patch new file mode 100644 index 0000000000000000000000000000000000000000..b74e70593eec71c6a79ec650a4f1419b6af1683f --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15_configure_intel.patch @@ -0,0 +1,95 @@ +--- hdf5-1.8.15/configure.orig 2015-05-01 20:56:59.000000000 +0200 ++++ hdf5-1.8.15/configure 2015-06-02 15:04:26.757168623 +0200 +@@ -5190,7 +5190,7 @@ + ac_link='$FC -o conftest$ac_exeext $FCFLAGS $LDFLAGS $ac_fcflags_srcext conftest.$ac_ext $LIBS >&5' + ac_compiler_gnu=$ac_cv_fc_compiler_gnu + if test -n "$ac_tool_prefix"; then +- for ac_prog in gfortran g95 xlf95 f95 fort ifort ifc efc pgfortran pgf95 lf95 ftn nagfor xlf90 f90 pgf90 pghpf epcf90 g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 ++ for ac_prog in gfortran g95 xlf95 f95 fort ifort mpif77 mpif90 ifc efc pgfortran pgf95 lf95 ftn nagfor xlf90 f90 pgf90 pghpf epcf90 g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. + set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +@@ -5234,7 +5234,7 @@ + fi + if test -z "$FC"; then + ac_ct_FC=$FC +- for ac_prog in gfortran g95 xlf95 f95 fort ifort ifc efc pgfortran pgf95 lf95 ftn nagfor xlf90 f90 pgf90 pghpf epcf90 g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 ++ for ac_prog in gfortran g95 xlf95 f95 fort ifort mpif77 mpif90 ifc efc pgfortran pgf95 lf95 ftn nagfor xlf90 f90 pgf90 pghpf epcf90 g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 + do + # Extract the first word of "$ac_prog", so it can be a program name with args. + set dummy $ac_prog; ac_word=$2 +@@ -11993,7 +11993,7 @@ + ;; + # icc used to be incompatible with GCC. + # ICC 10 doesn't accept -KPIC any more. +- icc* | ifort*) ++ icc* | mpicc*| ifort* | mpif77* | mpif90*) + lt_prog_compiler_wl='-Wl,' + lt_prog_compiler_pic='-fPIC' + lt_prog_compiler_static='-static' +@@ -12629,11 +12629,11 @@ + # Portland Group f77 and f90 compilers + whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` ${wl}--no-whole-archive' + tmp_addflag=' $pic_flag -Mnomain' ;; +- ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64 ++ ecc*,ia64* | icc*,ia64* | mpicc*,ia64*) # Intel C compiler on ia64 + tmp_addflag=' -i_dynamic' ;; +- efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64 ++ efc*,ia64* | ifort*,ia64* | mpif77*,ia64* | mpif90*,ia64*) # Intel Fortran compiler on ia64 + tmp_addflag=' -i_dynamic -nofor_main' ;; +- ifc* | ifort*) # Intel Fortran compiler ++ ifc* | ifort* | mpif77* | mpif90*) # Intel Fortran compiler + tmp_addflag=' -nofor_main' ;; + lf95*) # Lahey Fortran 8.1 + whole_archive_flag_spec= +@@ -13115,7 +13115,7 @@ + link_all_deplibs=yes + allow_undefined_flag="$_lt_dar_allow_undefined" + case $cc_basename in +- ifort*) _lt_dar_can_shared=yes ;; ++ ifort* | mpif77* | mpif90*) _lt_dar_can_shared=yes ;; + *) _lt_dar_can_shared=$GCC ;; + esac + if test "$_lt_dar_can_shared" = "yes"; then +@@ -16113,7 +16113,7 @@ + link_all_deplibs_CXX=yes + allow_undefined_flag_CXX="$_lt_dar_allow_undefined" + case $cc_basename in +- ifort*) _lt_dar_can_shared=yes ;; ++ ifort* | mpif77* | mpif90*) _lt_dar_can_shared=yes ;; + *) _lt_dar_can_shared=$GCC ;; + esac + if test "$_lt_dar_can_shared" = "yes"; then +@@ -19024,7 +19024,7 @@ + ;; + # icc used to be incompatible with GCC. + # ICC 10 doesn't accept -KPIC any more. +- icc* | ifort*) ++ icc* | mpicc* | ifort* | mpif77* | mpif90*) + lt_prog_compiler_wl_FC='-Wl,' + lt_prog_compiler_pic_FC='-fPIC' + lt_prog_compiler_static_FC='-static' +@@ -19645,11 +19645,11 @@ + # Portland Group f77 and f90 compilers + whole_archive_flag_spec_FC='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` ${wl}--no-whole-archive' + tmp_addflag=' $pic_flag -Mnomain' ;; +- ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64 ++ ecc*,ia64* | icc*,ia64* | mpicc*,ia64*) # Intel C compiler on ia64 + tmp_addflag=' -i_dynamic' ;; +- efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64 ++ efc*,ia64* | ifort*,ia64* | mpif77*,ia64* | mpif90*,ia64*) # Intel Fortran compiler on ia64 + tmp_addflag=' -i_dynamic -nofor_main' ;; +- ifc* | ifort*) # Intel Fortran compiler ++ ifc* | ifort* | mpif77* | mpif90*) # Intel Fortran compiler + tmp_addflag=' -nofor_main' ;; + lf95*) # Lahey Fortran 8.1 + whole_archive_flag_spec_FC= +@@ -20103,7 +20103,7 @@ + link_all_deplibs_FC=yes + allow_undefined_flag_FC="$_lt_dar_allow_undefined" + case $cc_basename in +- ifort*) _lt_dar_can_shared=yes ;; ++ ifort* | mpif77* | mpif90*) _lt_dar_can_shared=yes ;; + *) _lt_dar_can_shared=$GCC ;; + esac + if test "$_lt_dar_can_shared" = "yes"; then diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.4.0.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..4c1c1db1578db6be85e910c3e6e75f33e56f5094 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-5.4.0.eb @@ -0,0 +1,25 @@ +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': 'ictce', 'version': '5.4.0'} +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 = [ + 'HDF5_configure_ictce.patch', + 'configure_libtool.patch', + 'HDF5-%(version)s_mpi-includes_order_fix.patch', +] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-intel-2014b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..24af13ad70b0d0e2c7d768743b5c98f6cf11bdb7 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-intel-2014b.eb @@ -0,0 +1,25 @@ +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': 'intel', 'version': '2014b'} +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 = [ + 'HDF5_configure_ictce.patch', + 'configure_libtool.patch', + 'HDF5-%(version)s_mpi-includes_order_fix.patch', +] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5255f85ddcd37709b77b7063e1420b3759793394 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.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': 'intel', 'version': '2015a'} + +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-foss-2015b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..728ad9cf2ed2e878b157a4c9277d0696b734a900 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015b.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': '2015b'} +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-2015b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..fa34ec665e54f173d1b536839ea64eeed157db7f --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2015b.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': '2015b'} +toolchainopts = {'optarch': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..0118dd4b321394c81e947a4e24d53643924d98ea --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'HTSeq' +version = '0.6.1p1' + +homepage = 'http://www-huber.embl.de/users/anders/HTSeq/' +description = """A framework to process and analyze data from high-throughput sequencing (HTS) assays""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.8' +pyshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) +eggname = '%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % pyshortver + +dependencies = [ + (python, pythonver), + ('matplotlib', '1.3.1', versionsuffix), +] + +sanity_check_paths = { + 'files': ["bin/htseq-count", "bin/htseq-qa"], + 'dirs': ["lib/python%s/site-packages/%s" % (pyshortver, eggname)], +} + +options = {'modulename': '%(name)s'} + +moduleclass = 'data' 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 new file mode 100644 index 0000000000000000000000000000000000000000..465b0a7d53d7e7213cff80e758080e7de1f6444f --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.2.1-intel-2015b.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 = '1.2.1' + +homepage = "http://www.htslib.org/" +description = """ A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix """ + +toolchain = {'name': 'intel', 'version': '2015b'} + +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.so"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb index fea9291ff726a03922154f42c2567644117aab0e..0b189ca56d3f4dec1c9633a205696176c2ae5459 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb @@ -19,12 +19,15 @@ builddependencies = [ ('Maven', '3.2.3'), ('protobuf', '2.5.0'), ('CMake', '3.1.3'), + ('snappy', '1.1.2', '', ('GCC', '4.9.2')), ] dependencies = [(java, javaver)] build_native_libs = True +extra_native_libs = [('snappy', 'lib/libsnappy.so*')] + parallel = 1 moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.4.5-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.4.5-native.eb new file mode 100644 index 0000000000000000000000000000000000000000..e848ea7c2c2c85989f805e0465346ba195630013 --- /dev/null +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.4.5-native.eb @@ -0,0 +1,30 @@ +name = 'Hadoop' +version = '2.6.0-cdh5.4.5' +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', '3.3.3'), + ('protobuf', '2.5.0'), # *must* be this version + ('CMake', '3.3.1'), + ('snappy', '1.1.3', '', ('GCC', '4.9.3')), +] + +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-0.9.41-intel-2015a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..30ed702ef86d44117360b5f12f6125071e4e9670 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '0.9.41' + +homepage = 'http://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['HarfBuzz-%(version)s_no_symbolic.patch'] + +dependencies = [ + ('cairo', '1.14.2'), + ('GLib', '2.41.2'), +] + +sanity_check_paths = { + 'files': ["lib/libharfbuzz.so"], + 'dirs': [""], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41_no_symbolic.patch b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41_no_symbolic.patch new file mode 100644 index 0000000000000000000000000000000000000000..95722f9e5ea9047c01e7a3190447a7342c772fb7 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-0.9.41_no_symbolic.patch @@ -0,0 +1,11 @@ +--- configure.orig 2013-07-02 16:46:02.548302080 +0200 ++++ configure 2013-07-02 16:47:50.428410650 +0200 +@@ -16342,7 +16342,7 @@ + if test "x$GCC" = "xyes"; then + + # Make symbols link locally +- LDFLAGS="$LDFLAGS -Bsymbolic-functions" ++ LDFLAGS="$LDFLAGS" # -Bsymbolic-functions" + + # Make sure we don't link to libstdc++ + CXXFLAGS="$CXXFLAGS -fno-rtti -fno-exceptions" diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d96b54ef9349e23496e8739ddc6cad9ac3def7d0 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-1.0.1-intel-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '1.0.1' + +homepage = 'http://www.harfbuzz.org/' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('cairo', '1.14.2'), + ('GObject-Introspection', '1.44.0'), +] + +configopts = '--with-gobject --enable-introspection=yes ' + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.so', 'bin/hb-view'], + 'dirs': [] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.10.1-intel-2015b.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.10.1-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..aba4719bc98fb134770df85d856cda419055563e --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.10.1-intel-2015b.eb @@ -0,0 +1,22 @@ +name = 'Hypre' +version = '2.10.1' + +homepage = "https://computation.llnl.gov/casc/linear_solvers/sls_hypre.html" +description = """Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. + The problems of interest arise in the simulation codes being developed at LLNL and elsewhere + to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = ['https://computation.llnl.gov/project/linear_solvers/download/'] +sources = [SOURCELOWER_TAR_GZ] + +start_dir = 'src' + +sanity_check_paths = { + 'files': ['lib/libHYPRE.a'], + 'dirs': ['include'] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb similarity index 79% rename from easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb rename to easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb index d6f4de7c558d6d7859400e4dd714503fca77a074..f4b587afd4aa2054301c87265af5847f3def6a25 100644 --- a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9-gpfs.eb +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb @@ -17,12 +17,14 @@ sources = [SOURCE_TAR_GZ] python = 'Python' pyver = '2.7.9' pyshortver = '.'.join(pyver.split('.')[0:2]) -hdf5suff = '-gpfs' -versionsuffix = '-%s-%s%s' % (python, pyver, hdf5suff) +versionsuffix = '-%s-%s' % (python, pyver) + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' dependencies = [ (python, pyver), - ('HDF5', '1.8.14', hdf5suff), + ('HDF5', '1.8.14'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..f6063d9ec35a143e9b23bae2bc733ae1d1949d8f --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'hanythingondemand' +version = '2.2.2' + +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': '2015a'} + +source_urls = [ + 'https://github.com/hpcugent/hanythingondemand/archive/' +] +sources = ['%s.tar.gz' % version] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +dependencies = [ + (python, pythonver), + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), + ('netifaces', '0.10.4', versionsuffix), + ('netaddr', '0.7.14', versionsuffix), +] + +options = {'modulename': 'hod'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..9182229d2c9e1f13e0d42aaf6cd73d6df89c6bc2 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'hanythingondemand' +version = '2.2.3' + +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': '2015a'} + +source_urls = [ + 'https://github.com/hpcugent/hanythingondemand/archive/' +] +sources = ['%s.tar.gz' % version] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +dependencies = [ + (python, pythonver), + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), + ('netifaces', '0.10.4', versionsuffix), + ('netaddr', '0.7.14', versionsuffix), +] + +options = {'modulename': 'hod'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..73433b308159d427ef171befba8b28610014dbe4 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'hanythingondemand' +version = '2.2.4' + +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': '2015a'} + +source_urls = [ + 'https://github.com/hpcugent/hanythingondemand/archive/' +] +sources = ['%s.tar.gz' % version] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +dependencies = [ + (python, pythonver), + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), + ('netifaces', '0.10.4', versionsuffix), + ('netaddr', '0.7.14', versionsuffix), +] + +options = {'modulename': 'hod'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb b/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..bd8c70bf67223e9464b03585ce21bfc46b274acd --- /dev/null +++ b/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'hisat' +version = '0.1.5-beta' + +homepage = 'http://ccb.jhu.edu/software/hisat/index.shtml' +description = """HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one + global FM index that represents a whole genome, HISAT uses a large set of small FM indexes that collectively cover + the whole genome (each index represents a genomic region of ~64,000 bp and ~48,000 indexes are needed to cover the + human genome). These small indexes (called local indexes) combined with several alignment strategies enable effective + alignment of RNA-seq reads, in particular, reads spanning multiple exons. The memory footprint of HISAT is relatively + low (~4.3GB for the human genome). We have developed HISAT based on the Bowtie2 implementation to handle most of the + operations on the FM index. """ + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = ['%(name)s-%(version)s-source.zip'] +source_urls = ['http://ccb.jhu.edu/software/hisat/downloads/'] + +checksums = ['9524a0170d85c5b560b51e0087f4cf46'] + +executables = [name, 'hisat-build', 'hisat-inspect', 'hisat-build-s', 'hisat-inspect-s', 'hisat-align-s', + 'hisat-build-l', 'hisat-inspect-l', 'hisat-align-l'] +files_to_copy = [(executables, 'bin')] + + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.0-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..086602c3aaf50781106cfef41fc7f86d4fbcfcea --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.0-GNU-4.9.3-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.0' + +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': 'GNU', 'version': '4.9.3-2.25'} + +dependencies = [('numactl', '2.0.10')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..1f891126fda663c4c5aebf6d38c3e68af3503871 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = "1.7.2" + +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': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..0ee4a4f74034fad3f36869481aeeec6c9b721695 --- /dev/null +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb @@ -0,0 +1,41 @@ +# 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 + +# "make install" doesnt copy all the compiled binaries so we use the "MakeCp" easyblock +# to be sure everything is copied and we run ./configure in premakeopts +easyblock = 'MakeCp' + +name = 'IDBA-UD' +version = '1.1.1' + +homepage = 'http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/' +description = """ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads + Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. + IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth + contigs are removed iteratively with cutoff threshold from low to high to reduce the errors + in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled + locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD + can iterate k value of de Bruijn graph to a very large value with less gaps and less branches + to form long contigs in both low-depth and high-depth regions.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://hku-idba.googlecode.com/files/'] +sources = ['idba-%(version)s.tar.gz'] + +prebuildopts = './configure && ' + +# we delete every .o file which is left in bin folder +buildopts = ' && rm -fr bin/*.o && rm -fr bin/Makefile*' + +files_to_copy = ["bin", "script", "README", "ChangeLog", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["idba", "idba_hybrid", "idba_tran", + "idba_ud", "parallel_blat", "idba_tran_test"]], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb new file mode 100644 index 0000000000000000000000000000000000000000..0c2d1cc059f006bddc7a05b94fb798a5367e0932 --- /dev/null +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.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 = "Tarball" + +name = 'IMPUTE2' +version = '2.3.0' +versionsuffix = '_x86_64_dynamic' + +homepage = 'http://mathgen.stats.ox.ac.uk/impute/impute_v2.html' +description = """ IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation + and haplotype phasing program based on ideas from Howie et al. 2009 """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://mathgen.stats.ox.ac.uk/impute/'] +sources = ['%s_v%s%s.tgz' % (name.lower().rstrip('2'), version, versionsuffix)] + +sanity_check_paths = { + 'files': ["impute2"], + 'dirs': ["Example"] +} + +# add the top dir to PATH +modextrapaths = { + 'PATH': '' +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb new file mode 100644 index 0000000000000000000000000000000000000000..0fb795f7ebb564400e36a11a7e35d953cd58f5a7 --- /dev/null +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.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 = "Tarball" + +name = 'IMPUTE2' +version = '2.3.0' +versionsuffix = '_x86_64_static' + +homepage = 'http://mathgen.stats.ox.ac.uk/impute/impute_v2.html' +description = """ IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation + and haplotype phasing program based on ideas from Howie et al. 2009 """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://mathgen.stats.ox.ac.uk/impute/'] +sources = ['%s_v%s%s.tgz' % (name.lower().rstrip('2'), version, versionsuffix)] + +sanity_check_paths = { + 'files': ["impute2"], + 'dirs': ["Example"] +} + +# add the top dir to PATH +modextrapaths = { + 'PATH': '' +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-goolf-1.4.10.eb new file mode 100755 index 0000000000000000000000000000000000000000..690d220498ad0ff3898c804498cf8d4ef8983efe --- /dev/null +++ b/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-goolf-1.4.10.eb @@ -0,0 +1,23 @@ +easyblock = 'MakeCp' + +name = 'IMa2' +version = '8.27.12' + +homepage = 'https://bio.cst.temple.edu/~hey/software/software.htm#IMa2' +description = """IMa2 is a progam for population genetic analysis that can handle two or more populations.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://bio.cst.temple.edu/~hey/program_files/IMa2'] +sources = [SOURCELOWER_TAR_GZ] + +with_configure = True + +files_to_copy = [(['src/IMa2'], 'bin')] + +sanity_check_paths = { + 'files': ["bin/IMa2"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-ictce-5.5.0.eb b/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-ictce-5.5.0.eb new file mode 100755 index 0000000000000000000000000000000000000000..a3ed62f5d6aa488d3e79a67e80fa2d071732178d --- /dev/null +++ b/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-ictce-5.5.0.eb @@ -0,0 +1,23 @@ +easyblock = 'MakeCp' + +name = 'IMa2' +version = '8.27.12' + +homepage = 'https://bio.cst.temple.edu/~hey/software/software.htm#IMa2' +description = """IMa2 is a progam for population genetic analysis that can handle two or more populations.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['https://bio.cst.temple.edu/~hey/program_files/IMa2'] +sources = [SOURCELOWER_TAR_GZ] + +with_configure = True + +files_to_copy = [(['src/IMa2'], 'bin')] + +sanity_check_paths = { + 'files': ["bin/IMa2"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb index 3c52ea836c798912cb345632a59c5f5ce2a91da5..92f605169bdefe0d13a2793776b66062185261b6 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb @@ -14,11 +14,14 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://archive.ipython.org/release/%(version)s/'] +source_urls = [ + PYPI_LOWER_SOURCE, + 'http://archive.ipython.org/release/%(version)s/', +] python = 'Python' pyver = '2.7.3' -pyshortver = '2.7' +pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb index 377e6789046e456a8a2ccb9d4a0f5a0817da20bd..4ddce0d14217ddea9252339d3f412bfbf3096dc5 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb @@ -14,11 +14,14 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://archive.ipython.org/release/%(version)s/'] +source_urls = [ + PYPI_LOWER_SOURCE, + 'http://archive.ipython.org/release/%(version)s/', +] python = 'Python' pyver = '2.7.9' -pyshortver = '2.7' +pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..ca831cfe277d6b150831f9d9ed43addffeb5ac45 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,45 @@ +easyblock = "PythonPackage" + +name = 'IPython' +version = '3.2.0' + +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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + PYPI_LOWER_SOURCE, + 'http://archive.ipython.org/release/%(version)s/', +] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('pysqlite', '2.6.3', versionsuffix), + ('PyZMQ', '14.7.0', '%s-zmq3' % versionsuffix), + ('requests', '2.7.0', versionsuffix), + ('Pygments', '2.0.2', versionsuffix), +] + +# override extensions sanity check, default filter that imports a Python module doesn't work here +exts_filter = ('ipython -h', '') + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], +} + +sanity_check_commands = [('iptest','')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..5b0893e10be373866c73d86d2eb56554615bc7b7 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,45 @@ +easyblock = "PythonPackage" + +name = 'IPython' +version = '3.2.0' + +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'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + PYPI_LOWER_SOURCE, + 'http://archive.ipython.org/release/%(version)s/', +] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('pysqlite', '2.6.3', versionsuffix), + ('PyZMQ', '14.7.0', '%s-zmq3' % versionsuffix), + ('requests', '2.7.0', versionsuffix), + ('Pygments', '2.0.2', versionsuffix), +] + +# override extensions sanity check, default filter that imports a Python module doesn't work here +exts_filter = ('ipython -h', '') + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], +} + +sanity_check_commands = [('iptest','')] + +moduleclass = 'tools' 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 new file mode 100644 index 0000000000000000000000000000000000000000..4c966b0d8aa55b12cf8fad541c67d26de4513414 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.1-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,78 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '3.2.1' + +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'} + +python = 'Python' +pyver = '2.7.10' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('PyZMQ', '14.7.0', '%s-zmq4' % versionsuffix), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('pysqlite', '2.7.0', { + 'modulename': 'pysqlite2', + 'source_urls': ['https://pypi.python.org/packages/source/p/pysqlite/'], + }), + ('requests', '2.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + }), + ('tornado', '4.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.5', { + '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%s/site-packages' % pyshortver]} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1-intel-2015b.eb b/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..2a084a988257ef19593e239a09b0c648e83c21fa --- /dev/null +++ b/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1-intel-2015b.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'ISIS' +version = '4.2.1' + +homepage = 'https://gforge.irsn.fr/gf/project/isis/' +description = """ISIS is Computational Fluid Dynamics software based on CALIF3S and PELICANS libraries. It is + intensively used for simulation of fires and copes with a wide range of applications, including laminar or turbulent + flows, possibly reactive, governed by incompressible or low Mach number Navier-Stokes equations.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +# disable optimizing for host architecture, may cause tests to fail due to issues with result validation +toolchainopts = {'optarch': False} + +source_urls = ['https://gforge.irsn.fr/gf/download/frsrelease/3626/39835/'] +sources = [SOURCELOWER_TGZ] + +patches = [ + 'ISIS-%(version)s_impi.patch', + 'ISIS-%(version)s_specify-system-in-tests.patch', +] + +dependencies = [('METIS', '4.0.3')] + +skipsteps = ['configure', 'install'] + +unpack_options = '--strip-components=1' +buildininstalldir = True + +# options used both in build and test step +commonopts = 'CCC="$CC" ISISHOME=%(installdir)s/ISIS ' +commonopts += 'WITH_MPI=1 MPIRUN=$EBROOTIMPI/bin64/mpiexec.hydra ' +commonopts += 'WITH_METIS=1 METISPATH=$EBROOTMETIS/lib ' + +buildopts = "install LICENSE=accept " + commonopts + +parallel = 1 + +runtest = 'test ' + commonopts +runtest += '&& make test_install ' + commonopts +runtest += '&& make test_MPI ' + commonopts +runtest += '&& make test_METIS ' + commonopts + +binaries = ['isis', 'isis_batch', 'isis_run', 'isis_s2c', 'isis_sylvia'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['init.csh', 'init.sh', 'xisis'] + binaries], + 'dirs': ['CALIFS', 'ISIS', 'PELICANS'], +} + +modextrapaths = {'ISISHOME': 'ISIS'} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_impi.patch b/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_impi.patch new file mode 100644 index 0000000000000000000000000000000000000000..2a47d768253c090f75f83e0f46842e28db4a5b98 --- /dev/null +++ b/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_impi.patch @@ -0,0 +1,19 @@ +fix hardcoded MPI-related variables for EB-provided Intel MPI +author: Kenneth Hoste (Ghent University) +--- PELICANS/etc/extra-Linux.mak.orig 2015-09-04 11:28:14.263778000 +0200 ++++ PELICANS/etc/extra-Linux.mak 2015-09-04 11:31:37.180400000 +0200 +@@ -152,10 +152,10 @@ + CPPFLAGS += -I$(PELICANSHOME)/$(EXTPACKS)/MPI/include -DMPIRUN=\"$(MPIRUN)\" + endif + +-CPPFLAGS += -I$(MPIPATH)/include +-MPIPATH = $(EXTRA_LIBS_DIR)/openmpi +-LIBPATH += $(MPIPATH)/lib +-LDLIBS += -lmpi -lmpi_cxx ++MPIPATH = $(EBROOTIMPI) ++CPPFLAGS += -I$(MPIPATH)/include64 ++LIBPATH += $(MPIPATH)/lib64 ++LDLIBS += -lmpi -lmpicxx + endif + + diff --git a/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_specify-system-in-tests.patch b/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_specify-system-in-tests.patch new file mode 100644 index 0000000000000000000000000000000000000000..fdce1c97aa7689810f0891314fc8b24298d9b9ce --- /dev/null +++ b/easybuild/easyconfigs/i/ISIS/ISIS-4.2.1_specify-system-in-tests.patch @@ -0,0 +1,40 @@ +specify -system flag to fix path to binaries used by tests +author: Kenneth Hoste (Ghent University) +--- Makefile.orig 2015-09-17 14:21:50.947592000 +0200 ++++ Makefile 2015-09-17 14:22:33.015119930 +0200 +@@ -134,7 +134,7 @@ + @echo "| Test failed: ExternalAPI MPI not enabled" + @echo "--------------------------------------------------"; echo + else +- @ $(BIN_DIR)/isis $(PELICANS_DIR)/etc/ExternalAPI/MPI/tests_enabling/data.pel resu_MPI -no_check_data ++ @ $(BIN_DIR)/isis $(PELICANS_DIR)/etc/ExternalAPI/MPI/tests_enabling/data.pel resu_MPI -system Linux-$(CCC) -no_check_data + @ $(RM) resu_MPI + endif + +@@ -147,7 +147,7 @@ + @echo "| Test failed: ExternalAPI MPI not enabled" + @echo "--------------------------------------------------"; echo + else +- @ $(BIN_DIR)/isis $(PELICANS_DIR)/etc/ExternalAPI/MPI/tests_enabling/data.pel resu_MPI -no_check_data -opt2 ++ @ $(BIN_DIR)/isis $(PELICANS_DIR)/etc/ExternalAPI/MPI/tests_enabling/data.pel resu_MPI -system Linux-$(CCC) -no_check_data -opt2 + @ $(RM) resu_MPI + endif + @ cd $(APPLI_DIR) ; $(MAKE) test_install CCC=$(CCC) OPT_TEST=$(OPT_TEST) +@@ -161,7 +161,7 @@ + @echo "| Test failed: ExternalAPI METIS not enabled" + @echo "--------------------------------------------------"; echo + else +- @ $(BIN_DIR)/isis $(PELICANS_DIR)/etc/ExternalAPI/METIS_4.0.1/tests_enabling/data.pel resu_METIS -no_check_data ++ @ $(BIN_DIR)/isis $(PELICANS_DIR)/etc/ExternalAPI/METIS_4.0.1/tests_enabling/data.pel resu_METIS -system Linux-$(CCC) -no_check_data + @ $(RM) resu_METIS + endif + +@@ -174,7 +174,7 @@ + @echo "| Test failed: ExternalAPI METIS not enabled" + @echo "--------------------------------------------------"; echo + else +- @ $(BIN_DIR)/isis $(PELICANS_DIR)/etc/ExternalAPI/METIS_4.0.1/tests_enabling/data.pel resu_METIS -no_check_data -opt2 ++ @ $(BIN_DIR)/isis $(PELICANS_DIR)/etc/ExternalAPI/METIS_4.0.1/tests_enabling/data.pel resu_METIS -system Linux-$(CCC) -no_check_data -opt2 + @ $(RM) resu_METIS + endif + diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb index 3ba25676db502ead45b181e724635c338a3bc3a4..f6423e5d6eb43d9926048ed3846f1c38e871353e 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} source_urls = ['http://isl.gforge.inria.fr/'] sources = [SOURCELOWER_TAR_BZ2] -dependencies = [('GMP', '6.0.0')] +dependencies = [('GMP', '6.0.0a')] sanity_check_paths = { 'files': ['lib/libisl.so', 'lib/libisl.a'], diff --git a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb index 1ed83c45264e9253c0289137d110911f75f3673e..7dc3787320bc598d08a264e33b4b08762faf3e69 100644 --- a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb @@ -32,7 +32,7 @@ with_configure = True graphlib_version = '0.3' preconfigopts = "cd ../graphlib-%s && ./configure && make && " % graphlib_version # build isoinfer, make sure we can link to libgraph.a -preconfigopts += "cd ../isoinfer-%(version)s && " +preconfigopts += "cd ../%(namelower)s-%(version)s && " preconfigopts += 'export LDFLAGS="$LDFLAGS -L%%(builddir)s/graphlib-%s/src" && ' % graphlib_version files_to_copy = [ diff --git a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb index 3f65089c099e3b915fbbf0507c318aff46d4c66f..436dd9a680a2451f2d7f6ce26212a76346e6fe97 100644 --- a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb @@ -32,7 +32,7 @@ with_configure = True graphlib_version = '0.3' preconfigopts = "cd ../graphlib-%s && ./configure && make && " % graphlib_version # build isoinfer, make sure we can link to libgraph.a -preconfigopts += "cd ../isoinfer-%(version)s && " +preconfigopts += "cd ../%(namelower)s-%(version)s && " preconfigopts += 'export LDFLAGS="$LDFLAGS -L%%(builddir)s/graphlib-%s/src" && ' % graphlib_version files_to_copy = [ 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 new file mode 100644 index 0000000000000000000000000000000000000000..aca2626f977b0f84d2108eff3c8aaaaf53b859ee --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2015.3.187-GNU-4.9.3-2.25.eb @@ -0,0 +1,24 @@ +name = 'icc' +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'} + +sources = ['l_ccompxe_%(version)s.tgz'] + +gnu = 'GNU' +gnuver = '4.9.3-2.25' +versionsuffix = '-%s-%s' % (gnu, gnuver) + +dependencies = [(gnu, gnuver)] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' + diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..58c54bd7ef092dda0aa7ee86addf6ef8be241106 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -0,0 +1,17 @@ +easyblock = "Toolchain" + +name = 'iccifort' +version = '2015.3.187' +versionsuffix = '-GNU-4.9.3-2.25' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C, C++ and Fortran compilers""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' 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 new file mode 100644 index 0000000000000000000000000000000000000000..f944202e890a53a19f790165d933071c3bb78cc6 --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -0,0 +1,23 @@ +name = 'ifort' +version = '2015.3.187' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "Fortran compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_fcompxe_%(version)s.tgz'] + +gnu = 'GNU' +gnuver = '4.9.3-2.25' +versionsuffix = '-%s-%s' % (gnu, gnuver) + +dependencies = [(gnu, gnuver)] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..9b59992b23db95b8834b39120ddd169a2663666b --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5-GNU-4.9.3-2.25.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'iimpi' +version = '7.3.5' +versionsuffix = '-GNU-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 = '3.187' +compver = '2015.%s' % suff + +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', '5.0.3.048', '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..b76de536ee7110924bb05b528fbfdfaf234f528e --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5-GNU-4.9.3-2.25.eb @@ -0,0 +1,22 @@ +name = 'imkl' +version = '11.2.3.187' + +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': '7.3.5-GNU-4.9.3-2.25'} + +sources = ['l_mkl_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +interfaces = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb index 5f35cd6834769f295ae59b1a948027da1c4a7f86..e0aa55d8e10dfa8996f32c5f53af1f9ddef1e502 100644 --- a/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb +++ b/easybuild/easyconfigs/i/impi/impi-3.2.2.006.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb index 437532bb49a446ac6ac55cfdffdf59c4e79d5b7d..ed9f544efda8e76fcb5ddb1b2629a558dd400850 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-32bit.eb @@ -19,4 +19,7 @@ license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic m32 = True +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb index b47595dda38e162a04f89f035f056f9992f5d8c3..cdfb37e60d4dcc453dc912194f3f6ad523607e56 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073-32bit.eb @@ -18,4 +18,7 @@ license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic m32 = True +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb index 7b8162cea322e5d94b3feac97600730a25261f37..05a3dcd5242f446c626d51dca9270a1528e5967d 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028-iccifort-11.1.073.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb index a551f577861f9d2cfe510f030718b1b893dff0fd..6a5c58b965a5e6f8fdcc6f86717eb6b1367160cc 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.0.028.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb index 153ba081b1751e1f8c0933f5c08738e0578d438a..32c938b850a847594f09070fa4304b9cc580d9d8 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.10.319.eb @@ -18,4 +18,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb index da8581e61f9000a1ee742148e4d41d37cbe5a591..c9a73b1fbdf5bfe297bb1ba43aa370ef9a9d8f04 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003-iccifort-2011.6.233.eb @@ -18,4 +18,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb index 4830b5c3c8a5607ac3ede7138941cdf045b8c893..321fcf953c4ddb596d7d4ee1153ff88ef870ec72 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.0.2.003.eb @@ -18,4 +18,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb index 16a82416aab9857bdc2dc0f29ebacedd43356d4b..03f1826816789abec94c4bfb56363d4d2092dd87 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2011.13.367.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb index d81cc168ff3554aba673893fe9957b6a92bd133c..61d1d122580027cebc3c781bc12045d3d7b8fdbf 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027-iccifort-2013.1.117.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb index 839fe8f60479697300ef5dbf751bf4520739c920..52c561052296eb08d575e13fbc256fdd80701b13 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.027.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb index 0f49c7d2123c2599795f996b9086d2fde11df9dd..10206cc86fdb1523153e1e13955db7e332b7b661 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.2.146.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb index 178d95d4156fb61ff11c55b80b848279f7ea692f..14cfad4a95fb037c70d2147f2d09944e757aa95a 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.3.163.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb index 16d697d7065a7534932717c7593764123af326f9..5e54731d6a6a248dc9a4b6c9fbdedf5be7894bdb 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030-iccifort-2013.4.183.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb index 875b582066aca796928cc2f6fc00f769b757900e..9d7dcdffc597e7e30d6c66ce91ef1a9533fe3598 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.0.030.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb index 00ee030d34f072ef17e780e76da6632a82eea431..5b383c2276ae68082139398ec4593e8c4d9d8eb6 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb index 1440a8a1b0edaa335ea932c742a6a4262bf6d57d..2aeefc2cd908f2fc832088258ea7c22392ae26f7 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb index f3bb7b6e5edac1d3691d6a9609c942afa15d39e2..6f91af21b338e5394291a178c67501fcb2d25890 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013_sp1.0.080.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb index 97c88ff999b20e090a54b94fd44d5029fa72ef70..48ea7b9ce580731d0df7fbddfafea24e70b3c343 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb index 839d937043ccd762e31ea88e582c5453dca1d804..d88a37c91f84cbb1f2dfd6a3c71802e669018c97 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.2.040.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb index 1b64e97c4604c0119f1ffaa9945042657d8d165c..048251c331ae1486d20bb8c2118c43ae41cb1370 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045-iccifort-2013_sp1.1.106.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb index d31c2924c887ecb27381fef588ce2f711f9f1160..5843dfe20093c8bf455ba0f90ed8771bf58cf331 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.045.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb index 478cc2645d4795671fb5354ce94815681cb5e92c..9e56e74b2d2ec897605056ddb6cb385851aa4d08 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-GCC-4.8.3.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb index ddba0fe1d651350e7318b888f9e4cdde7b726ba4..07bd2d77cd46d9a9b7a3a849390951f0e43b1dd6 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013.5.192-GCC-4.8.3.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb index 5732c5fbd3ca426c51f3aff3afdcf1fd24e084f7..d3e34f99af61e979bb818acc023c55c082dda51a 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.2.144.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb index b9d7d5e20bf4d4a8ae487f735282c5de6511dfae..54e5d17b0fa8386d395426ea23675c041b970f49 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049-iccifort-2013_sp1.3.174.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb index e55725a62a895cd1821b4a0254b6579865ca1838..23f4c4874467e9e694bd6c0eb221ad69ebad8ed9 100644 --- a/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb +++ b/easybuild/easyconfigs/i/impi/impi-4.1.3.049.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb index 5f63a18d7bab1b0d7a3281c7b0827ccf85d314dc..57ed02ab9ad3369924f5c137e45a2a8bd90656ce 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090-GCC-4.9.2.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb index 43da00f4ab81f655bbf0a17b4ad5f379e96f8b8d..107a4290a36bea440320068c53e4b04153b1c1b0 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.1.035-iccifort-2015.0.090.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb index 64a9011ae4a33b76f3abe88ce5074a64e160096f..85451943cd1eda1d79b720ed736594ff0b2cccda 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.2.044-iccifort-2015.1.133-GCC-4.9.2.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb index d23a27639e609602466190fa211f608b05f70d5a..0bd01e5fe2b5c8ede0ae36fc473877c2a4d00451 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.2.164-GCC-4.9.2.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..7b891134eb4bc5a82bbe4f0d3fa3bef2c6af606e --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187-GNU-4.9.3-2.25.eb @@ -0,0 +1,22 @@ +name = 'impi' +version = '5.0.3.048' + +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': '2015.3.187-GNU-4.9.3-2.25'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb index 5e0972d8f3ef5fbe04aa75c53478eb9144f08cdd..baf8e132f9ad902849d92abc719d695cd1961a30 100644 --- a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb @@ -16,4 +16,7 @@ dontcreateinstalldir = 'True' import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb new file mode 100644 index 0000000000000000000000000000000000000000..10fe208f63220697300a147f9c364309effcb959 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb @@ -0,0 +1,23 @@ +name = 'impi' +version = '5.1.0.079' + +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': '2015.3.187'} + +# source tarball doesn't match actual version?! +sources = ['l_mpi_p_5.1.0.038.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +# set up all the mpi wrappers to work as expected with intel compilers (e.g. mpicc wraps icc not the default gcc) +# set_mpi_wrappers_all = 'True' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel/intel-2015b.eb b/easybuild/easyconfigs/i/intel/intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..e0b4b71ab1ed505936f260629330b5a33ac57ccd --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2015b.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'intel' +version = '2015b' + +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 = '2015.3.187' +gccsuff = '-GNU-4.9.3-2.25' + +dependencies = [ + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '5.0.3.048', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '11.2.3.187', '', ('iimpi', '7.3.5%s' % gccsuff)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..903be570eba76b8d092434cb05f7d7991af2b900 --- /dev/null +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb @@ -0,0 +1,23 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'JUBE' +version = '2.0.3' + +homepage = "http://www.fz-juelich.de/jsc/jube" +description = """The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, + run those sets on different computer systems and evaluate the results.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] +sources = [SOURCE_TAR_GZ] +checksums = ['8afc5e3959752e7541f5f59b07fd1e1c'] + +options = {'modulename': 'jube2'} + +sanity_check_paths = { + 'files': ['bin/jube'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..545b5785eada40b34061adf8097d4741040ecd91 --- /dev/null +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb @@ -0,0 +1,23 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'JUBE' +version = '2.0.4' + +homepage = "http://www.fz-juelich.de/jsc/jube" +description = """The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, + run those sets on different computer systems and evaluate the results.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] +sources = [SOURCE_TAR_GZ] +checksums = ['96a7946d38d678b25ba4bbd539482a14'] + +options = {'modulename': 'jube2'} + +sanity_check_paths = { + 'files': ['bin/jube'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..b270f53d57e3e3d997743f6207a0f4a5e01843dd --- /dev/null +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb @@ -0,0 +1,23 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'JUBE' +version = '2.0.5' + +homepage = "http://www.fz-juelich.de/jsc/jube" +description = """The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, + run those sets on different computer systems and evaluate the results.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] +sources = [SOURCE_TAR_GZ] +checksums = ['f506e9f39898af3d7456890ba219ab90'] + +options = {'modulename': 'jube2'} + +sanity_check_paths = { + 'files': ['bin/jube'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2015a.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..02cb1d4f4c8f76a6dec82b0400463ea2d02d393b --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2015a.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': 'foss', 'version': '2015a'} +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_45.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_45.eb new file mode 100644 index 0000000000000000000000000000000000000000..50a687a0505c8706344f43480761d4e8ac222c6d --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_45.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.8.0_45' + +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-2.1.3-foss-2014b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..bd77b8e773e08f359083cb4fae7603cc6e9b2004 --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb @@ -0,0 +1,28 @@ +# 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 = '2.1.3' + +homepage = 'http://www.genome.umd.edu/jellyfish.html' +description = """ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.""" + +toolchain = {'name': 'foss', 'version': '2014b'} + +source_urls = ['ftp://ftp.genome.umd.edu/pub/jellyfish/'] +sources = [SOURCELOWER_TAR_GZ] + +parallel = 1 + +# The tests for the Bloom filter are statistical tests and can randomly fail, they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb index 595bb566df9266eb5e928cd0dd4ddb07d4ca7954..e874c0503026a44dbee2ecc595f8b54b422f12c6 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb @@ -18,7 +18,8 @@ sources = [SOURCELOWER_TAR_GZ] parallel = 1 -runtest = "check" +# The tests for the Bloom filter are statistical tests and can randomly fail, they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" sanity_check_paths = { 'files': ['bin/jellyfish'], diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.3-intel-2015b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.3-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..5e170ee4c542fbc013c66ce4678aece3d6e54600 --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.3-intel-2015b.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 = 'Jellyfish' +version = '2.2.3' + +homepage = 'http://www.genome.umd.edu/jellyfish.html' +description = """ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] + +parallel = 1 + +# The tests for the Bloom filter are statistical tests and can randomly fail, they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" + +postinstallcmds = ["cp config.h %(installdir)s/include/%(namelower)s-%(version)s/%(namelower)s/"] + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +modextrapaths = {'CPATH': 'include/%(namelower)s-%(version)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-3.6.0-foss-2015a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-3.6.0-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b9fa5705295ca629a151410b07ea096ff684d318 --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-3.6.0-foss-2015a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '3.6.0' + +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': 'foss', 'version': '2015a'} + +source_urls = ['http://www.canonware.com/download/jemalloc/'] +sources = [SOURCE_TAR_BZ2] + +sanity_check_paths = { + 'files': ['bin/pprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.so', + 'lib/libjemalloc.so.1', 'include/jemalloc/jemalloc.h'], + 'dirs': ['share'], +} + +modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.so.1']} + +moduleclass = 'lib' 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 new file mode 100644 index 0000000000000000000000000000000000000000..62923f260f75b2e09b1850a3cba8f59e1c2c4838 --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.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': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +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/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0-headless.eb b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0-headless.eb new file mode 100644 index 0000000000000000000000000000000000000000..d4e5cc4292a396e45f6841e909438acb44ef6f8a --- /dev/null +++ b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0-headless.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'LAMARC' +version = '2.1.9' +versionsuffix = '-headless' + +homepage = 'http://evolution.genetics.washington.edu/lamarc/' +description = """LAMARC is a program which estimates population-genetic parameters such as population size, + population growth rate, recombination rate, and migration rates.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://evolution.genetics.washington.edu/lamarc/download/'] +sources = ['%(namelower)s-%(version)s-src.tgz'] + +patches = ['LAMARC-2.1.9_Makefile-fix.patch'] + +configopts = "--disable-converter --disable-gui" + +sanity_check_paths = { + 'files': ["bin/lamarc"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9_Makefile-fix.patch b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9_Makefile-fix.patch new file mode 100644 index 0000000000000000000000000000000000000000..74db39ff1cb9940d4fc4ecadde6a029acbdf6878 --- /dev/null +++ b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9_Makefile-fix.patch @@ -0,0 +1,10 @@ +--- lamarc/Makefile.in.orig 2014-03-19 14:25:08.261820031 +0100 ++++ lamarc/Makefile.in 2014-03-19 14:25:15.382031107 +0100 +@@ -1810,7 +1810,6 @@ + doc/html/genotype.html \ + doc/html/glossary.html \ + doc/html/growthmenu.html \ +- doc/html/forces.html \ + doc/html/index.html \ + doc/html/insumfile.2reg3rep.html \ + doc/html/insumfile.2reg3rep.xml \ diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0e2be216c94c5ae847a28bccbafc9b00711ebf4e --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.6.2-intel-2015a.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.6.2' + +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': '2015a'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.2.3'), + ('Python', '2.7.10'), +] + +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-3.7.0-intel-2015a.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..622b77ee482378dbd02727ca5412e6bf82c328c4 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.7.0-intel-2015a.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.7.0' + +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': '2015a'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('CMake', '3.2.3'), + ('Python', '2.7.10'), +] + +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/LibTIFF/LibTIFF-4.0.3-goolf-1.7.20.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..46a3c3ee49fd8d5df3ad41acd37397ff284c70fb --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.7.20.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.3' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5b2c252b76084d2497e44c2424b0dbf7498e78bc --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2015a.eb @@ -0,0 +1,30 @@ +## +# 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 = 'LibTIFF' +version = '4.0.3' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +source_urls = ['ftp://ftp.remotesensing.org/pub/libtiff/'] +sources = ['tiff-%(version)s.tar.gz'] + +toolchain = {'name': 'intel', 'version': '2015a'} + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..70578c5f23ecd7eae1d286fe27ec6f9160d09924 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb @@ -0,0 +1,34 @@ +# Built with EasyBuild version 2.2.0dev on 2015-06-16_10-51-42 +## +# 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 +# $Id$ +# +# 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 = '4.0.4' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'foss', 'version': '2015a'} + +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/LibTIFF/LibTIFF-4.0.4-goolf-1.7.20.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..8858538d5aefcfa8f7fa47729bc16a6769daee8d --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-goolf-1.7.20.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.4' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6b0d237d173faa8e8c9cbc79a3d8ab1c2d8af7fe --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb @@ -0,0 +1,34 @@ +# Built with EasyBuild version 2.2.0dev on 2015-06-16_10-51-42 +## +# 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 +# $Id$ +# +# 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 = '4.0.4' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'intel', 'version': '2015a'} + +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/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..accbb2bb0a71dcbc746fb52a30f151707c1e2fcc --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb @@ -0,0 +1,35 @@ +# Built with EasyBuild version 2.2.0dev on 2015-06-16_10-51-42 +## +# 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 +# $Id$ +# +# 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' +# misleading name, this is a 'stable' release +version = '4.0.4beta' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +toolchain = {'name': 'foss', 'version': '2015a'} + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-foss-2015b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ba9b735bea8175f438671d27fa45c371e20354a5 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-foss-2015b.eb @@ -0,0 +1,24 @@ +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': 'foss', 'version': '2015b'} +toolchainopts = {'opt': True, 'optarch': True, '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.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs':[], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2015b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..1e71a38b555915bd997380294f0e7a6549acb613 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2015b.eb @@ -0,0 +1,24 @@ +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': '2015b'} +toolchainopts = {'opt': True, 'optarch': True, '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.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs':[], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..9c513d4634cfe420d8a127ad8c7c8408ed7539c3 --- /dev/null +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libX11' +version = '1.6.3' +versionsuffix = '-Python-2.7.10' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', versionsuffix), + ('inputproto', '2.3.1'), + ('xproto', '7.0.27'), + ('kbproto', '1.0.6'), +] + +dependencies = [ + ('libxcb', '1.11', versionsuffix), + ('xtrans', '1.3.5'), +] + +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/libXScrnSaver/libXScrnSaver-1.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libXScrnSaver/libXScrnSaver-1.2.2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0889930509402b0b32bc7a0bd8de6ba4c9cfdf34 --- /dev/null +++ b/easybuild/easyconfigs/l/libXScrnSaver/libXScrnSaver-1.2.2-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libXScrnSaver' +version = '1.2.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 Screen Saver extension client library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libX11', '1.6.3', '-Python-2.7.9'), + ('libXext', '1.3.3') +] + +sanity_check_paths = { + 'files': ['lib/libXss.a', 'lib/libXss.so', 'include/X11/extensions/scrnsaver.h'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..0cb53836e382ccebf106804266a25f116b16dd6e --- /dev/null +++ b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libXdamage' +version = '1.1.4' +versionsuffix = '-Python-2.7.10' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Damage extension library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libX11', '1.6.3', versionsuffix), + ('libxcb', '1.11', versionsuffix), + ('libXau', '1.0.8'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/Xdamage.h', 'lib/libXdamage.so', 'lib/libXdamage.a'], + 'dirs': [], +} + +moduleclass = 'vis' 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 new file mode 100644 index 0000000000000000000000000000000000000000..a959a12b0ade1d798c8452b1a08e98d1e73b845e --- /dev/null +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libXext' +version = '1.3.3' +versionsuffix = '-Python-2.7.10' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """Common X Extensions library""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xproto', '7.0.27'), + ('xextproto', '7.3.0'), +] + +dependencies = [ + ('libX11', '1.6.3', versionsuffix), + ('libXdmcp', '1.1.2'), +] + +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/libXfont/libXfont-1.5.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..c14d0fe75e7fcc8fcae9ff657274648ee461d4ef --- /dev/null +++ b/easybuild/easyconfigs/l/libXfont/libXfont-1.5.1-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libXfont' +version = '1.5.1' +versionsuffix = '-Python-2.7.10' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X font libary""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fontsproto', '2.1.3'), + ('xproto', '7.0.27'), + ('xtrans', '1.3.5'), + ('libfontenc', '1.1.3'), +] +dependencies = [ + ('libX11', '1.6.3', versionsuffix), +] + +sanity_check_paths = { + 'files': ['lib/libXfont.so', 'lib/libXfont.a'], + 'dirs': ['include/X11/fonts'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3-Python-2.7.10.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..306d4728389afbe13778a131ec4d6b257c9951a8 --- /dev/null +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3-Python-2.7.10.eb @@ -0,0 +1,35 @@ +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': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.6'), + ('renderproto', '0.11'), +] + +libx11ver = '1.6.3' +pysuff = '-Python-2.7.10' +versionsuffix = '-libX11-%s%s' % (libx11ver, pysuff) + +dependencies = [ + ('libX11', libx11ver, pysuff), + ('libXrender', '0.9.9', pysuff), + ('freetype', '2.6'), + ('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-2015a-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..65123b2fae75491d544f2a8225532a30c136786d --- /dev/null +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3.eb @@ -0,0 +1,34 @@ +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': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.6'), + ('renderproto', '0.11'), +] + +libx11ver = '1.6.3' +versionsuffix = '-libX11-%s' % libx11ver + +dependencies = [ + ('libX11', libx11ver, '-Python-2.7.9'), + ('libXrender', '0.9.9'), + ('freetype', '2.5.5'), + ('fontconfig', '2.11.93'), +] + +sanity_check_paths = { + 'files': ['lib/libXft.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-intel-2015a-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-intel-2015a-libX11-1.6.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..083f86b1a3805db508cf9038bf42d57e7d772ff9 --- /dev/null +++ b/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-intel-2015a-libX11-1.6.3.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libXmu' +version = '1.1.2' +versionsuffix = '-libX11-1.6.3' + +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': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libXt', '1.1.4', versionsuffix), + ('libXpm', '3.5.11'), +] +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['%(name)s.a', '%(name)s.so']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2015a.eb b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..69fda1c84a0f87d164d49cfc10c227069788092e --- /dev/null +++ b/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-intel-2015a.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': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [('gettext', '0.19.4', '', ('GCC', '4.9.2'))] + +sanity_check_paths = { + 'files': ['lib/%s' % x for x in ['libXpm.a', 'libXpm.so']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb index 778cd1670cc7f85fc419bb7b4c592dd8c77df7b9..cea866f2b70edc72597ed741ce9f067862012f5b 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb @@ -12,11 +12,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('kbproto', '1.0.6'), ('renderproto', '0.11'), ] dependencies = [ - ('kbproto', '1.0.6'), ('libX11', '1.6.2', '-Python-2.7.8'), ] diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb index fe8ecdca33913919ab4509674cd319a77c345d67..80e0f6ea245a0d1779817f08d5d5a1bd2730d8f2 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb @@ -12,11 +12,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('kbproto', '1.0.6'), ('renderproto', '0.11'), ] dependencies = [ - ('kbproto', '1.0.6'), ('libX11', '1.6.2', '-Python-2.7.8'), ] diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..e6f3cd47ac01e34f4fd4beb7399a10eb2a25baac --- /dev/null +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libXrender' +version = '0.9.9' +versionsuffix = '-Python-2.7.10' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), +] + +dependencies = [ + ('libX11', '1.6.3', versionsuffix), +] + +sanity_check_paths = { + 'files': ['lib/libXrender.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..52e06388f33af85749323d1f1fcd9f3305e6a94e --- /dev/null +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.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': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), +] + +dependencies = [ + ('libX11', '1.6.3', '-Python-2.7.9'), +] + +sanity_check_paths = { + 'files': ['lib/libXrender.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libbeef/libbeef-0.1.1-intel-2015a.eb b/easybuild/easyconfigs/l/libbeef/libbeef-0.1.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d5d17f503c50987e0f186439d0326cb118897bee --- /dev/null +++ b/easybuild/easyconfigs/l/libbeef/libbeef-0.1.1-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libbeef' +version = '0.1.1' + +homepage = 'https://confluence.slac.stanford.edu/display/SUNCAT/BEEF+Functional+Software' +description = """libbeef is a package providing the class of BEEF-vdW functionals and + Bayesian error estimates to Fortran- or C-based DFT codes.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://confluence.slac.stanford.edu/download/attachments/146704476'] +sources = [SOURCE_TAR_GZ] + +configopts = 'CC="$CC"' + +sanity_check_paths = { + 'files': ['bin/bee', 'lib/libbeef.a'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goalf-1.1.0-no-OFED.eb index 5c7544aa886565d6bddc483ec9b298f0c9d3d37c..92ffc337ddd59b79bfe0667b79d77a7aa1551748 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goalf-1.1.0-no-OFED.eb @@ -6,22 +6,20 @@ version = '2.4.27' homepage = 'http://dri.freedesktop.org' description = """Direct Rendering Manager runtime library.""" +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} + source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] -toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} - dependencies = [ - ('libpthread-stubs', '0.3'), - ('libpciaccess', '0.13.1') - ] - -configopts = '--enable-nouveau-experimental-api' + ('libpthread-stubs', '0.3'), + ('libpciaccess', '0.13.1'), +] sanity_check_paths = { - 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', - 'lib/libdrm_radeon.so', 'lib/libdrm_nouveau.so', 'lib/libdrm.so', 'lib/libkms.so'], - 'dirs': ['include/libdrm', 'include/libkms', 'include/nouveau', 'lib/pkgconfig'] - } + 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', + 'lib/libdrm_radeon.so', 'lib/libdrm.so', 'lib/libkms.so'], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goolf-1.4.10.eb index e4bdd39b89b3646f56abb8f025f9ab13c562273e..b1d2fbfdf4022b01eef815daaa39b934300b2896 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goolf-1.4.10.eb @@ -6,21 +6,20 @@ version = '2.4.27' homepage = 'http://dri.freedesktop.org' description = """Direct Rendering Manager runtime library.""" +toolchain = {'name': 'goolf', 'version': '1.4.10'} + source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] -toolchain = {'name': 'goolf', 'version': '1.4.10'} dependencies = [ - ('libpthread-stubs', '0.3'), - ('libpciaccess', '0.13.1') - ] - -configopts = '--enable-nouveau-experimental-api' + ('libpthread-stubs', '0.3'), + ('libpciaccess', '0.13.1'), +] sanity_check_paths = { - 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', - 'lib/libdrm_radeon.so', 'lib/libdrm_nouveau.so', 'lib/libdrm.so', 'lib/libkms.so'], - 'dirs': ['include/libdrm', 'include/libkms', 'include/nouveau', 'lib/pkgconfig'] - } + 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', + 'lib/libdrm_radeon.so', 'lib/libdrm.so', 'lib/libkms.so'], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.0.6.eb index d970534cf1e3634213d3618c372fb7dd806a0622..c3030842e986744a09fdbfe8795ee9bfcc3dedc4 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.0.6.eb @@ -6,22 +6,20 @@ version = '2.4.27' homepage = 'http://dri.freedesktop.org' description = """Direct Rendering Manager runtime library.""" +toolchain = {'name': 'ictce', 'version': '4.0.6'} + source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] -toolchain = {'name': 'ictce', 'version': '4.0.6'} - dependencies = [ - ('libpthread-stubs', '0.3'), - ('libpciaccess', '0.13.1') - ] - -configopts = '--enable-nouveau-experimental-api' + ('libpthread-stubs', '0.3'), + ('libpciaccess', '0.13.1'), +] sanity_check_paths = { - 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', - 'lib/libdrm_radeon.so', 'lib/libdrm_nouveau.so', 'lib/libdrm.so', 'lib/libkms.so'], - 'dirs': ['include/libdrm', 'include/libkms', 'include/nouveau', 'lib/pkgconfig'] - } + 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', + 'lib/libdrm_radeon.so', 'lib/libdrm.so', 'lib/libkms.so'], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.1.13.eb index 844b065646118c65d0b76bac85e99acb51f43482..153b29cec154354e3bdc86f0afee51fe0a0db864 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.1.13.eb @@ -6,22 +6,20 @@ version = '2.4.27' homepage = 'http://dri.freedesktop.org' description = """Direct Rendering Manager runtime library.""" +toolchain = {'name': 'ictce', 'version': '4.1.13'} + source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] -toolchain = {'name': 'ictce', 'version': '4.1.13'} - dependencies = [ ('libpthread-stubs', '0.3'), ('libpciaccess', '0.13.1'), ] -configopts = '--enable-nouveau-experimental-api' - sanity_check_paths = { 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', - 'lib/libdrm_radeon.so', 'lib/libdrm_nouveau.so', 'lib/libdrm.so', 'lib/libkms.so'], - 'dirs': ['include/libdrm', 'include/libkms', 'include/nouveau', 'lib/pkgconfig'], + 'lib/libdrm_radeon.so', 'lib/libdrm.so', 'lib/libkms.so'], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.3.0.eb index e1a66cadcc78dfe033d7dc1306c956cfe210b85d..c5883cb6dbd425f4eebbbaca2fca21d40a29b304 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.3.0.eb @@ -6,23 +6,20 @@ version = '2.4.27' homepage = 'http://dri.freedesktop.org' description = """Direct Rendering Manager runtime library.""" +toolchain = {'name': 'ictce', 'version': '5.3.0'} + source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] - -toolchain = {'name': 'ictce', 'version': '5.3.0'} - dependencies = [ - ('libpthread-stubs', '0.3'), - ('libpciaccess', '0.13.1') - ] - -configopts = '--enable-nouveau-experimental-api' + ('libpthread-stubs', '0.3'), + ('libpciaccess', '0.13.1'), +] sanity_check_paths = { - 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', - 'lib/libdrm_radeon.so', 'lib/libdrm_nouveau.so', 'lib/libdrm.so', 'lib/libkms.so'], - 'dirs': ['include/libdrm', 'include/libkms', 'include/nouveau', 'lib/pkgconfig'] - } + 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', + 'lib/libdrm_radeon.so', 'lib/libdrm.so', 'lib/libkms.so'], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.5.0.eb index 1e464e3679f82084064caf74058c68052b56aa01..d46e9edefed2775fd9b3cc54a18a7de2fff32b24 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-5.5.0.eb @@ -6,22 +6,20 @@ version = '2.4.27' homepage = 'http://dri.freedesktop.org' description = """Direct Rendering Manager runtime library.""" +toolchain = {'name': 'ictce', 'version': '5.5.0'} + source_urls = ['http://dri.freedesktop.org/libdrm/'] sources = [SOURCELOWER_TAR_GZ] -toolchain = {'name': 'ictce', 'version': '5.5.0'} - dependencies = [ ('libpthread-stubs', '0.3'), ('libpciaccess', '0.13.1'), ] -configopts = '--enable-nouveau-experimental-api' - sanity_check_paths = { 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', - 'lib/libdrm_radeon.so', 'lib/libdrm_nouveau.so', 'lib/libdrm.so', 'lib/libkms.so'], - 'dirs': ['include/libdrm', 'include/libkms', 'include/nouveau', 'lib/pkgconfig'], + 'lib/libdrm_radeon.so', 'lib/libdrm.so', 'lib/libkms.so'], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2015a.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..3b516fcaacf3904c52e285f395cc002771916ecf --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.59-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libdrm' +version = '2.4.59' + +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': '2015a'} + +dependencies = [ + ('libpthread-stubs', '0.3'), + ('libpciaccess', '0.13.1'), +] + +sanity_check_paths = { + 'files' : ['include/xf86drm.h', 'include/xf86drmMode.h', 'lib/libdrm_intel.so', + 'lib/libdrm_radeon.so', 'lib/libdrm.so', 'lib/libkms.so'], + 'dirs': ['include/libdrm', 'include/libkms', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libedit/libedit-20150325-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libedit/libedit-20150325-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..fe54474a05f46484d6a53eb80628a3c46bc00c4c --- /dev/null +++ b/easybuild/easyconfigs/l/libedit/libedit-20150325-GNU-4.9.3-2.25.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libedit' +version = '20150325' + +homepage = 'http://thrysoee.dk/editline/' +description = """ +This BSD-style licensed command line editor library provides generic line editing, +history, and tokenization functions, similar to those found in GNU Readline. +""" + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} + +sources = ['libedit-20150325-3.1.tar.gz'] +source_urls = ['http://thrysoee.dk/editline/'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ['include/editline/readline.h', 'lib/libedit.so', 'lib/libedit.a'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb index 75b8531ffaaa500714c335017d3f542fa9a2d3ba..b12575ef8969916ad060e1a2d24d206771458aba 100644 --- a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GCC-4.9.2.eb @@ -11,8 +11,8 @@ description = """The libevent API provides a mechanism to execute a callback fun toolchain = {'name': 'GCC', 'version': '4.9.2'} source_urls = [ - 'https://sourceforge.net/projects/levent/files/%(name)s/%(name)s-%(version_major_minor)s/', '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'] diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..3b555aa6f7f7695a711e40ec9bcfb70114de30e0 --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.0.22-GNU-4.9.3-2.25.eb @@ -0,0 +1,19 @@ +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': 'GNU', 'version': '4.9.3-2.25'} + +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'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..ba1db82dae7639a1c9c100a2084f49d0f4fcae5e --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.1' + +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': 'goolf', 'version': '1.7.20'} + +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-2015a.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..17a9f263e81c3fa579796c73b5cc0c9727d802a1 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015a.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': '2015a'} + +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-intel-2015a.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..385b07e0ea24a13f4022cceeb095e36f16ccc492 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-intel-2015a.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': 'intel', 'version': '2015a'} + +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-intel-2015a.eb b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b6a5cba0dbc9b17505219d9bd09369ecf2e9297b --- /dev/null +++ b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-intel-2015a.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': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('xproto', '7.0.27'), +] + +sanity_check_paths = { + 'files': ['include/X11/fonts/fontenc.h', 'lib/libfontenc.so', 'lib/libfontenc.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..b5f853d5af4fcb0651cb8fceb9c37f813438c254 --- /dev/null +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.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 = '0.6.1' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['http://hannonlab.cshl.edu/fastx_toolkit'] + +sanity_check_paths = { + 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..16d490f92bf2bccaa322f74f12cf17471598c078 --- /dev/null +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.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 = '0.6.1' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['http://hannonlab.cshl.edu/fastx_toolkit'] + +sanity_check_paths = { + 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..d2b54d01ffffcd7378cc4f9c50b53ab0222acd4d --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-goolf-1.7.20.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.3.1' + +homepage = 'http://sourceforge.net/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': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.05'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2015a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d6bc643d578d7a83bb3cb8b97749e7681fe92881 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.3.1' + +homepage = 'http://sourceforge.net/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': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.05'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-ictce-7.3.5.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-ictce-7.3.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..24b1cf1a07384678a528f0a37f68701277867390 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-ictce-7.3.5.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.0' + +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': 'ictce', 'version': '7.3.5'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.06'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-foss-2015b.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..eb2697c94d08b4710f1cffa66b8fce30553cdaa9 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-foss-2015b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.1' + +homepage = 'http://sourceforge.net/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': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.08'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..af63e0180b6b98482efd3f63120aa269b0e705cb --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-goolf-1.7.20.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.1' + +homepage = 'http://sourceforge.net/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': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.05'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..3f922516d94cf412d1116db53cd2f7f811bdac65 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.1' + +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': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.08'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015b.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..49b99b98b32ddc0fbac101c331e38e452186e871 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.1' + +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': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.08'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' 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 new file mode 100644 index 0000000000000000000000000000000000000000..ce77f3502c1b3bfd484cc33b8b316d852459faab --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.13.1' + +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': '2015a'} + +builddependencies = [ + ('Autotools', '20150119', '', ('GCC', '4.9.2')), + ('xorg-macros', '1.17'), +] + +preconfigopts = "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-1.6.12-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.12-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..11dd528148faed80e5058bef5b735a55be0a49e4 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.12-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.12' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..21ff2f77640e9e1bc4e63949562f324f53355dc6 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-intel-2015b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.16' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-foss-2015b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..e421fa225d15c1e7c46f8a1224bec26380f038ab --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-foss-2015b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.17' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..fd641ddebc59bcdb3310a0de75cad47a92c4265c --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.17' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-intel-2015b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..4c66e1d2243e5fd8a767f49e8c8629d4fd570221 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-intel-2015b.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.17' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' 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 new file mode 100644 index 0000000000000000000000000000000000000000..1247037f85fbb5513db6d5e4da35dcf161c204c7 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GNU-4.9.3-2.25.eb @@ -0,0 +1,29 @@ +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': 'GNU', 'version': '4.9.3-2.25'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +preconfigopts = " LDFLAGS='-ltinfo' " + +dependencies = [('ncurses', '5.9')] + +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-foss-2015.05.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..c23d9ba71113a7bd731c278228c714475ecfe121 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb @@ -0,0 +1,27 @@ +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': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +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-foss-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..1c079c55a64f9a8d31e218f5d0fac16ab88d634d --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015b.eb @@ -0,0 +1,27 @@ +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': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +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-1.4.10.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..918bfc4406c603be5cc2e35ab37b5800581cd0cf --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.4.10.eb @@ -0,0 +1,27 @@ +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': '1.4.10'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +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-ictce-7.3.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..34ea8a516d62e173e32ccd411b57632f66a3e2f4 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb @@ -0,0 +1,29 @@ +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': 'ictce', 'version': '7.3.5'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +preconfigopts = " LDFLAGS='-ltinfo' " + +dependencies = [('ncurses', '5.9')] + +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-2015b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..de61e222ce41598587eeec4c004dd445759d61ca --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2015b.eb @@ -0,0 +1,27 @@ +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': '2015b'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +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/libsigc++/libsigc++-2.4.1-intel-2015a.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.4.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f4b4e3a392d224afe9554a8242b924484fe297ce --- /dev/null +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-2.4.1-intel-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libsigc++' +version = '2.4.1' + +homepage = 'http://www.gtk.org/' +description = """The libsigc++ package implements a typesafe callback system for standard C++.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://ftp.gnome.org/pub/gnome/sources/%(name)s/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s.tar.xz'] + +sanity_check_paths = { + 'files': ['lib/libsigc-2.0.so'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.3-intel-2015a.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.3-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..761355fc9f515a8aabebf8582db27bb77d24f5a1 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.3-intel-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.3' + +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': '2015a'} + +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/libtool/libtool-2.4.6-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..99efd1e796649386114cc5847624d00d32ca5cb7 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.3-2.25.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': 'GNU', 'version': '4.9.3-2.25'} + +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-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..33c6f3867ed98f6470bff34307768d7b5e142edf --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-5.1.0-2.25.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': 'GNU', 'version': '5.1.0-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [('M4', '1.4.17')] + +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 new file mode 100644 index 0000000000000000000000000000000000000000..74be1e3d78a12d5a0d1553607b2466396e5bd102 --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2015a.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 = {'version': '2015a', 'name': 'foss'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SAVANNAH_SOURCE] + +sanity_check_paths = { + 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..355b1a14f908d1f52d0918d42c362de9a87c731b --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-foss-2015b.eb @@ -0,0 +1,32 @@ +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': 'foss', 'version': '2015b'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a', 'lib/libxc.so'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..25c12f798e5de9a8b1f4c2961dabb2520d5d2d31 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.2' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc.a', 'lib/libxc.so'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..b07c35e53185c016113075b962ee4a172ee2bde5 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.2' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$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/libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..c1b10ef129b17a1ca369339b4f7cb365ef5a4ba0 --- /dev/null +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libxcb' +version = '1.11' + +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': 'intel', 'version': '2015a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('xcb-proto', '1.11', versionsuffix), + ('libXau', '1.0.8'), + ('libpthread-stubs', '0.3'), +] + +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/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index aaf4c869fd8f2d510c16bc6d43fa64475688df26..22eb3e4fce6e0812ff6758559ec0c62fb7f7161e 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -6,6 +6,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -24,4 +25,9 @@ dependencies = [ ('Python', pythonver), ] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb index c67963ba182bd282643c30a3259cc5b7dac66901..7557598cd64d9613aad91a05f3e48ab9362c474b 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -19,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb index d6a8666d27dfe2d7b0e4bd388fe8625e3cf37551..60c64c147dcde840645808f5a4bab5a90e895337 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb @@ -5,6 +5,7 @@ homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -23,4 +24,9 @@ dependencies = [ ('Python', pythonver), ] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb index 3d1f3f2077131d745835dfdb2acbfb98e789657a..53eca5aa25a0d500aa46bc8d938e4eae1f912a91 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb @@ -7,6 +7,7 @@ homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -18,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb index ddf8c959891d1b635637e624fa2a5d22d8f1a3f4..3e93f2c23c41f4c3e905945608cf06bb517cdd57 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb @@ -6,6 +6,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '4.0.6'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -24,4 +25,9 @@ dependencies = [ ('Python', pythonver), ] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb index c92bb71719aa1a28deec72a2a8efa3a33d999bb9..36c184b95a294c22da7af4f0c60ce46c7e11ade9 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '4.0.6'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -19,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb index e56d2ad35387bc1da3b636f7aaf3b49f168c8d13..5c84637a7e6a7b228fb1699ee76c90d5a2189eff 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb @@ -6,6 +6,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -24,4 +25,9 @@ dependencies = [ ('Python', pythonver), ] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb index e014507e31ff21bd5329ef731e5912d3e04388ba..47ab2a1eaf30dd30964e015ddb10b2ea26fba74a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb @@ -6,6 +6,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -24,4 +25,9 @@ dependencies = [ ('Python', pythonver), ] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb index 1a06b1ab67e14d975baab04f8ebef8a709750d2a..0297dc62f16c0ccd9c36fac6e1c780f88227ffb1 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -19,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb index 833381d4b24b18d167a600acdf6d91a2dc8161cf..b747d1108f7d76dfb72c59840a63611941fbdef6 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb @@ -6,6 +6,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -24,4 +25,9 @@ dependencies = [ ('Python', pythonver), ] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb index 1babda58a00c8a770d4edc83e454656b694791f1..461d52a9c8e2bacdd93b664eddd517f93e811fe5 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -19,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb index 9c2538dce193148c178766bd2a60e2c1e0f1aa96..9780466535460c5720cb016319abc989dad304af 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb @@ -7,6 +7,7 @@ homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -18,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb index 34aa5f2ec628855c40cd45e53aee9079e941176d..f10ab602a59aef8feed069751ca5be3364e77548 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '4.0.6'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -19,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb index 59de5c01a760075da72be964b215f9a9943466f1..5d91dfdb96ccb962a58b42d5c22d1ae068f04512 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -19,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb index 5618053aba929a71e04c9a5492e21bded5a6abec..e91eeeeabc9b78aff7a0b393a085ea1af7a91dd2 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -19,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..f98f4a1b675989bebc5ccb067a9f521b2c8faea7 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable +outside of the Gnome platform).""" + +toolchain = {'name': 'gmpolf', 'version': '1.4.8'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb index 0d54f03977331560d8edf3b64ef7972fbb0a2289..728af8a94693e5f43c52fed7d0718b8ebed7597e 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -19,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb index 2145f1ccf3642751064d553c446ec9a92bc61f18..ddfc201d2da00595c64b401afea6adf0a2c7acd2 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'goalf', 'version': '1.5.12-no-OFED'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -19,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000000000000000000000000000000000..04f39a5a5e2afe2c82664100754626c7d2f21f4f --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb index b46d67c8c8252d034aeeb50bdb636ee30ffd1e1b..85c8e40fd53130964b09bd1952f3619a86f2a9e4 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -19,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..dc6262f297f24a8310ff036f4f88ca3ef2eab526 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable +outside of the Gnome platform).""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb index 02c5f8e418e1939158f4168b88c62f3c0705ff83..63cf588844b53a52703445f235635f5512955f19 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno (but usable outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '4.0.6'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -19,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb index b3eac90a5135fc738be54f4dd7e99e44fc6869e9..5849c68e0ba5f8f15f5e8386014de4ce131ba6b8 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno (but usable outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -19,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..00ef91bfbe0bd50a4e193754a90f44b6c833fbe3 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'ictce', 'version': '5.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb index e18bbcef3bbe722866f0425285e25dfa7a6ceef1..6454b3c5bcd485aaf2da86d0e79d04e06a571b2c 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno (but usable outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -19,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb index ef442f4bb59b2ad3581e62c7593b6e643358c012..8b4ebb1f971939825aca07609205eeff84036118 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb @@ -6,6 +6,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -24,4 +25,9 @@ dependencies = [ ('Python', pythonver), ] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb index 5c7f304740e63f95bf22fb48d9d0b3a6aed8d297..32892101ebaac548d2e3de5529f506708e00a150 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb @@ -8,6 +8,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno (but usable outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -19,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb index 3194637d11d4b6021ff32f38c77d4469f1d361ca..4ca7d2ddd74a9b760744b9b090da6af80f95ba95 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb @@ -9,6 +9,7 @@ toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" toolchain = {'name': 'ictce', 'version': '7.1.2'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -20,4 +21,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb index 102c2914dbfbed3a7a942047bc970703f0db36be..0fdd037332ea1c5035cdbc942c6bfee3f8d8a1ee 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb @@ -9,6 +9,7 @@ toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -20,4 +21,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb index 25967be1173d9792dd44e3f95f615e9c4e74dc37..4f3853dc8b4fc821dd7656c8025c6847e5816fc4 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb @@ -9,6 +9,7 @@ toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -20,4 +21,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..aa7e3a45276411fd154df845dcb4f998252079e8 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb index 12454bc9c490647eeffee3f3707f9803095c0854..60f233de3e2288bb1bcc8f82b6f7959142fdf05a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb @@ -9,6 +9,7 @@ toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -20,4 +21,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..4af0891c8abb0e79ef12e21bb654a7c4a529cfb8 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..f85a2b61718f864d4770d3e097dc5988c7093c88 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..8b3729f893206d3afe1fbdb461d78ff0bcb67dbf --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..22b90777374860b36500eff766c4220b3fa3de1a --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..22727637dc909b79e688b6b2178b09df5edbf3a5 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..e102ff79f513a26a4e0fa66f6605b8a3e51658eb --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,28 @@ +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic' + +pythonver = '2.7.10' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..da831a62f319b4e41021d03e5ea392741029a2b1 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,28 @@ +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable + outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic' + +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +dependencies = [ + ('zlib', '1.2.8'), + ('Python', pythonver), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb index 84a2d133c68d3ed02c317d55937dbc20880915a5..c052dd338dba35e323aa2cfa315090435e1bbe9f 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb @@ -9,6 +9,7 @@ toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -20,4 +21,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..6b29a23daad4f87a9a3d758e565ec78dd6825e8d --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.2' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2014b.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..da4b7d1bbdd20d19a39c5064b9cae1065c9f06e9 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2014b.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': '2014b'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.2'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2015b.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..6524ad39ef89ca3b1dc9465f879bd660f8e94f37 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-intel-2015b.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': '2015b'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.2'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015b.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..581b8cb56bb2a8eed622664de0d48af2cc4d4cab --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015b.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:: Nils Christian +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.1.6' + +homepage = 'http://pyyaml.org/wiki/LibYAML' +description = """LibYAML is a YAML 1.1 parser and emitter written in C.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = ['yaml-%(version)s.tar.gz'] +source_urls = ['http://pyyaml.org/download/libyaml/'] + +sanity_check_paths = { + 'files': ["include/yaml.h", "lib/libyaml.a", "lib/libyaml.so"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lxml/lxml-3.4.2-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/l/lxml/lxml-3.4.2-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..c64a9a648dc446f149b4dd836ba7bc422eac9034 --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-3.4.2-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'lxml' +version = '3.4.2' + +homepage = 'http://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://lxml.de/files/'] +sources = [SOURCE_TGZ] + +python = 'Python' +pythonversion = '2.7.8' +pyshortver = '.'.join(pythonversion.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('libxml2', '2.9.2'), + ('libxslt', '1.1.28'), +] + +pylibdir = "lib/python%s/site-packages/%%(name)s" % pyshortver + +sanity_check_paths = { + 'files': [], + 'dirs': [('%s-%%(version)s-py%s.egg' % (pylibdir, pyshortver), + '%s-%%(version)s-py%s-linux-x86_64.egg' % (pylibdir, pyshortver))], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lxml/lxml-3.4.4-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/l/lxml/lxml-3.4.4-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..6f981f8afada86a39fd42e3df900b48a0732ae1b --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-3.4.4-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'lxml' +version = '3.4.4' + +homepage = 'http://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['http://lxml.de/files/'] +sources = [SOURCE_TGZ] + +python = 'Python' +pythonversion = '2.7.10' +pyshortver = '.'.join(pythonversion.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('libxml2', '2.9.2'), + ('libxslt', '1.1.28'), +] + +pylibdir = "lib/python%s/site-packages/%%(name)s" % pyshortver + +sanity_check_paths = { + 'files': [], + 'dirs': [('%s-%%(version)s-py%s.egg' % (pylibdir, pyshortver), + '%s-%%(version)s-py%s-linux-x86_64.egg' % (pylibdir, pyshortver))], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-6.1.5.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-6.1.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..062e490de1ec9700d054e4168e374334cc701f3a --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-6.1.5.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.16' + +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': 'ictce', 'version': '6.1.5'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +patches = ['M4-%(version)s-no-gets.patch'] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000000000000000000000000000000000..a79d153988e395f5ecf8028734d4ae26f9a94afe --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.2-binutils-2.25.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': 'GCC', 'version': '4.9.2-binutils-2.25'} + +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" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000000000000000000000000000000000..89984f9bafa395c2faeedb88f29ee71e079670c0 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-4.9.3-binutils-2.25.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': 'GCC', 'version': '4.9.3-binutils-2.25'} + +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" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000000000000000000000000000000000..e856a3fd434a4481589f2c44fdc0d2860aaf8433 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.1.0-binutils-2.25.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': 'GCC', 'version': '5.1.0-binutils-2.25'} + +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" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000000000000000000000000000000000..ad83091b2bf417349aeb8cbf74bc223951fd67fd --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.3-2.25.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': 'GNU', 'version': '4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000000000000000000000000000000000..e83b261924d4a2783a0f5e6aa1151bd2864ee363 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.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': 'GNU', 'version': '5.1.0-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000000000000000000000000000000000..94ec58056bd19a15fe6fe924516739ca49f4cb6e --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.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': 'foss', 'version': '2014b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000000000000000000000000000000000..411820a76bb3e8fef73e6da7d5917889be8273ee --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.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': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000000000000000000000000000000000..3b4187acd1295cd2cee41412784368927dbb1cc2 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-ictce-5.4.0.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': 'ictce', 'version': '5.4.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb new file mode 100644 index 0000000000000000000000000000000000000000..3f396ce26b1f9699142abde0d13df234d7552e9a --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17.eb @@ -0,0 +1,25 @@ +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': 'dummy', 'version': 'dummy'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..fe54887474e69d6cc812349117bcc55422812757 --- /dev/null +++ b/easybuild/easyconfigs/m/MACS/MACS-1.4.2-1-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,41 @@ +# 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 + +easyblock = 'PythonPackage' + +name = 'MACS' +version = '1.4.2-1' + +homepage = 'http://liulab.dfci.harvard.edu/MACS/' +description = """ Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers + such as Genome Analyzer (Illumina / Solexa). MACS empirically models the length of + the sequenced ChIP fragments, which tends to be shorter than sonication or library + construction size estimates, and uses it to improve the spatial resolution of predicted + binding sites. MACS also uses a dynamic Poisson distribution to effectively capture + local biases in the genome sequence, allowing for more sensitive and robust prediction.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +# automagic download doesn't work, download manually from https://github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.5' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +options = {'modulename': 'MACS14'} + +sanity_check_paths = { + 'files': ['bin/macs14'], + 'dirs': [''], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..79d3f53e5ad6a9edbab99b0717ef9196c15d60ff --- /dev/null +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb @@ -0,0 +1,24 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'MATIO' +version = '1.5.2' + +homepage = 'http://sourceforge.net/projects/matio/' +description = """matio is an C library for reading and writing Matlab MAT files.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_ZIP] + +dependencies = [('zlib','1.2.7')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..acdae43db5801fa2c7705d9c7068144a62839aa9 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2015a.eb @@ -0,0 +1,20 @@ +name = 'MATLAB' +version = '2015a' + +homepage = 'http://www.mathworks.com/products/matlab' +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'} + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Java', '1.8.0_45')] + +import os +license_server = os.getenv('EB_MATLAB_LICENSE_SERVER', 'license.example.com') +license_server_port = os.getenv('EB_MATLAB_LICENSE_SERVER_PORT', '00000') +key = os.getenv('EB_MATLAB_KEY', '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000') + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7efec1287d0f127808fe9078fdcfd5ff60230223 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2014a.eb @@ -0,0 +1,16 @@ +name = 'MCR' +version = 'R2014a' + +homepage = 'http://www.mathworks.com/products/compiler/mcr/' +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'} + +source_urls = ['http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/'] +sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] + +dependencies =[('Java', '1.8.0_31')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e0b5326bd60b3ce84d093900ae7237193704baf6 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2015a.eb @@ -0,0 +1,16 @@ +name = 'MCR' +version = 'R2015a' + +homepage = 'http://www.mathworks.com/products/compiler/mcr/' +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'} + +source_urls = ['http://www.mathworks.com/supportfiles/downloads/%(version)s/deployment_files/%(version)s/installers/glnxa64/'] +sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] + +dependencies =[('Java', '1.8.0_31')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MDP/MDP-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/m/MDP/MDP-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 3818ea1e1b1d412cf5c8311ea5502c4c5bd89e8c..ebdb88d2e4f472258e628921d026248289211dad 100644 --- a/easybuild/easyconfigs/m/MDP/MDP-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/MDP/MDP-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -13,12 +13,17 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = [('http://sourceforge.net/projects/mdp-toolkit/files/mdp-toolkit/%s' % version, 'download')] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +python = 'Python' +pyver = '2.7.3' -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) -dependencies = [(python, pythonversion)] +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/bimdp' % pyshortver, 'lib/python%s/site-packages/mdp' % pyshortver], + 'dirs': [], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/MDP/MDP-3.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/MDP/MDP-3.3-goolf-1.4.10-Python-2.7.3.eb index e0c55493525845fcba846a7b2612852f5b8bd65e..d72a56800d805635890b6fba3906ced9490f8fde 100644 --- a/easybuild/easyconfigs/m/MDP/MDP-3.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/MDP/MDP-3.3-goolf-1.4.10-Python-2.7.3.eb @@ -13,12 +13,17 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [('http://sourceforge.net/projects/mdp-toolkit/files/mdp-toolkit/%s' % version, 'download')] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +python = 'Python' +pyver = '2.7.3' -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) -dependencies = [(python, pythonversion)] +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/bimdp' % pyshortver, 'lib/python%s/site-packages/mdp' % pyshortver], + 'dirs': [], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/MDP/MDP-3.3-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/m/MDP/MDP-3.3-ictce-4.0.6-Python-2.7.3.eb index ecbabdb0020d077635eaa37f9bdb305f7ba0192b..97479dc022b19a248a4688facafac9d8ec9dbb48 100644 --- a/easybuild/easyconfigs/m/MDP/MDP-3.3-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/MDP/MDP-3.3-ictce-4.0.6-Python-2.7.3.eb @@ -13,12 +13,17 @@ toolchain = {'name': 'ictce', 'version': '4.0.6'} source_urls = [('http://sourceforge.net/projects/mdp-toolkit/files/mdp-toolkit/%s' % version, 'download')] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +python = 'Python' +pyver = '2.7.3' -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) -dependencies = [(python, pythonversion)] +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/bimdp' % pyshortver, 'lib/python%s/site-packages/mdp' % pyshortver], + 'dirs': [], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/MDP/MDP-3.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/MDP/MDP-3.3-ictce-5.3.0-Python-2.7.3.eb index 007fc91caa964f1c61eb9e92f6beca35bd701959..5538ab064d4f6dc2cb747d231b3236cdfe02eeb9 100644 --- a/easybuild/easyconfigs/m/MDP/MDP-3.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/MDP/MDP-3.3-ictce-5.3.0-Python-2.7.3.eb @@ -14,12 +14,17 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = [('http://sourceforge.net/projects/mdp-toolkit/files/mdp-toolkit/%s' % version, 'download')] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +python = 'Python' +pyver = '2.7.3' -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) -dependencies = [(python, pythonversion)] +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/bimdp' % pyshortver, 'lib/python%s/site-packages/mdp' % pyshortver], + 'dirs': [], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/METIS/METIS-4.0.3-intel-2015b.eb b/easybuild/easyconfigs/m/METIS/METIS-4.0.3-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..c24b8fd216ecfa43198565a4c8b8efdbdbc4aa16 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-4.0.3-intel-2015b.eb @@ -0,0 +1,18 @@ +name = 'METIS' +version = '4.0.3' + +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': '2015b'} +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', +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-3.6.11-intel-2015a.eb b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-3.6.11-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9d2b2c9a3034b785d2acc231025891b7065caaa8 --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-3.6.11-intel-2015a.eb @@ -0,0 +1,39 @@ +easyblock = "ConfigureMake" + +name = "MIGRATE-N" +version = "3.6.11" + +homepage = 'http://popgen.sc.fsu.edu/Migrate/Migrate-n.html' +description = """Migrate estimates effective population sizes and past migration rates + between n population assuming a migration matrix model + with asymmetric migration tates and different subpopulation sizes.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'http://popgen.sc.fsu.edu/currentversions/', + 'http://popgen.sc.fsu.edu/oldversions/%(version_major)s.x/%(version_major_minor)s', + 'http://popgen.sc.fsu.edu/oldversions/', +] +sources = ['migrate-%(version)s.src.tar.gz'] + +patches = [ + 'migrate-%(version)s_icc.patch', + 'migrate-%(version)s_install.patch', +] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-A4 "CC=$CC" ' +prebuildopts = 'make mpis && make clean && ' + +start_dir = 'src' + +sanity_check_paths = { + 'files': ['bin/migrate-n', 'bin/migrate-n-mpi'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MIGRATE-N/migrate-3.6.11_icc.patch b/easybuild/easyconfigs/m/MIGRATE-N/migrate-3.6.11_icc.patch new file mode 100644 index 0000000000000000000000000000000000000000..5c06ee45aac15fb2159f0defece92b291b271ccf --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/migrate-3.6.11_icc.patch @@ -0,0 +1,13 @@ +#icc does not find -lpthread, if -fast defined +#B. Hajgato 3rd September 2015 +--- src/configure.old 2015-05-02 14:42:10.000000000 +0200 ++++ src/configure 2015-09-03 10:00:54.320014335 +0200 +@@ -3333,7 +3333,7 @@ + pgcc) CFLAGS="-B -fast "; + SYSTEM="gcc";; + # icc) CFLAGS=" -O3 -tpp7 -xKW -pad -ip "; +- icc) CFLAGS+=" -fast "; ++ icc) CFLAGS+=""; + SYSTEM="icc";; + cc) case "$host_vendor" in + ibm) CFLAGS="-O3 -Dinline='/*inline*/' -q cpluscmt -DIBM"; diff --git a/easybuild/easyconfigs/m/MIGRATE-N/migrate-3.6.11_install.patch b/easybuild/easyconfigs/m/MIGRATE-N/migrate-3.6.11_install.patch new file mode 100644 index 0000000000000000000000000000000000000000..77600f365c946cdb9e2d6eefaa28ab27ce7bbd83 --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/migrate-3.6.11_install.patch @@ -0,0 +1,13 @@ +#Create parent directories during install +#B. Hajgato 3rd September 2015 +--- src/configure.old 2015-05-02 14:42:10.000000000 +0200 ++++ src/configure 2015-09-03 10:00:54.320014335 +0200 +@@ -3412,7 +3412,7 @@ + test -s conftest.dir/conftest.one && + test -s conftest.dir/conftest.two + then +- ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c" ++ ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c -D" + break 3 + fi + fi diff --git a/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..922c0e05aba193c9df76c6e14afe1fc3ccb94fa9 --- /dev/null +++ b/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'MIRA' +version = '4.0.2' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://sourceforge.net/p/mira-assembler/wiki/Home/' +description = """MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), + IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads).""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['%(namelower)s-%(version)s.tar.bz2'] +source_urls = [('http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/', 'download')] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = '--with-boost-libdir=$EBROOTBOOST/lib --with-expat=$EBROOTEXPAT' + +patches = ['MIRA-%(version)s-quirks.patch'] + +builddependencies = [('flex', '2.5.39')] +dependencies = [ + ('Boost', '1.58.0', versionsuffix), + ('expat', '2.1.0'), + ('zlib', '1.2.8'), + ('gperftools', '2.4'), +] + +sanity_check_paths = { + 'files': ["bin/mira"], + 'dirs': ["bin", "share"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-quirks.patch b/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-quirks.patch new file mode 100644 index 0000000000000000000000000000000000000000..062ec9454fa7b9f3f41888c1d106312198b4286d --- /dev/null +++ b/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-quirks.patch @@ -0,0 +1,13 @@ +# solve error reported: https://github.com/Homebrew/homebrew-science/issues/2268 +# +--- a/src/progs/quirks.C.old ++++ b/src/progs/quirks.C +@@ -22,7 +22,7 @@ + * + */ + +- ++#include + #include + + // make the "tcmalloc: large alloc" messages from TCMallom disappear diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c0d8ea5a4855626565738cd1a3b91cd3781f4c53 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-foss-2015a-GMP-6.0.0a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.2' + +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': '2015a'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['MPFR_ictce_remove-deprecated-mp.patch'] + +gmp='GMP' +gmpver='6.0.0a' +versionsuffix='-%s-%s' % (gmp,gmpver) + +#GMP does not compile correctly with ICC on Haswell architecture +dependencies = [(gmp, gmpver, '', ('GCC', '4.9.2'))] + +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-3.1.2-intel-2015a-GMP-6.0.0a.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4afd6ab5dcbbf3c162902a2aebe47808f8973563 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.2-intel-2015a-GMP-6.0.0a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.2' + +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': '2015a'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['MPFR_ictce_remove-deprecated-mp.patch'] + +gmp='GMP' +gmpver='6.0.0a' +versionsuffix='-%s-%s' % (gmp,gmpver) + +#GMP does not compile correctly with ICC on Haswell architecture +dependencies = [(gmp, gmpver, '', ('GCC', '4.9.2'))] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.0.1-intel-2015a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.0.1-intel-2015a-metis.eb new file mode 100644 index 0000000000000000000000000000000000000000..a7272f2a494ed8676b219dac39551053c6964ca1 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.0.1-intel-2015a-metis.eb @@ -0,0 +1,22 @@ +name = 'MUMPS' +version = '5.0.1' +versionsuffix = '-metis' + +homepage = 'http://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://mumps.enseeiht.fr/'] +sources = ['%(name)s_%(version)s.tar.gz'] + +dependencies = [ + ('SCOTCH', '6.0.4'), + ('METIS', '5.1.0'), +] + +parallel = 1 +buildopts = 'all' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.0.1-intel-2015a-parmetis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.0.1-intel-2015a-parmetis.eb new file mode 100644 index 0000000000000000000000000000000000000000..d258742e329ca7e6b9ccd46026da7862bf7eb656 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.0.1-intel-2015a-parmetis.eb @@ -0,0 +1,22 @@ +name = 'MUMPS' +version = '5.0.1' +versionsuffix = '-parmetis' + +homepage = 'http://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://mumps.enseeiht.fr/'] +sources = ['%(name)s_%(version)s.tar.gz'] + +dependencies = [ + ('SCOTCH', '6.0.4'), + ('ParMETIS', '4.0.3'), +] + +parallel = 1 +buildopts = 'all' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..c56c34addfc7ef62f532258a699ae28a0d99b8fd --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.0.21-GNU-4.9.3-2.25.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '10.0.21' + +homepage = 'https://mariadb.org/' +description = """MariaDB An enhanced, drop-in replacement for MySQL.""" + +toolchain = {'name': 'GNU' , 'version': '4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://downloads.mariadb.org/f/mariadb-10.0.21/source/'] + +dependencies = [ + ('zlib', '1.2.8'), + ('ncurses' , '5.9'), + ('libedit', '20150325'), + ('libxml2', '2.9.2'), +] + +builddependencies = [ + ('CMake', '3.3.2'), + ('Bison', '3.0.4'), +] + +# remove prebundled version of libedit +preconfigopts = "rm -rf cmd-line-utils/libedit && " + +configopts = "-DCURSES_LIBRARY=$EBROOTNCURSES/lib/libncurses.so -DCURSES_INCLUDE_PATH=$EBROOTNCURSES/include" +# do not use ld.gold +configopts += " -DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.so', 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb b/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..a18f09ae418a5d25f75584ad42ee248606984084 --- /dev/null +++ b/easybuild/easyconfigs/m/Maven/Maven-3.3.3.eb @@ -0,0 +1,23 @@ +easyblock = 'PackedBinary' + +name = 'Maven' +version = '3.3.3' + +homepage = 'http://maven.apache.org/index.html' +description = """Binary maven install, Apache Maven is a software project management and comprehension tool. Based on +the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a +central piece of information. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['apache-maven-%(version)s-bin.tar.gz'] +source_urls = ['http://apache.org/dist/maven/maven-%(version_major)s/%(version)s/binaries/'] + + +sanity_check_paths = { + 'files': ["bin/mvn"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb b/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb index 822615186c2965e75e9b266626cab2e2625a1b94..baee3155cfdb2c7e519d33b9cc6bccc97c15aa35 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb @@ -20,7 +20,7 @@ patches = ['Meep-%(version)s_version-string-without-spaces.patch'] dependencies = [ ('Harminv', '1.4'), - ('HDF5', '1.8.14', '-gpfs'), + ('HDF5', '1.8.14'), ('libctl', '3.2.2'), ('GSL', '1.16'), ('FFTW', '3.3.4') diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..9f2977a63e37ca2723f34e76c3a86bc17cc7c6ac --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-10.5.5-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,74 @@ +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '10.5.5' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] + +pythonver = '2.7.10' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % ('Python', pythonver) + +builddependencies = [ + ('flex', '2.5.39', '', ('GCC', '4.9.2')), + ('Bison', '3.0.4', '', ('GCC', '4.9.2')), + ('Autotools', '20150119', '', ('GCC', '4.9.2')), + ('pkg-config', '0.28', '', ('GCC', '4.9.2')), + ('glproto', '1.4.17'), + ('kbproto', '1.0.6'), + ('xextproto', '7.3.0'), + ('xproto', '7.0.27'), + ('makedepend', '1.0.5'), + ('M4', '1.4.17', '', ('GCC', '4.9.2')), +] + +dependencies = [ + ('Python', pythonver), + ('libxml2', '2.9.2'), + ('libdrm', '2.4.59'), + ('libX11', '1.6.3', versionsuffix), + ('libXext', '1.3.3', versionsuffix), + ('libXfixes', '5.0.1'), + ('libXdamage', '1.1.4', versionsuffix), + ('libXfont', '1.5.1', versionsuffix), + ('LLVM', '3.6.2'), + ('eudev', '3.0'), +] + +#Use the os provided libudev or the EB provided eudev +#osdependencies = ['libudev'] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri --enable-xlib-glx" +configopts += " --disable-driglx-direct --with-gallium-drivers='swrast' --disable-egl --with-osmesa-bits=32 --enable-texture-float " + +# package-config files for os dependencies are in an os specific place +#preconfigopts = 'libtoolize && PKG_CONFIG_PATH="$PKG_CONFIG_PATH:/usr/lib64/pkgconfig/:/usr/share/pkgconfig" ' +preconfigopts = ' libtoolize && ' + +prebuildopts = 'CPATH="$EBROOTLIBDRM/include/libdrm" ' + +sanity_check_paths = { + 'files': ['lib/libGL.so', 'lib/libOSMesa.so', + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/wglext.h', 'include/GL/gl.h', + 'include/GL/glxext.h', 'include/GL/glx_mangle.h', + 'include/GL/wmesa.h'], + 'dirs': [] +} + +maxparallel = 1 + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-2012.1.27-intel-2015a.eb b/easybuild/easyconfigs/m/Molpro/Molpro-2012.1.27-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..bfa90c0102678c6848c8e75e748d21d5471dd1b9 --- /dev/null +++ b/easybuild/easyconfigs/m/Molpro/Molpro-2012.1.27-intel-2015a.eb @@ -0,0 +1,17 @@ +name = 'Molpro' +version = '2012.1.27' + +homepage = 'https://molpro.net' +description = """Molpro is a complete system of ab initio programs for molecular electronic structure calculations.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +# no source URL available, requires registration to download +sources = ['%(namelower)s.%(version)s.tar.gz'] + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), 'licenses', name, 'license.lic') + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb new file mode 100644 index 0000000000000000000000000000000000000000..afe163b841159ca2b65c40ae7fabd895702189dc --- /dev/null +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.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 = 'MuTect' +version = '1.1.4' + +homepage = 'http://www.broadinstitute.org/cancer/cga/mutect' +description = """ MuTect is a method developed at the Broad Institute for the reliable + and accurate identification of somatic point mutations in next generation sequencing + data of cancer genomes. """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutect/'] +sources = ['muTect-%(version)s-bin.zip'] + +java = 'Java' +javaver = '1.7.0_76' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': ["muTect-%(version)s.jar"], + 'dirs': [], +} + +modloadmsg = """ +to execute: java -jar \\$EBROOTMUTECT/muTect-%(version)s.jar +""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_80.eb new file mode 100644 index 0000000000000000000000000000000000000000..1434f1c176673a77f9c7a5beca3de356227eb32e --- /dev/null +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-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 +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'Tarball' + +name = 'MuTect' +version = '1.1.4' + +homepage = 'http://www.broadinstitute.org/cancer/cga/mutect' +description = """ MuTect is a method developed at the Broad Institute for the reliable + and accurate identification of somatic point mutations in next generation sequencing + data of cancer genomes. """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutect/'] +sources = ['muTect-%(version)s-bin.zip'] + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': ["muTect-%(version)s.jar"], + 'dirs': [], +} + +modloadmsg = """ +to execute: java -jar \\$EBROOTMUTECT/muTect-%(version)s.jar +""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb new file mode 100644 index 0000000000000000000000000000000000000000..bae1276ac2d48d9a72e315d8d3c9d31a18d629be --- /dev/null +++ b/easybuild/easyconfigs/m/MySQL/MySQL-5.6.26-GNU-4.9.3-2.25-clientonly.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'MySQL' +version = '5.6.26' +versionsuffix = '-clientonly' + +homepage = 'http://www.mysql.com/' +description = """MySQL is (as of March 2014) the world's second most widely used + open-source relational database management system (RDBMS).""" + +source_urls = ['http://dev.mysql.com/get/Downloads/MySQL-%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} + +dependencies = [ + ('libevent', '2.0.22'), + ('ncurses', '5.9'), + ('libedit', '20150325'), + ('zlib', '1.2.8'), +# ('OpenSSL', '1.0.1p'), # OS dependency should be preferred for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +builddependencies = [ + ('CMake', '3.3.2'), +] + +configopts = "-DWITHOUT_SERVER=ON -DWITH_EDITLINE=system" + +sanity_check_paths = { + 'files': ['bin/mysql'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/MySQLdb/MySQLdb-1.2.5-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/m/MySQLdb/MySQLdb-1.2.5-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..93f03d3fd48fc896bb6c46220e3d7f58459b0fcd --- /dev/null +++ b/easybuild/easyconfigs/m/MySQLdb/MySQLdb-1.2.5-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,37 @@ +easyblock = "PythonPackage" + +name = 'MySQLdb' +version = '1.2.5' + +homepage = 'https://pypi.python.org/pypi/MySQL-python/' + +description = """MySQLdb is an interface to the popular MySQL database server for Python.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['https://pypi.python.org/packages/source/M/MySQL-python/'] +sources = ['MySQL-python-%(version)s.zip'] +checksums = ['654f75b302db6ed8dc5a898c625e030c'] + +python = 'Python' +pythonversion = '2.7.8' +pyshortver = '.'.join(pythonversion.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('MySQL', '5.6.20', '-clientonly'), +] + +options = {'modulename': '%(name)s'} + +pylibdir = "lib/python%s/site-packages/MySQL_python" % pyshortver + +sanity_check_paths = { + 'files': [], + 'dirs': [('%s-%%(version)s-py%s.egg' % (pylibdir, pyshortver), + '%s-%%(version)s-py%s-linux-x86_64.egg' % (pylibdir, pyshortver))], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..080aad8636fe87fb99761a076cee7d48f1692260 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.2.1' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.10' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('freetype', '2.5.5'), + ('libpng', '1.6.16'), +] + +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..959081d6a063e88f758756f942dcc3fa4453c214 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.2.1' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('zlib', '1.2.8'), + ('freetype', '2.5.5'), + ('libpng', '1.6.16'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/matplotlib' % pythonshortversion], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..765f86a131a7f3bcf20cf09eb927b6db81eee965 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,37 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.3.1' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.8' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('zlib', '1.2.8'), + ('freetype', '2.5.3'), + ('libpng', '1.6.12'), +] + +# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..0f1262c9db2b683f3714146676fba9e14dd317db --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,37 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.4.3' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = [('matplotlib-%(version)s_Qhull-intel-fix.patch')] + +python = "Python" +pythonversion = '2.7.10' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('freetype', '2.5.5'), + ('libpng', '1.6.16'), +] + +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..df9c676c65282e929bd7956f2d3411f63239ffd1 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,37 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.4.3' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = [('matplotlib-%(version)s_Qhull-intel-fix.patch')] + +python = 'Python' +pythonversion = '2.7.10' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('freetype', '2.5.5'), + ('libpng', '1.6.16'), +] + +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015b-Python-3.5.0.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015b-Python-3.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..741df4d0ff7938b6484bf301a544ebc081fcde05 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015b-Python-3.5.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'matplotlib' +version = '1.4.3' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = [('matplotlib-%(version)s_Qhull-intel-fix.patch')] + +python = 'Python' +pythonversion = '3.5.0' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('freetype', '2.5.5'), + ('libpng', '1.6.16'), +] + +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..5d19338ab330d70960ae54b3f6d6f8abb6792cf9 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'molmod' +version = '1.0' + +homepage = 'http://molmod.github.io/molmod/' +description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://users.ugent.be/~tovrstra/molmod'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.10' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.2.1', versionsuffix), +] + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/molmod' % pythonshortversion], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..b6703cee3099afdb0d973de768d2723f09f54be8 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'molmod' +version = '1.0' + +homepage = 'http://molmod.github.io/molmod/' +description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://users.ugent.be/~tovrstra/molmod'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.2.1', versionsuffix), +] + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/molmod' % pythonshortversion], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 832a044412960f49cfb3e22b3099f048dbba6363..98f6b375dfec77f5e8f773681483a034c6e86d98 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -23,4 +23,10 @@ dependencies = [ (python, pyver), ] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/mpi4py' % pyshortver], +} + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb index d7ce479c30cb6b92dfa5ff4094b5e16c95ad144f..58e1efec953d6fd93286aa4b10b8a37d7ecd387d 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-2.7.3.eb @@ -23,4 +23,10 @@ dependencies = [ (python, pyver), ] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/mpi4py' % pyshortver], +} + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..8d1017dab1d5529822d9b1a8e68480c9d24dc6b3 --- /dev/null +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'mpi4py' +version = '1.3' + +homepage = 'https://code.google.com/p/mpi4py/' +description = """MPI for Python (mpi4py) provides bindings of the +Message Passing Interface (MPI) standard for the Python programming +language, allowing any Python program to exploit multiple processors.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [ + BITBUCKET_DOWNLOADS, + GOOGLECODE_SOURCE, +] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '3.2.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/mpi4py' % pyshortver], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb index 52e2739364c4f7e22c0fd5c00df4ea5f2887dc85..fff549de1f9e5125088caae9bd42a07e5552d25d 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb @@ -23,4 +23,10 @@ dependencies = [ (python, pyver), ] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/mpi4py' % pyshortver], +} + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb index 5878a3a0a6ecb468186f41fd3790ab0904b08afb..9fe2a5f319af2b39d5a680874013722ab102c943 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb @@ -23,4 +23,10 @@ dependencies = [ (python, pyver), ] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/mpi4py' % pyshortver], +} + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb index 989b264cf78b11f9f555d9df54619a783517edd6..eaf599c8ab0e5c4731710f43b7e0e35ef4456665 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.3.0-Python-2.7.3.eb @@ -21,4 +21,10 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/mpi4py' % pyshortver], +} + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb index 6f9b95ae80b25c89c58848e5aeacd16bb84911ac..07635c8d39050512fdcc0a4c0c28c8a05624d81a 100644 --- a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-5.5.0-Python-2.7.5.eb @@ -21,4 +21,10 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/mpi4py' % pyshortver], +} + moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-goolf-1.7.20.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..61250ef0ab190312acd0bd996109c6b7efb7a30c --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +## +# 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/HPCBIOS_2012-90.html +## +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.05' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2015a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9bf83664591478f6e96cede8f460c06bd3767ffd --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2015a.eb @@ -0,0 +1,31 @@ +## +# 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/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.05' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +toolchain = {'name': 'intel', 'version': '2015a'} + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-ictce-7.3.5.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-ictce-7.3.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..d2c0dab761544f931fca8e6b3d552c1b29c0576d --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-ictce-7.3.5.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.06' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2015b.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..bcb04e784170e74ffa5fb8edd101eec1f6efcaff --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-foss-2015b.eb @@ -0,0 +1,31 @@ +## +# 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/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.08' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..77ceaa2d9a8cb9485589e5d6aa8467335b855b98 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015a.eb @@ -0,0 +1,31 @@ +## +# 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/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.08' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015b.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..92d511ac9cd6bfc946b6d508bac6a433d757d39b --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015b.eb @@ -0,0 +1,31 @@ +## +# 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/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.08' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..010a358d9234751705d9c4ad1d6456c266c924a4 --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-ictce-5.4.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '4.4.4' + +homepage = "http://nco.sourceforge.net" +description = """manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5""" + +toolchain = {'name': 'ictce', 'version': '5.4.0'} + +source_urls = ['http://nco.sourceforge.net/src'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('UDUNITS', '2.1.24'), + ('expat', '2.1.0'), + ('ANTLR', '2.7.7'), + ('GSL', '1.16'), + ('netCDF', '4.2.1.1'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ncap2', 'ncatted', 'ncbo', 'ncdiff', 'ncea', 'ncecat', 'nces', 'ncflint', + 'ncks', 'ncpdq', 'ncra', 'ncrcat', 'ncrename']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..434cce1376537213ffbbb9f26142a26595eb6743 --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-4.4.4-intel-2014b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '4.4.4' + +homepage = "http://nco.sourceforge.net" +description = """manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://nco.sourceforge.net/src'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('UDUNITS', '2.1.24'), + ('expat', '2.1.0'), + ('ANTLR', '2.7.7'), + ('GSL', '1.16'), + ('netCDF', '4.2.1.1'), +] + +sanity_check_paths = { + 'files': ['bin/nc%s' % x for x in ['ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', 'flint', + 'ks', 'pdq', 'ra', 'rcat', 'rename']] + + ['lib/libnco.a', 'lib/libnco.so', 'lib/libnco_c++.a', 'lib/libnco_c++.so'], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5-IC3.eb b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5-IC3.eb new file mode 100644 index 0000000000000000000000000000000000000000..3f22d894436ef0799bd9c4092a0c7e13cebe953f --- /dev/null +++ b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5-IC3.eb @@ -0,0 +1,29 @@ +name = 'NEMO' +version = '3.4-r5541' +versionsuffix = '-IC3' + +homepage = 'http://www.nemo-ocean.eu/' +description = """NEMO (Nucleus for European Modelling of the Ocean) is a state-of-the-art modeling framework for + oceanographic research, operational oceanography seasonal forecast and climate studies.""" + +toolchain = {'name': 'ictce','version': '6.1.5'} +toolchainopts = {'opt': False, 'optarch': False} + +# authenticated SVN access required +# svn --username 'login' co http://forge.ipsl.jussieu.fr/nemo/svn/branches/2012/dev_v3_4_STABLE_2012 +# tar cfvz NEMO-3.4-r.tar.gz dev_v3_4_STABLE_2012 +sources = [SOURCE_TAR_GZ] + +dependencies = [('netCDF-Fortran', '4.2')] + +# setting specific to IC3 +# enable ocean model and Louvain-la-Neuve sea-ice model +# see http://www.nemo-ocean.eu/About-NEMO +with_components = ['OPA_SRC', 'LIM_SRC_3'] +# enable LIM3, MPI, IOM, global ORCA config at 1 degree resolution (& more) +# disable LIM2, global ORCA config at 2 degree resolution, tides induced vertical mixing +# see http://www.nemo-ocean.eu/About-NEMO, http://www.nemo-ocean.eu/Using-NEMO/User-Guides/Basics/cpp-keys-v3_4 +add_keys = ['key_dtasal', 'key_dtatem', 'key_lim3', 'key_iomput', 'key_mpp_mpi', 'key_orca_r1=75', 'key_tradmp'] +del_keys = ['key_lim2', 'key_orca_r2', 'key_zdftmx'] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..dca0868591c7aa4baa077e3c315ac42bbdccc353 --- /dev/null +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-CrayGNU-5.2.40.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'NFFT' +version = '3.3.0' + +homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine + library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more + dimensions, of arbitrary input size, and of complex data.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = { 'dynamic': True } + +source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-foss-2015a.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..263c3c6dac7d48ea5b196aced4a54d1cf082ca1c --- /dev/null +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-foss-2015a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'NFFT' +version = '3.3.0' + +homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine + library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more + dimensions, of arbitrary input size, and of complex data.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('FFTW', '3.3.4', '', ('gompi', '2015a'))] + +sanity_check_paths = { + 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-intel-2015a.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0e939b4038921b7dd6cf0b7b16e44776fe6fe957 --- /dev/null +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.3.0-intel-2015a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'NFFT' +version = '3.3.0' + +homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine + library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more + dimensions, of arbitrary input size, and of complex data.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://www-user.tu-chemnitz.de/~potts/nfft/download/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('FFTW', '3.3.4')] + +sanity_check_paths = { + 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..2eefc9a7f35a4bb722e574829d36ffd5702995fb --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb @@ -0,0 +1,31 @@ +name = 'NWChem' +version = '6.5.revision26243' + +homepage = 'http://www.nwchem-sw.org' +description = """NWChem aims to provide its users with computational chemistry tools that are scalable both in + their ability to treat large scientific computational chemistry problems efficiently, and in their use of available + parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. + NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all + combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties + and relativity.""" + +toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'i8': True} + +source_urls = [ 'http://www.nwchem-sw.org/download.php?f='] +verdate = '2014-09-10' +sources = ['Nwchem-%s-src.%s.tar.bz2' % (version, verdate)] + +patches = [ + 'NWChem_fix-date.patch', + 'NWChem-%(version)s-parallelbuild.patch', +] + +python = 'Python' +pyver = '2.7.8' +versionsuffix = '-%s-%s-%s' % (verdate, python, pyver) +dependencies = [(python, pyver)] + +modules = 'all python' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch new file mode 100644 index 0000000000000000000000000000000000000000..c3a7a329824e6bdd5e084025e8f42ab5892e1945 --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch @@ -0,0 +1,92 @@ +# corrected parallel builds, no debug info and no vec reports +# B. Hajgato Nov 13 2014 +--- src/config/makefile.h.orig 2014-09-10 20:08:39.000000000 +0200 ++++ src/config/makefile.h 2014-11-12 11:33:06.449137413 +0100 +@@ -1231,7 +1231,7 @@ + _FC=ifort + #ifort 9.1 + # LINK.f = ifort $(LDFLAGS) +- FOPTIONS += -align -mp1 -w -g -vec-report1 ++ FOPTIONS += -align -mp1 -w + ifdef USE_GPROF + FOPTIONS += -qp + endif +@@ -1394,7 +1394,7 @@ + CORE_SUBDIRS_EXTRA = blas lapack + CC = gcc + RANLIB = ranlib +- MAKEFLAGS = -j 1 --no-print-directory ++ MAKEFLAGS = -j 8 --no-print-directory + INSTALL = @echo $@ is built + CPP = gcc -E -nostdinc -undef -P + FCONVERT = (/bin/cp $< /tmp/$$$$.c; \ +@@ -1527,7 +1527,7 @@ + DEFINES += -DGFORTRAN + endif + ifeq ($(_FC),ifc) +- FOPTIONS = -align -mp1 -w -g -vec-report1 ++ FOPTIONS = -align -mp1 -w + ifdef USE_GPROF + FOPTIONS += -qp + endif +@@ -1602,7 +1602,7 @@ + endif + + ifeq ($(CC),icc) +- COPTIONS = -mp1 -w -g -vec-report1 ++ COPTIONS = -mp1 -w + COPTIMIZE = -O3 -unroll + ifeq ($(_CPU),i586) + COPTIMIZE += -tpp5 -xi # this are for PentiumII +@@ -1814,7 +1814,7 @@ + endif + endif + DEFINES += -DEXT_INT +- MAKEFLAGS = -j 1 --no-print-directory ++ MAKEFLAGS = -j 8 --no-print-directory + _CPU = $(shell uname -m ) + ifeq ($(BLAS_LIB),) + CORE_SUBDIRS_EXTRA += blas +@@ -1923,7 +1923,7 @@ + endif # end of ia32 bit + ifeq ($(_CPU),x86_64) + # +- MAKEFLAGS = -j 2 --no-print-directory ++ MAKEFLAGS = -j 8 --no-print-directory + COPTIMIZE = -O1 + ifeq ($(NWCHEM_TARGET),CATAMOUNT) + FC=pgf90 +@@ -1959,19 +1959,17 @@ + ifeq ($(_IFCV15ORNEWER), Y) + FOPTIONS += -qopt-report-file=stderr + ifdef USE_OPTREPORT +- FOPTIONS += -qopt-report=1 -qopt-report-phase=vec ++ FOPTIONS += -qopt-report=0 -qopt-report-phase=vec + endif + ifdef USE_OPENMP + FOPTIONS += -qopenmp +- FOPTIONS += -qopt-report-phase=openmp + COPTIONS += -qopenmp + DEFINES+= -DUSE_OPENMP + endif + else +- FOPTIONS += -vec-report6 ++ FOPTIONS += -vec-report0 + ifdef USE_OPENMP + FOPTIONS += -openmp +- FOPTIONS += -openmp-report2 + COPTIONS += -openmp + DEFINES+= -DUSE_OPENMP + endif +@@ -2086,9 +2084,9 @@ + ICCV15ORNEWER=$(shell icc -V 2>&1|egrep "Version "|head -n 1 | sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 15) {print "Y";exit}}') + COPTIONS += -xHOST -ftz + ifeq ($(ICCV15ORNEWER), Y) +- COPTIONS += -qopt-report-phase:openmp -vec-report=1 ++ COPTIONS += -qopt-report-phase:openmp + else +- COPTIONS += -openmp-report=2 -vec-report=1 ++ COPTIONS += -openmp-report0 + endif + #old COPTIMIZE = -O3 -hlo -mP2OPT_hlo_level=2 + COPTIMIZE = -O3 diff --git a/easybuild/easyconfigs/n/NetLibIDN/Net-LibIDN-0.12-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/n/NetLibIDN/Net-LibIDN-0.12-intel-2014b-Perl-5.20.0.eb index e208935ff8b7fcf216b592165eda70a4b9dfdeb2..0dbda2b162fcee271706fd4a690573cec44cbfab 100644 --- a/easybuild/easyconfigs/n/NetLibIDN/Net-LibIDN-0.12-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/n/NetLibIDN/Net-LibIDN-0.12-intel-2014b-Perl-5.20.0.eb @@ -23,5 +23,10 @@ dependencies = [ options = {'modulename': 'Net::LibIDN'} -moduleclass = 'system' +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/Net/LibIDN.pm' % (perlmajver, perlver)], + 'dirs': [], +} +moduleclass = 'system' diff --git a/easybuild/easyconfigs/n/ncdf/ncdf-1.6.6-ictce-5.3.0-R-2.15.3.eb b/easybuild/easyconfigs/n/ncdf/ncdf-1.6.6-ictce-5.3.0-R-2.15.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..ba779e4d32adeb7d0d406e5d973fa12ffd32a365 --- /dev/null +++ b/easybuild/easyconfigs/n/ncdf/ncdf-1.6.6-ictce-5.3.0-R-2.15.3.eb @@ -0,0 +1,34 @@ +easyblock = 'RPackage' + +name = 'ncdf' +version = '1.6.6' + +homepage = 'http://cran.r-project.org/web/packages/ncdf4' +description = """This package provides a high-level R interface to data files written using Unidata's netCDF library + (version 4 or earlier), which are binary data files that are portable across platforms and include metadata + information in addition to the data sets.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = [ + 'http://cran.freestatistics.org/src/contrib', + 'http://cran.r-project.org/src/contrib/Archive/ncdf', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +r = 'R' +rver = '2.15.3' + +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [ + (r, rver), + ('netCDF', '4.2.1.1', '-zlib-1.2.5'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['ncdf'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-2.15.3.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-2.15.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..92ad89bc5d64fb916a6b05a7779e0c917d2d39e5 --- /dev/null +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-2.15.3.eb @@ -0,0 +1,34 @@ +easyblock = 'RPackage' + +name = 'ncdf4' +version = '1.10' + +homepage = 'http://cran.r-project.org/web/packages/ncdf4' +description = """This package provides a high-level R interface to data files written using Unidata's netCDF library + (version 4 or earlier), which are binary data files that are portable across platforms and include metadata + information in addition to the data sets.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = [ + 'http://cran.freestatistics.org/src/contrib', + 'http://cran.r-project.org/src/contrib/Archive/ncdf4', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +r = 'R' +rver = '2.15.3' + +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [ + (r, rver), + ('netCDF', '4.2.1.1', '-zlib-1.2.5'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['ncdf4'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-3.0.2-bare.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-3.0.2-bare.eb index 0f47ffdcefb7f320ce2eb2788a20ba5a129b2f57..420a463745d0b93ffa06ae9e6d3fa5c625d1687c 100644 --- a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-3.0.2-bare.eb +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-3.0.2-bare.eb @@ -27,4 +27,9 @@ dependencies = [ ('netCDF', '4.2.1.1'), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['ncdf4'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-3.0.2.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-3.0.2.eb index 20417f1a1fd0bb5f7a402f97b26c89e95b38ba16..e2d4470245803ca09aba9c93b11ad02fe1f92898 100644 --- a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-3.0.2.eb +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-3.0.2.eb @@ -26,4 +26,9 @@ dependencies = [ ('netCDF', '4.2.1.1'), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['ncdf4'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..93af22628cc9421e02f8276013adac9cb45acca5 --- /dev/null +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb @@ -0,0 +1,32 @@ +easyblock = 'RPackage' + +name = 'ncdf4' +version = '1.13' + +homepage = 'http://cran.r-project.org/web/packages/%(name)s' +description = """ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [ + 'http://cran.r-project.org/src/contrib/', + 'http://cran.r-project.org/src/contrib/Archive/$(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +r = 'R' +rver = '3.1.1' +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [ + (r, rver), + ('netCDF', '4.3.2'), + ('cURL', '7.37.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['ncdf4'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2-bare.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2-bare.eb index 491a03c606147945c5d1f37db7448af3b668a96f..4ef7a218bc9727a13f77d6a46daa71efb6e8cf23 100644 --- a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2-bare.eb +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2-bare.eb @@ -27,4 +27,9 @@ dependencies = [ ('netCDF', '4.2.1.1'), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['ncdf4'], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2.eb index 17bf529b5ec3ab6c149a50ba2fdb1da03e7f9ab5..ab54113dccf49d01130b558171d35f956e3191ec 100644 --- a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2.eb +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.6.1-ictce-5.3.0-R-3.0.2.eb @@ -26,4 +26,9 @@ dependencies = [ ('netCDF', '4.2.1.1'), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['ncdf4'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb index 3522f8a87b99bd3113a31f70abdce86546a0d556..634fda5b4d876573afd6dfb3890e690f923f1745 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' @@ -14,7 +16,26 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb index f954a9b12a271effc56ef267704bb2377c1bfc15..4f21474dcf5c3864913bd453cf823ed7be3e8e0b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' @@ -14,7 +16,26 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb index 6a10d2ec63c363e31a77a54902e499945eed7dcf..a71c6aab72a3fb8caac5c469b119b2773d35b886 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' @@ -14,7 +16,26 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb index 4913ef008f8ebac65148f362d32443fcf595b7e6..f2a6bbb76a64f147336529b6ffe1f392c5a11593 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' @@ -9,12 +11,31 @@ function-key mapping, and has all the other SYSV-curses enhancements over BSD Cu toolchain = {'name': 'cgmvolf', 'version': '1.2.7'} toolchainopts = {'optarch': True, 'pic': True} -sources = [SOURCE_TGZ] # In future, this URL will not be sufficient to obtain this tarball, because # the directory contains only a couple of older ncurses 5.9 snapshots. source_urls = ['ftp://invisible-island.net/ncurses/current/'] +sources = [SOURCE_TGZ] + +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb index 8b7d3a2416c6ff2c10fe61a11447786c85987d29..5ef3e822adb21f9c224561aa2163a10ee719df8e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' @@ -14,7 +16,26 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb index 1632ef23de6428be684ed244393e5390c6598973..96cc600747164cd4fca476a0954e658e52fc79bf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' @@ -14,7 +16,26 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb index 43375f2a293e09e47e1f46aac131252f7ffcc4ec..a1409a10e65d3f1c7bcd5d1ae0d6f59415770380 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' @@ -14,7 +16,26 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406_configure_darwin.patch b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406_configure_darwin.patch new file mode 100644 index 0000000000000000000000000000000000000000..067ec128f9927e469df5df128fdf4e1ee93444c0 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406_configure_darwin.patch @@ -0,0 +1,11 @@ +--- ncurses-5.9-20130406/configure.orig 2013-04-07 00:09:21.000000000 +0200 ++++ ncurses-5.9-20130406/configure 2015-06-03 12:20:33.765043843 +0200 +@@ -5587,7 +5587,7 @@ + chmod +x mk_shared_lib.sh + ;; + darwin*) #(vi +- cf_try_cflags="no-cpp-precomp" ++ #cf_try_cflags="no-cpp-precomp" + CC_SHARED_OPTS="-dynamic" + MK_SHARED_LIB='${CC} ${CFLAGS} -dynamiclib -install_name ${libdir}/`basename $@` -compatibility_version ${ABI_VERSION} -current_version ${ABI_VERSION} -o $@' + test "$cf_cv_shlib_version" = auto && cf_cv_shlib_version=abi diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb index 23ac2489aa09b3ac1c5002bc30cf1c40e8221da5..6b7bb1c3472d6faa7a233f230a19c91c05b04dd3 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -7,16 +9,28 @@ description = """The Ncurses (new curses) library is a free software emulation o function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} -toolchainopts = {'pic': True, 'dynamic': True} +toolchainopts = {'optarch': True, 'shared': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb index 95c1010bbcc66582fe393a4bc7ebfe7f70e51ca7..01680ab5b7d7480e3f51ccc11cc8751a58a70653 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -7,16 +9,28 @@ description = """The Ncurses (new curses) library is a free software emulation o function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} -toolchainopts = {'pic': True, 'dynamic': True} +toolchainopts = {'optarch': True, 'shared': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb index af63de1cff91c7bec349c8d7c74c4f6fcd687ecf..6f00fdbd514cfcb8d9a437c6a016daff6de25974 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -7,16 +9,28 @@ description = """The Ncurses (new curses) library is a free software emulation o function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} -toolchainopts = {'pic': True, 'dynamic': True} +toolchainopts = {'optarch': True, 'shared': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb index ad58285a8513af8aa7faca7eaaf8f469e2546599..37a2fff35a8b069cbc61d625bebc22aebefb37d2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb index f972b6a4ffc003ebba3bababe376213801a7a1c8..96e1f454725a74c213ddbfa4b42b16958050853a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb index 5f56a5562114b5dfa1c257b65e92645b508b2607..5dd295c39e5434be465784d56190ab8a5df450ca 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb index 3068c78b44596e55e60ecb5be5483fd68b29f21b..3071876ad25b05ad6e61d3e2cab624d1afc84766 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -6,13 +8,29 @@ description = """The Ncurses (new curses) library is a free software emulation o and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html -patches = ['ncurses-5.9_configure_darwin.patch'] - toolchain = {'name': 'GCC', 'version': '4.8.2'} toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb index 52e0aac9ea3c614e3b263a864e2ed3826ad23033..c5e4c7e93d2561686ae904effb7417780d164d0b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb index 946a1c53383958239960c9bb5cd2b587d04feeeb..a769a56170102b10c9a568d33c1aef99ee6fc728 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb @@ -14,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb index 78b7618284c00eea1b85b0f2cfbe07486554ba27..512532996644497e265f5777fb4c6a1662437b69 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..82fd4d66d07f4797cd222c5cee19a0d0190f8e67 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GNU-4.9.3-2.25.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb index b4ea71f97f0685c284357c6709729be956b08ec8..7278bb4ccf3979c0fe1c6796273eb42f6d728500 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..37d7e0480953a411415f85fd60d72913cf8b5bc6 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb index 2f9501c9ae8a4cdab8fef461a1288387b751d442..cff4af273d5accf82686c9ab1e1909be6614758c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..fd95bcc678fe34e001e6a3535986cd83d2b67ee0 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015b.eb @@ -0,0 +1,18 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +# see https://bbs.archlinux.org/viewtopic.php?id=194029&p=3 +buildopts = 'CPP="$CC -E -P"' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb index 15745294d9f475b510c91ff6fee807b7427c33d0..b529181479679c9688afe923db69e6eb1da965dd 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb index 062cbaeab624e4a1beceaaebcf9e41ebeb8994ab..aaa5b2bd78231932fa7427cb44eb37ee1ae49ee3 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -14,7 +16,26 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb index a372492a64aafbef666f0010ff48d63122214623..f8ee92d0944a25c7ccd20ffdeb5b6455eaf672e0 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,7 +14,26 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb index 38b356d5e1a763c4d098b5f53c18174b4aaa155e..9936cdbc6cdb6baa6b81ce5240396139575e01d8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb index 947e8e3afaf18759ff1a65ee0644e43086a5a411..b5428d27b07354508f725b3e6392f2a825824bb1 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb index 4084c938c1c2a7782ffad1379754c2afd617a78a..21128a21c58cfc993c0cf129ed680a85f373221e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb index 9f6619baca56f6dd3813e005f73c170690c3208a..e272a823d6614bb8925b410002e8a92100a21885 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb index 33bb21037fd7ac4a65074b61bf3ce9ce27fe6e58..fa8d19afbbd1e5e93a2e837630a4038815f3cedc 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb index e67f480463340aeb85025cfe155c7007d32a4cad..cdf8cdb5ce9e70c915b5161862b9d950fa2ebe29 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb index a62ac8f66802cea59e5aa9ad00abee4177129795..9a1708ba34ae2398814813b6de4c9c4e581e4fb3 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb index 5a698183f4f79d5d5b3f3f7b4f42c0ffb3999300..36b5053e62a60abae1f717693dc908ea34b2a781 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb index 4e33e95089d0a624fd05522fadf7811e2abeb808..292cec33e2bc3921dc6b5b481fb41cf2d544290b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://ftpmirror.gnu.org/%(name)s'] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb index c0284ad94f484ff092d1be2ca13001b0672cb2f1..0b4bbba9adc30ef5d48081dffd653c3839a0f10b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb index 95388cfc5b6d2e549dfe51de58b354a4abfab48e..b5099d8795a6848fdd057092b96b3d36bc8e02c8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb index 731485e77bb044ec79ba33d3a1fc5d357ba0406d..94e44f7817caddf76091fff227e9685266e954f3 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb index 8cb79c351b8087fe72e0ad91d2734e6effb94df3..b1c1a88d7577aa59bfaabeb478debe832afe4055 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb index ee127c7a3c35601056fd67f032ae7d9b2050208d..fed58a89dd1f2373cf76550ce214f954c5c1781e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb index 020778b318ecb01f7c95c411c83762ec6a49c88c..bf996a362f89c915867564a47acc1d457d2a38d1 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb index a81155369d140411cd90b282723fa67c5a7b9cda..671b5796ac95d1834954ef17b311a0c30f00e242 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb index 84c486d4d929b95f9216aa4feb913fb6c0b2f709..61118f900516a33e99efa0b231d9b1730251b746 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb index ab5e8538f310a9b7db8fbfc439d47f8dbb93805b..278cc8d64a005f42fe4393c5ed8fa81fda2c0569 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -14,4 +16,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb index 2a7094da2181c35d84d55cbe5b65727abb8b8b48..38c7d0798803c85c251a0de30028904f91aa3e72 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.3.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..a12e4726630cca29876db01c1352d71ecc1052fa --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.3.5.eb @@ -0,0 +1,15 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb index e1045e7b9f8e67ca96c460b26c008578d7a15e76..d67fc45cbf74de2b745b55b8a787038105ef7e8b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb index 4aface2738e4be2af300db0b78beb5078d9da889..9fa751952c5838fd56e21106ba31e1b0fdf3e9ea 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 867d190ac8821b748d3d97dbba140bc2846b9615..24097805bc3a9413673fea1452241d1dba4b5ac7 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,11 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' ] +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..7a48798be876242cae44d0f5a073f97c1415c5a0 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015b.eb @@ -0,0 +1,18 @@ +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +# see https://bbs.archlinux.org/viewtopic.php?id=194029&p=3 +buildopts = 'CPP="$CC -E -P"' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb index 9963e053c2ff37d9944dbbbd70e2452c8996e988..115d1bd981375350fa3b16238bffd34d11d45bde 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb index decfe9bc04b5d0a8b9dd9938a6ded2fea1eabc2d..e4351873f4eeb066925a1439d18deba08b7abc25 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb index f4b42632c95c69520cb058504ffa7e2c0b6ac29a..529b47259fc05498939d6f0744b21441088b9c26 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb index 6ab79de61f05db056443ca5117e231bf95dc29dc..dd70b0800a4df8ac05a21610aa6ae59cf96d69e6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch b/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch index cbc78d120b898add4dc0050f506cc38492bb903d..293f47532a0c63bb189db74ba802f248ed848f3a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch @@ -1,3 +1,5 @@ +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +# tried/proposed by Fotis, meant for MacOSX compatible ncurses builds... --- ncurses-5.9.orig/configure 2014-10-25 21:11:31.000000000 +0200 +++ ncurses-5.9/configure 2014-10-25 21:11:10.000000000 +0200 @@ -5584,7 +5584,7 @@ diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..4012f0e69bde30c60bcc4568189782260e4fd448 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GNU-4.9.3-2.25.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.so' % (x, y) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.2-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.2-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..01beb0993132c83db0026a35794d1c30d2ece86c --- /dev/null +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.2-goolf-1.4.10.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'ncview' +version = '2.1.2' + +homepage = 'http://meteora.ucsd.edu/~pierce/ncview_home_page.html' +description = """Ncview is a visual browser for netCDF format files. +Typically you would use ncview to get a quick and easy, push-button +look at your netCDF files. You can view simple movies of the data, +view along various dimensions, take a look at the actual data values, +change color maps, invert the data, etc.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} + +source_urls = ['ftp://cirrus.ucsd.edu/pub/ncview/'] +sources = [SOURCE_TAR_GZ] + +configopts = "--with-udunits2_incdir=$EBROOTUDUNITS/include --with-udunits2_libdir=$EBROOTUDUNITS/lib" + +dependencies = [ + ('netCDF-Fortran', '4.2'), + ('UDUNITS', '2.1.24'), +] + +sanity_check_paths = { + 'files': ['bin/ncview'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/ncview/ncview-2.1.2-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncview/ncview-2.1.2-ictce-5.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..26ed84e0cab6fdb983ca08e64f71190ae63115bc --- /dev/null +++ b/easybuild/easyconfigs/n/ncview/ncview-2.1.2-ictce-5.3.0.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'ncview' +version = '2.1.2' + +homepage = 'http://meteora.ucsd.edu/~pierce/ncview_home_page.html' +description = """Ncview is a visual browser for netCDF format files. +Typically you would use ncview to get a quick and easy, push-button +look at your netCDF files. You can view simple movies of the data, +view along various dimensions, take a look at the actual data values, +change color maps, invert the data, etc.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} + +source_urls = ['ftp://cirrus.ucsd.edu/pub/ncview/'] +sources = [SOURCE_TAR_GZ] + +configopts = "--with-udunits2_incdir=$EBROOTUDUNITS/include --with-udunits2_libdir=$EBROOTUDUNITS/lib" + +dependencies = [ + ('netCDF-Fortran', '4.2'), + ('UDUNITS', '2.1.24'), +] + +sanity_check_paths = { + 'files': ['bin/ncview'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-goolf-1.4.10.eb index b46d95de455ed7cf103dcc5b897dc5da94856310..e0cfb1558e3ee268b3cfee1869c975f91e0305d3 100644 --- a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-goolf-1.4.10.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = ['netcdf-cxx-%(version)s.tar.gz'] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb index 57f1d3e4bb87ad0c08e3f8493c1f7f8263c0f10e..d47cb17c759e7cd7920c9d7158c04cfd5198a69e 100644 --- a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb @@ -13,7 +13,10 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True, 'openmp': True} sources = ['netcdf-cxx-%(version)s.tar.gz'] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('netCDF', '4.2.1.1', versionsuffix), diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb index 7a7c4b81bc1d579b5b25067a6a42e8654ab789e4..400224b911f0f03f51b8476caa8b5c378e77d8e6 100644 --- a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True} sources = ['netcdf-cxx-%(version)s.tar.gz'] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-5.3.0.eb index 3b4f3e5332f61645e898b28a4e59051ab7ad0646..16ea5317c44ad2e4ce3acbefe0d99483abd17034 100644 --- a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-5.3.0.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} sources = ['netcdf-cxx-%(version)s.tar.gz'] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-iqacml-3.7.3.eb index de008bf23555d4d20f93fd960eb202fd5a1321a0..d8cdaf41c40323ce847ca3ddbe5c1bc41c70c602 100644 --- a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-iqacml-3.7.3.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'pic': True} sources = ['netcdf-cxx-%(version)s.tar.gz'] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.2.1-foss-2014b.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.2.1-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..5fcb22ae6f56dabbb79b5bb89da19e82cea41bdf --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.2.1-foss-2014b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.2.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2014b'} +toolchainopts = {'pic': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] + +dependencies = [('netCDF', '4.3.2')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.so'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goalf-1.1.0-no-OFED.eb index 091c9e9f897d879fca8b8a83653375fdbb1981c2..adc9cf91dce8705937f049531d0ae5891ac5ebd5 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', version)] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.4.10.eb index f4a44d81d372d3caab433671e5b83dcb65c56c8f..2caeeaf083e69a79e8a902d073bf3ec063200c31 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.4.10.eb @@ -5,11 +5,15 @@ homepage = 'http://www.unidata.ucar.edu/software/netcdf/' description = """NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb index a8cbfe5ddb1455f8d33c0106591d09829954ad4d..bd158f66c56af7e8f4cd8334a66a873497547b5b 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-3.2.2.u3.eb index fac88a30ba22ecbe6072ae301a0bc4a33114d93b..d4ddc1b2b51651134f94313c4d1fc0974cf375e6 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-3.2.2.u3.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', version)] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb index 6b36f2c00bc417ca6deb2dd17b7a36f2d7a3dfa2..b50fb138ef03d9d48c8042a1ca76aefcdf0af319 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True, 'openmp': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1', versionsuffix)] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13.eb index ef015a9175c618e7c70da65b94ebaa7cd1155038..40fd553f1f782847bb2b4300505360f5647c5b0a 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-5.3.0.eb index 4686402139143a8e419bd541bb60323a924b5216..09084630c19ea94ec3392e6903ac439a930d007e 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-5.3.0.eb @@ -6,12 +6,14 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..87478cf832f5e9c7202aa7f0c6116d5b29d03995 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb @@ -0,0 +1,18 @@ +name = 'netCDF-Fortran' +version = '4.2' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + + +toolchain = {'name': 'ictce', 'version': '6.1.5'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [('netCDF', '4.2.1.1')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-iqacml-3.7.3.eb index b0bef7e67a1df40bcfef0efdd93c3cea7826effb..f7f72fcd3221fdd38f3d1b1e16f915dfee6d7de1 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-iqacml-3.7.3.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..c51e1a79417f0f36af65a0ce5d1416721988d5ca --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb @@ -0,0 +1,20 @@ +name = 'netCDF-Fortran' +version = '4.4.0' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2014b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [('netCDF', '4.3.2')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9b2aa29afe29efa0b1678fb196ff54cb3ee9e16a --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb @@ -0,0 +1,20 @@ +name = 'netCDF-Fortran' +version = '4.4.0' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [('netCDF', '4.3.2')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2014b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2014b.eb index 59ed0da09a80bc6eb812f550428a97327e6aa593..7823a5fa7da5d39fe723d2a57ba9865dd58ac9fd 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2014b.eb @@ -6,12 +6,14 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" - toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.3.2')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2015a.eb index ed31b043f1f29beaa08e1e5c0be905dd1c1de180..39adb73d6e43fdf3ce98084f3905cb6a098ee684 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2015a.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.3.2')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goalf-1.1.0-no-OFED.eb index e83acc3cca390c27b1f7b1af16aefc6b2e03d675..aaee694b4f58ae06541ec2a031439c1e8c738c7b 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.7')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb index 8bf5c28625a7b91f9e6676e8808c2081d7bfcdf4..6aa937d650d348e77a1b382adc58ef1ef7169b1b 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb @@ -9,7 +9,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.7')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-3.2.2.u3.eb index c00c2955522225cc4333739b4f807f311ca5351f..3d4e4b80346fe4a17108fecd10912e830b8d871a 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-3.2.2.u3.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.7')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb index 4a0335f76409425c82f4fd171076d7bf03af3bac..1cf87a93d6b03b8ef32c01fe8f698438edbe4114 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic':True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('HDF5', '1.8.9'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb index eef9aa4fe1fbabad97bcae1d770c685093639ac4..2e121dba814b25d0730e17363cacb14e1c75bb2e 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb @@ -6,16 +6,18 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic':True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ - ('HDF5', '1.8.9'), - ('Doxygen', '1.8.1.1') - ] + ('HDF5', '1.8.9'), + ('Doxygen', '1.8.1.1'), +] moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goalf-1.1.0-no-OFED.eb index 827d6154dadc5c4db557e45cc3c6ce8273e60100..8a0164a41a6bb2016123103f7c22de95bce49532 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('HDF5', '1.8.9'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goolf-1.4.10.eb index 3f8634ce6672e1d61619e2ad4c001c4b307f49e5..9278dcabb794b6cbf07553e64fa8febd1b251c1d 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goolf-1.4.10.eb @@ -9,7 +9,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('HDF5', '1.8.9'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-3.2.2.u3.eb index 738b574b640d44c88a7487eb2c559a70501336ac..70579f3686ec9decd7a8e2d716e6aceb433a41cb 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-3.2.2.u3.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('HDF5', '1.8.9'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.3.0.eb index b51011ebf8fd44e6c16d9136b9a1cc61bbeeef81..bf3bcad88f2eea802decbf9374295c7d59902011 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.3.0.eb @@ -6,16 +6,18 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ - ('HDF5', '1.8.9'), - ('Doxygen', '1.8.1.1') - ] + ('HDF5', '1.8.9'), + ('Doxygen', '1.8.1.1'), +] moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.4.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..a0f0b6f197829d460796378a2bf93d05029bdcf3 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.4.0.eb @@ -0,0 +1,21 @@ +name = 'netCDF' +version = '4.2' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries +and machine-independent data formats that support the creation, access, and sharing of array-oriented +scientific data.""" + +toolchain = {'name': 'ictce', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +configopts = ['--disable-doxygen'] + +dependencies = [ + ('HDF5', '1.8.9'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-intel-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..fc24bdb27fe483c90e503dc2ca37235de0afdce5 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-intel-2014b.eb @@ -0,0 +1,21 @@ +name = 'netCDF' +version = '4.2' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries +and machine-independent data formats that support the creation, access, and sharing of array-oriented +scientific data.""" + +toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +configopts = ['--disable-doxygen'] + +dependencies = [ + ('HDF5', '1.8.9'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb index 4f975041bc7545bfd52457ba719ab15f692121c8..8ae8d0db4f380f1dbfea9665a56bb2241fdd1c7a 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10-patch1')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb index a8fa0bc40a20c8c6cc7a1f2429f2a3119a417d59..452797370468a8d706be4e1a1e7b04df67788b83 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10-patch1')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb index 1d208f1301b2d4915c6e4f480180b6d95df7810c..a518b2a451eaadd896c49f43988710278a7d6dcc 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb @@ -11,7 +11,10 @@ toolchain = {'name':'ictce','version':'4.1.13'} toolchainopts = {'pic': True, 'openmp': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10', '-gpfs-mt')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb index a43794119f16467be15736098adb5779bc3052a3..9caf198302785c53e936ddd4eb64d6fa6afc46ca 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb @@ -10,7 +10,10 @@ toolchain = {'name':'ictce','version':'4.1.13'} toolchainopts = {'pic':True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10', '-gpfs')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb new file mode 100755 index 0000000000000000000000000000000000000000..081ab64f4b1abdbb590a0262cded9e6e016235c6 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb @@ -0,0 +1,24 @@ +name = 'netCDF' +version = '4.2.1.1' +versionsuffix = '-zlib-1.2.5' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [ + ('HDF5', '1.8.10', '-gpfs%(versionsuffix)s'), + ('Doxygen', '1.8.2'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb index b2e2392049f2b9eb925c8946e7e574327dcf51c0..59a30799c776e9d9f53a634b0cd55f13b1c6d9c0 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10', '-gpfs')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.4.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..49f253f65d210c826640d7360697328b523e6b0d --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.4.0.eb @@ -0,0 +1,19 @@ +name = 'netCDF' +version = '4.2.1.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'ictce', 'version': '5.4.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [('HDF5', '1.8.10', '-gpfs')] + +builddependencies = [('Doxygen', '1.8.3.1')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.5.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.5.0.eb index 5e5d78307e82e1dc24b359fe54207bda48e0f909..a238c0cf33d0bc4c628e97ac4131702e959fb4b9 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.5.0.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10', '-gpfs')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..262ebc70b918d1801205fae5d973ed950294ed97 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb @@ -0,0 +1,19 @@ +name = 'netCDF' +version = '4.2.1.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'ictce', 'version': '6.1.5'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [('HDF5', '1.8.10', '-gpfs')] + +builddependencies = [('Doxygen', '1.8.3.1')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-intel-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-intel-2014b.eb index fa034d149822eb5571e4f90abd218b57540e679a..69ddb9f9ca998864fbff669e24c70152abf714f0 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-intel-2014b.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10', '-gpfs')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb index dd168910be3759ffd3e336830fe90766fecfbe6f..741f74cd63020f76f7c14a483f0fc3a3a1b773c7 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10-patch1')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb index 78d6d431c3e7005756656263aaf7b7eeb26d08c8..a3bce6fa83fc4fad45d72a032aa6e99a5bba358a 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] patches = [('netCDF-4.3.0_nc-config.in.cmake', 'netcdf-4.3.0')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..f0b637b12c033d26d77ddc2ce58d0f484c7a0089 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb @@ -0,0 +1,38 @@ +name = 'netCDF' +version = '4.3.2' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2014b'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +patches = [ + 'netCDF-4.3.2-with-HDF-1.8.13.patch', + 'netCDF-4.3.2-parallel-HDF.patch', +] + +dependencies = [('HDF5', '1.8.13')] + +builddependencies = [ + ('CMake', '3.0.0'), + ('Doxygen', '1.8.7'), + ('cURL', '7.37.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=ON", + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=OFF", +] + +moduleclass = 'data' + diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d7b013c4185862449d8a96e37bda747cca799d2c --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb @@ -0,0 +1,37 @@ +name = 'netCDF' +version = '4.3.2' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +patches = [ + 'netCDF-4.3.2-with-HDF-1.8.13.patch', + 'netCDF-4.3.2-parallel-HDF.patch', +] + +dependencies = [('HDF5', '1.8.13')] + +builddependencies = [ + ('CMake', '3.0.0'), + ('Doxygen', '1.8.7'), + ('cURL', '7.37.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=ON", + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=OFF", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb index 5ab91b52fe086690d652f385c7e066e631199b6a..e848a71eec8578203e512fbc0567bc996c53a47c 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb @@ -10,9 +10,15 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] -patches = ['netCDF-4.3.2-with-HDF-1.8.13.patch'] +patches = [ + 'netCDF-4.3.2-with-HDF-1.8.13.patch', + 'netCDF-4.3.2-parallel-HDF.patch', +] dependencies = [('HDF5', '1.8.13')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb index bb04604455283e68b4441597d9f019c8a77b7dd4..623ceccdb3dd0dabbbae570c719850035eedc5ee 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb @@ -10,9 +10,15 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] -patches = ['netCDF-4.3.2-with-HDF-1.8.13.patch'] +patches = [ + 'netCDF-4.3.2-with-HDF-1.8.13.patch', + 'netCDF-4.3.2-parallel-HDF.patch', +] dependencies = [('HDF5', '1.8.13')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-parallel-HDF.patch b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-parallel-HDF.patch new file mode 100644 index 0000000000000000000000000000000000000000..d097592f1514f7e7fa84d23c3301e7d072d85f02 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-parallel-HDF.patch @@ -0,0 +1,21 @@ +#If a system installed sequential HDF5 exist and we use an external +#parallel HDF5 intsllation then the system installed h5cc will be used +#instead of the external h5pcc. Inspiration from netCDF 4.3.3.1 +#B. Hajgato March 1st 2015 +--- netcdf-4.3.2/CMakeLists.txt.org 2014-04-23 23:35:20.000000000 +0200 ++++ netcdf-4.3.2/CMakeLists.txt 2015-03-01 21:07:55.000000000 +0100 +@@ -637,8 +637,13 @@ + ENDIF(NOT MSVC) + + # Assert HDF5 version. ++ IF(HDF5_IS_PARALLEL) ++ SET(HDF5_CC h5pcc) ++ ELSE() ++ SET(HDF5_CC h5cc) ++ ENDIF() + SET(HDF5_VERSION_REQUIRED 1.8.6) +- execute_process(COMMAND sh -c "h5cc -showconfig | grep -i \"HDF5 version\" | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*$/\\1/'" ++ execute_process(COMMAND sh -c "${HDF5_CC} -showconfig | grep -i \"HDF5 version\" | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*$/\\1/'" + OUTPUT_VARIABLE HDF5_VERSION + ERROR_QUIET + ) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..ee5055dfe4f1dd64a3e72dd55d1a8f6cc958bb35 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.3.1-intel-2015a.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.3.3.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [ + ('HDF5', '1.8.15'), + ('cURL', '7.43.0'), +] + +builddependencies = [ + ('CMake', '3.2.2'), + ('Doxygen', '1.8.9.1', '', ('GCC', '4.9.2')), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=OFF ", + "-DBUILD_SHARED_LIBS=ON ", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb index 26cfac901b2e0a074459208268830a1f673a7d44..bd3aec85fa1264a97802750330fd347501063728 100644 --- a/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb @@ -14,14 +14,19 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' -pythonver = '2.7.9' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % (python, pythonver) +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - (python, pythonver), + (python, pyver), ] options = {'modulename': 'netifaces'} +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (pyshortver, pyshortver)], + 'dirs': [], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/netifaces/netifaces-0.8-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/n/netifaces/netifaces-0.8-ictce-5.5.0-Python-2.7.6.eb index 7994c5fb6eaec57e428028d8adc4716afaefca6a..c636b30fb58f9772dd62704e7082591ff5c5acb9 100644 --- a/easybuild/easyconfigs/n/netifaces/netifaces-0.8-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/n/netifaces/netifaces-0.8-ictce-5.5.0-Python-2.7.6.eb @@ -14,14 +14,19 @@ source_urls = ['http://alastairs-place.net/projects/netifaces/'] sources = [SOURCE_TAR_GZ] python = 'Python' -pythonver = '2.7.6' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % (python, pythonver) +pyver = '2.7.6' +versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - (python, pythonver), + (python, pyver), ] options = {'modulename': 'netifaces'} +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (pyshortver, pyshortver)], + 'dirs': [], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..422e3c89403504132f2b004d0fd3c82fef2b4197 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '1.10' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s.egg' % (pyshortver, pyshortver)], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..3968711a0e7efa4c3ecb48a180065eebb892de3e --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '1.10' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s.egg' % (pyshortver, pyshortver)], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015b-Python-3.5.0.eb b/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015b-Python-3.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..089cc6d27d443ab753d85c62099bdc06010e55f0 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-1.10-intel-2015b-Python-3.5.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '1.10' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '3.5.0' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s.egg' % (pyshortver, pyshortver)], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb index f6ae1e74b7a2539793d7a25daabd7c84d7620e75..bedaf28b91182f897a19c901bfffe381f5b5a267 100644 --- a/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb @@ -13,12 +13,18 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' -pythonver = '2.7.9' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % (python, pythonver) +pyver = '2.7.9' +pythonshortver = '.'.join(pyver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - (python, pythonver), + (python, pyver), ] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s.egg' % (pyshortver, pyshortver)], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..9346ee7b4c1fe70e9d785cb97ce0c09b9f3d1c61 --- /dev/null +++ b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'ngspice' +version = '26' + +homepage = 'http://ngspice.sourceforge.net' +description = """Ngspice is a mixed-level/mixed-signal circuit simulator. Its code + is based on three open source software packages: Spice3f5, Cider1b1 + and Xspice. +""" + +toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +builddependencies = [ + ('Bison', '3.0.2'), + ('flex', '2.5.39'), +] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ngmakeidx', 'ngmultidec', 'ngnutmeg', 'ngproc2mod', 'ngsconvert', 'ngspice']], + 'dirs': [], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..04cd4b9e23de46364477bf7ad7d5f7a358db7bc2 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.3-2.25.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.10' + +checksums = ['682c38305b2596967881f3d77bc3fc9c'] + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.so', 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6a2ab2df295538ba8e9251e633c4844994418c4e --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb @@ -0,0 +1,34 @@ +# 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 = "OPARI2" +version = "1.1.2" + +homepage = 'http://www.score-p.org' +description = """OPARI2, the successor of Forschungszentrum Juelich's OPARI, + is a source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls to + the POMP2 measurement interface.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/opari2/'] + +checksums = [ + '9a262c7ca05ff0ab5f7775ae96f3539e', # opari2-1.1.2.tar.gz +] + +sanity_check_paths = { + 'files': ["bin/opari2", "include/opari2/pomp2_lib.h"], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..34e2fdbcea5512d2a15da831f62ae07863f27b20 --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb @@ -0,0 +1,29 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Authors:: Jordi Blasco +# License:: New BSD +# +## + +easyblock = 'ConfigureMake' + +name = "OPARI2" +version = "1.1.2" + +homepage = 'http://www.score-p.org' +description = """OPARI2, the successor of Forschungszentrum Juelich's OPARI, + is a source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls to + the POMP2 measurement interface.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +# http://www.vi-hps.org/upload/packages/opari2/opari2-1.1.1.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/opari2/'] + +sanity_check_paths = { + 'files': ["bin/opari2", "include/opari2/pomp2_lib.h"], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d96cc487d50b0e3de4adc13cb941e826ad8eef0a --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '4.4.1' + +homepage = 'http://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$MPICC"' + +benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..60c9ce8691c6e8f36bbdec05df5fac58981f76a5 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb @@ -0,0 +1,32 @@ +# 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 = 'EB_Score_minus_P' + +name = "OTF2" +version = "1.2.1" + +homepage = 'http://www.score-p.org' +description = """The Open Trace Format 2 is a highly scalable, memory efficient event + trace data format plus support library. It will become the new standard trace format + for Scalasca, Vampir, and Tau and is open for other tools.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +# http://www.vi-hps.org/upload/packages/otf2/otf2-1.2.1.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] + +sanity_check_paths = { + # note by Bernd Mohr: on some systems libraries end up in lib/ + 'files': ["bin/otf2-config", "include/otf2/otf2.h", ("lib64/libotf2.a", "lib/libotf2.a")], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4f583c01b16b6ce7120e5003306b9460ad846819 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb @@ -0,0 +1,34 @@ +# 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 = 'EB_Score_minus_P' + +name = "OTF2" +version = "1.5.1" + +homepage = 'http://www.score-p.org' +description = """The Open Trace Format 2 is a highly scalable, memory efficient event + trace data format plus support library. It will become the new standard trace format + for Scalasca, Vampir, and Tau and is open for other tools.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] + +checksums = [ + '16a9df46e0da78e374f5d12c8cdc1109', # otf2-1.5.1.tar.gz +] + +sanity_check_paths = { + # note by Bernd Mohr: on some systems libraries end up in lib/ + 'files': ["bin/otf2-config", "include/otf2/otf2.h", ("lib64/libotf2.a", "lib/libotf2.a")], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/Oases/Oases-0.2.08-intel-2015a.eb b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9c657fda4a8d08e46f554b1283952fcbd0f96145 --- /dev/null +++ b/easybuild/easyconfigs/o/Oases/Oases-0.2.08-intel-2015a.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Fotis Georgatos +# License:: MIT/GPL +# +## + +easyblock = "MakeCp" + +name = 'Oases' +version = '0.2.08' + +homepage = 'http://www.ebi.ac.uk/~zerbino/oases/' +description = """Oases is a de novo transcriptome assembler designed to produce transcripts from + short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +velvetver = '1.2.09' + +sources = [ + '%(namelower)s_%(version)s.tgz', + 'velvet_%s.tgz' % velvetver, +] + +source_urls = [ + 'http://www.ebi.ac.uk/~zerbino/%(namelower)s', + 'http://www.ebi.ac.uk/~zerbino/velvet', +] + +# listed make targets exclude 'doc' on purpose +buildopts = ['VELVET_DIR=../velvet_%s cleanobj velvet oases' % velvetver] +parallel = 1 + +files_to_copy = [(["oases"], 'bin'), "data", "scripts", "src", "doc", "LICENSE.txt", "README.txt"] + +sanity_check_paths={ + 'files': ["bin/oases", "LICENSE.txt", "README.txt"], + 'dirs': ["data", "scripts", "src", "doc"] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..b11768a1504a439bf31ff0bcec0e0e824335e602 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.3-2.25-LAPACK-3.5.0.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.14' + +lapackver = '3.5.0' +versionsuffix = '-LAPACK-%s' % lapackver + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +buildopts = 'BINARY=64 USE_THREAD=1 CC="$CC" FC="$F77" NO_AFFINITY=1' +installopts = "USE_THREAD=1 PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +#runtest = 'PATH=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..4055b16ed1e8466669bd0bdb11db31cae2817589 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb @@ -0,0 +1,38 @@ +name = 'OpenFOAM' +version = '2.3.1' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + 'OpenFOAM-2.3.0_libreadline.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +# fix for cyclic symlink issue, which may cause unpacking to fail +# see also http://www.openfoam.org/mantisbt/view.php?id=1191 +# fixed in recent versions: https://github.com/OpenFOAM/OpenFOAM-2.3.x/commit/f7a485069c778495cc39b308580289f6c2d47163 +unpack_options = "--exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/backgroundMeshDecomposition" +unpack_options += " --exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/cellShapeControlMesh" + +dependencies = [ + ('libreadline', '6.3'), + ('SCOTCH', '6.0.4'), + ('ncurses', '5.9'), +] + +builddependencies = [('flex', '2.5.39')] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..645bcba3514e373c5de5136e4b803b28baf10009 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015b.eb @@ -0,0 +1,38 @@ +name = 'OpenFOAM' +version = '2.3.1' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + 'OpenFOAM-2.3.0_libreadline.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +# fix for cyclic symlink issue, which may cause unpacking to fail +# see also http://www.openfoam.org/mantisbt/view.php?id=1191 +# fixed in recent versions: https://github.com/OpenFOAM/OpenFOAM-2.3.x/commit/f7a485069c778495cc39b308580289f6c2d47163 +unpack_options = "--exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/backgroundMeshDecomposition" +unpack_options += " --exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/cellShapeControlMesh" + +dependencies = [ + ('libreadline', '6.3'), + ('SCOTCH', '6.0.4'), + ('ncurses', '5.9'), +] + +builddependencies = [('flex', '2.5.39')] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015a.eb index 06ceafc8c9695cf5c5e1cecf7fe1e87dcff93860..5eecb4a977c204201c080f225ae079ecbaab78c5 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015a.eb @@ -21,6 +21,12 @@ patches = [ ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir ] +# fix for cyclic symlink issue, which may cause unpacking to fail +# see also http://www.openfoam.org/mantisbt/view.php?id=1191 +# fixed in recent versions: https://github.com/OpenFOAM/OpenFOAM-2.3.x/commit/f7a485069c778495cc39b308580289f6c2d47163 +unpack_options = "--exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/backgroundMeshDecomposition" +unpack_options += " --exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/cellShapeControlMesh" + dependencies = [ ('libreadline', '6.3'), ('SCOTCH', '6.0.4'), diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..944836d77d3b159e4b8db55bf682b67edaa0431f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2015b.eb @@ -0,0 +1,38 @@ +name = 'OpenFOAM' +version = '2.3.1' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + 'OpenFOAM-2.3.0_libreadline.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +# fix for cyclic symlink issue, which may cause unpacking to fail +# see also http://www.openfoam.org/mantisbt/view.php?id=1191 +# fixed in recent versions: https://github.com/OpenFOAM/OpenFOAM-2.3.x/commit/f7a485069c778495cc39b308580289f6c2d47163 +unpack_options = "--exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/backgroundMeshDecomposition" +unpack_options += " --exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/cellShapeControlMesh" + +dependencies = [ + ('libreadline', '6.3'), + ('SCOTCH', '6.0.4'), + ('ncurses', '5.9'), +] + +builddependencies = [('flex', '2.5.39')] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.4.0-intel-2015b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.4.0-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..68a091945cb0dbd8e64da0ca309f0d86e7576818 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.4.0-intel-2015b.eb @@ -0,0 +1,38 @@ +name = 'OpenFOAM' +version = '2.4.0' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + 'OpenFOAM-2.3.0_libreadline.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +# fix for cyclic symlink issue, which may cause unpacking to fail +# see also http://www.openfoam.org/mantisbt/view.php?id=1191 +# fixed in recent versions: https://github.com/OpenFOAM/OpenFOAM-2.3.x/commit/f7a485069c778495cc39b308580289f6c2d47163 +unpack_options = "--exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/backgroundMeshDecomposition" +unpack_options += " --exclude=*tutorials/mesh/foamyHexMesh/mixerVessel/system/cellShapeControlMesh" + +dependencies = [ + ('libreadline', '6.3'), + ('SCOTCH', '6.0.4'), + ('ncurses', '5.9'), +] + +builddependencies = [('flex', '2.5.39')] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.4.0.patch b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.4.0.patch new file mode 100644 index 0000000000000000000000000000000000000000..879e7e0b731de04113ead7ed478924c6a328e39e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.4.0.patch @@ -0,0 +1,107 @@ +add support for picking up dependencies (i.e. SCOTCH) provided via EasyBuild +author: Kenneth Hoste (kenneth.hoste@ugent.be) +diff -ru OpenFOAM-2.4.0/etc/config/scotch.sh OpenFOAM-2.4.0.patched/etc/config/scotch.sh +--- OpenFOAM-2.4.0/etc/config/scotch.sh 2015-05-22 11:50:30.000000000 +0200 ++++ OpenFOAM-2.4.0.patched/etc/config/scotch.sh 2015-09-16 09:53:43.280706774 +0200 +@@ -33,7 +33,11 @@ + # during the wmake process + #------------------------------------------------------------------------------ + +-export SCOTCH_VERSION=scotch_6.0.3 +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$SCOTCH_VERSION ++if [ -n "${SCOTCH_ROOT}" ] ; then ++ export SCOTCH_ARCH_PATH="${SCOTCH_ROOT}" ++else ++ export SCOTCH_VERSION=scotch_6.0.3 ++ export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$SCOTCH_VERSION ++fi + + # ----------------------------------------------------------------------------- +diff -ru OpenFOAM-2.4.0/etc/config/settings.csh OpenFOAM-2.4.0.patched/etc/config/settings.csh +--- OpenFOAM-2.4.0/etc/config/settings.csh 2015-05-22 11:50:30.000000000 +0200 ++++ OpenFOAM-2.4.0.patched/etc/config/settings.csh 2015-09-16 09:47:42.863934554 +0200 +@@ -339,7 +339,7 @@ + # Communications library + # ~~~~~~~~~~~~~~~~~~~~~~ + +-unsetenv MPI_ARCH_PATH MPI_HOME FOAM_MPI_LIBBIN ++#unsetenv MPI_ARCH_PATH MPI_HOME FOAM_MPI_LIBBIN + + switch ("$WM_MPLIB") + case SYSTEMOPENMPI: +diff -ru OpenFOAM-2.4.0/etc/config/settings.sh OpenFOAM-2.4.0.patched/etc/config/settings.sh +--- OpenFOAM-2.4.0/etc/config/settings.sh 2015-05-22 11:50:30.000000000 +0200 ++++ OpenFOAM-2.4.0.patched/etc/config/settings.sh 2015-09-16 09:47:42.883935006 +0200 +@@ -359,7 +359,7 @@ + # Communications library + # ~~~~~~~~~~~~~~~~~~~~~~ + +-unset MPI_ARCH_PATH MPI_HOME FOAM_MPI_LIBBIN ++#unset MPI_ARCH_PATH MPI_HOME FOAM_MPI_LIBBIN + + case "$WM_MPLIB" in + SYSTEMOPENMPI) +@@ -573,6 +573,11 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib64 + ;; ++ ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; ++ + *) + export FOAM_MPI=dummy + ;; +diff -ru OpenFOAM-2.4.0/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-2.4.0.patched/src/parallel/decompose/ptscotchDecomp/Make/options +--- OpenFOAM-2.4.0/src/parallel/decompose/ptscotchDecomp/Make/options 2015-05-22 11:50:30.000000000 +0200 ++++ OpenFOAM-2.4.0.patched/src/parallel/decompose/ptscotchDecomp/Make/options 2015-09-16 09:54:52.402822251 +0200 +@@ -3,10 +3,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt +diff -ru OpenFOAM-2.4.0/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C OpenFOAM-2.4.0.patched/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C +--- OpenFOAM-2.4.0/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2015-05-22 11:50:30.000000000 +0200 ++++ OpenFOAM-2.4.0.patched/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2015-09-16 09:47:42.903935458 +0200 +@@ -112,6 +112,8 @@ + + \*---------------------------------------------------------------------------*/ + ++#include "mpi.h" ++ + #include "ptscotchDecomp.H" + #include "addToRunTimeSelectionTable.H" + #include "Time.H" +@@ -121,8 +123,8 @@ + + extern "C" + { +-#include + #include "mpi.h" ++#include + #include "ptscotch.h" + } + +diff -ru OpenFOAM-2.4.0/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-2.4.0.patched/src/parallel/decompose/scotchDecomp/Make/options +--- OpenFOAM-2.4.0/src/parallel/decompose/scotchDecomp/Make/options 2015-05-22 11:50:30.000000000 +0200 ++++ OpenFOAM-2.4.0.patched/src/parallel/decompose/scotchDecomp/Make/options 2015-09-16 09:47:42.903935458 +0200 +@@ -7,10 +7,8 @@ + + EXE_INC = \ + $(PFLAGS) $(PINC) \ +- -I$(SCOTCH_ROOT)/include \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ROOT)/lib -L$(FOAM_EXT_LIBBIN) -lscotch -lscotcherrexit -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN) -lscotch -lscotcherrexit -lrt diff --git a/easybuild/easyconfigs/o/OpenFOAM/cleanup-ThirdParty-2.4.0.patch b/easybuild/easyconfigs/o/OpenFOAM/cleanup-ThirdParty-2.4.0.patch new file mode 100644 index 0000000000000000000000000000000000000000..58e0c4eaf607ea99192e8000c3ab1d7786b67350 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/cleanup-ThirdParty-2.4.0.patch @@ -0,0 +1,57 @@ +fix lib dir, using an external SCOTCH +author: Kenneth Hoste (kenneth.hoste@ugent.be) +diff -ru ThirdParty-2.4.0.ORIG/Allwmake ThirdParty-2.4.0/Allwmake +--- ThirdParty-2.4.0.ORIG/Allwmake 2014-02-06 16:31:37.000000000 +0100 ++++ ThirdParty-2.4.0/Allwmake 2014-07-08 00:32:02.955084962 +0200 +@@ -110,12 +110,12 @@ + ;; + + MPICH) +- if [ -r $MPI_ARCH_PATH/lib/libmpich.so ] ++ if [ -r $MPI_ARCH_PATH/lib64/libmpich.so ] + then + echo " have $WM_MPLIB shared library ($FOAM_MPI)" + echo + echo +- elif [ -r $MPI_ARCH_PATH/lib/libmpich.a ] ++ elif [ -r $MPI_ARCH_PATH/lib64/libmpich.a ] + then + echo " have $WM_MPLIB static library ($FOAM_MPI)" + echo +@@ -195,6 +195,13 @@ + echo " scotch header in $SCOTCH_ARCH_PATH/include" + echo " scotch libs in $FOAM_EXT_LIBBIN" + echo ++elif [ -f $SCOTCH_ARCH_PATH/include/scotch.h \ ++ -a \( -r $SCOTCH_ARCH_PATH/lib/libscotch.so -o -r $SCOTCH_ARCH_PATH/lib/libscotch.a \) \ ++ -a \( -r $SCOTCH_ARCH_PATH/lib/libscotcherrexit.so -o -r $SCOTCH_ARCH_PATH/lib/libscotcherrexit.a \) ] ++then ++ echo " scotch header in $SCOTCH_ARCH_PATH/include" ++ echo " scotch libs in $SCOTCH_ARCH_PATH/lib" ++ echo + else + ( + set -x +@@ -256,6 +263,13 @@ + echo " ptscotch header in $SCOTCH_ARCH_PATH/include/$FOAM_MPI" + echo " ptscotch libs in $FOAM_EXT_LIBBIN/$FOAM_MPI" + echo ++ elif [ -f $SCOTCH_ARCH_PATH/include/ptscotch.h \ ++ -a \( -r $SCOTCH_ARCH_PATH/lib/libptscotch.so -o -r $SCOTCH_ARCH_PATH/lib/libptscotch.a \) \ ++ -a \( -r $SCOTCH_ARCH_PATH/lib/libptscotcherrexit.so -o -r $SCOTCH_ARCH_PATH/lib/libptscotcherrexit.a \) ] ++ then ++ echo " ptscotch header in $SCOTCH_ARCH_PATH/include" ++ echo " ptscotch libs in $SCOTCH_ARCH_PATH/lib" ++ echo + else + ( + set -x +@@ -296,7 +310,7 @@ + fi + + # verify existence of scotch include +- [ -f $SCOTCH_ARCH_PATH/include/$FOAM_MPI/ptscotch.h ] || { ++ [ -f $SCOTCH_ARCH_PATH/include/$FOAM_MPI/ptscotch.h -o -f $SCOTCH_ARCH_PATH/include/ptscotch.h ] || { + echo + echo " WARNING: required include file 'ptscotch.h' not found!" + echo diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb index e568f8411eb1f656a81e3868d9bd8b1aeade2765..e2dcab157e948b20e9e328f43a4805ed7821250f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb @@ -17,11 +17,10 @@ patches = ['pax_disable.patch'] configopts = '--with-threads=posix --enable-shared --enable-mpi-threads --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "open-pal", "open-rte"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "open-pal", "open-rte"]], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb index fe72e01efd4a0a9c5a3f4cb63224971c3da2232f..af837e08152447032188101eaaa88fc5f04944c1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb @@ -17,11 +17,10 @@ configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "open-pal", "open-rte"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "open-pal", "open-rte"]], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..70d3c85032a28e19b0e16e7ef6cf63f13e131d4a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = "1.4.5" + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +builddependencies = [ + ('Automake', '1.14'), + ('Autoconf', '2.69'), +] + +dependencies = [('hwloc', '1.7.2')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-openib +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "open-pal", "open-rte"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb index 3f5d4cafd7932522ba9bf619518ebb02422b19e6..d88a606fa0874e2b4b4eddd005397d49a5617cf0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb @@ -20,14 +20,11 @@ dependencies = [('hwloc', '1.6')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "otfaux", "otf", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb index 68114cf721a0f3006cfdc073c4a0c48ddc3e3ddb..b42d9a8b03342c501a030c846654b30116370dec 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb @@ -21,12 +21,11 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb index 109447fa55dfbac944c050be136588b18a837429..fc479108fe13c08eb88b87078db0458a24537bc7 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb @@ -21,12 +21,11 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb index 983eb22945063bf4bc7bb4a77f041348e340fd08..8b588833b0c12bbf66e7797020c3a94ca1a0e326 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb @@ -19,15 +19,14 @@ configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77" ,"mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], - 'dirs': ["include/openmpi/ompi/mpi/cxx"], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], } moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb index 7d3922cea0136cb2867301cafe5283861876c889..168f6f9d236888fabac64ade04e006292e2fb169 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb @@ -21,12 +21,11 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb index 21bd882ac7c7d5cd897257b259cd66a684b78f1a..933369e32b802a241d5f062949027dd85601f6cc 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb @@ -24,12 +24,13 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", - "mpif-mpi-io", "mpi", "mpi_portable_platform"]], + "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb index 90dc3e34495caafd9ecb1eb1212fe9d483784332..ccbc9394ec9eed2af9e1eccbe052d90063a61f14 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb @@ -12,18 +12,19 @@ toolchain = {'name': 'GCC', 'version': '4.7.3'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb index 5e9b5fcda835e62b138981267948153f87cccf49..ce23f55355012b7649e9e014603456c3b077bab5 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb @@ -12,18 +12,19 @@ toolchain = {'name': 'GCC', 'version': '4.8.1'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb index 394c231617a2cff59c9de1e4ccb7c84e213d8165..c6b40582c811ab933be965e5e3d4a70972a3c210 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb @@ -11,7 +11,9 @@ toolchain = {'name': 'GCC', 'version': '4.8.1'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path @@ -20,12 +22,11 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb index 6cac76d97d59e0e7575f8b51fb4e11f8cd057013..2afbc4733e247f52c6237f6660133c85b8f746f6 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb @@ -12,7 +12,9 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path @@ -21,12 +23,11 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' dependencies = [('hwloc', '1.8.1')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb index 908f092bfae6509365da49a239152a4b3017abe1..8af372736a44fabbbb08930300abd29c4e875038 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb @@ -11,7 +11,9 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path @@ -23,12 +25,11 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb index c9d45613dfcaa2cc5f82e6c8135f163547b72c27..2ae7377c3711c9dc395ade0bda8a717d614b459a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb @@ -11,7 +11,9 @@ toolchain = {'name': 'GCC', 'version': '4.8.3'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path @@ -23,12 +25,11 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev','libibverbs-devel')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb index 85b6644c9f22372ab8669187e7c9309ffa6728e2..4fc8978e4dd5bda028cdc3019bcd9366074d5edf 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb @@ -20,14 +20,11 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "otfaux", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb index 4d2c94f271e8b1dc99698983c024d4e67251d9f8..0bb4349893a40dbd2b9e1ac16432eeb08305d867 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb @@ -18,18 +18,14 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support dependencies = [('hwloc', '1.9')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "otfaux", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } moduleclass = 'mpi' - diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb index 79c31e1c3d020b4877cef79fbff6c3e7366c29f1..e9f2f244ec124a54d581a97c0e27e3266c7903bb 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb @@ -20,14 +20,11 @@ dependencies = [('hwloc', '1.9')] # needed for --with-openib osdependencies = [('libibverbs-dev','libibverbs-devel')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", "open-rte", + "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "otfaux", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb index 1f4d38649b5ca572a646ba41325cbaad671b894c..6687a0ffa048b153e13d236b53057589a5e6ff9b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb @@ -23,12 +23,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb index 094489afc48e54abae3315a707f56c4481b3c3b7..10774dff41ae6028fb5708e770c44b6a5efdb2b3 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb @@ -11,7 +11,15 @@ toolchain = {'name': 'gcccuda', 'version': '2.6.10'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-%(version)s-vt_cupti_events.patch'] +patches = [ + 'OpenMPI-%(version)s_common-cuda-lib.patch', + 'OpenMPI-%(version)s-vt_cupti_events.patch', +] + +builddependencies = [ + ('Automake', '1.14'), + ('Autoconf', '2.69') +] dependencies = [('hwloc', '1.8')] @@ -23,12 +31,10 @@ configopts += '--with-cuda=$CUDA_HOME ' # CUDA-aware build; N.B. --d # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3_common-cuda-lib.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3_common-cuda-lib.patch new file mode 100644 index 0000000000000000000000000000000000000000..4ba9ebab68df8a17794440a7e9657c4a2645d391 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3_common-cuda-lib.patch @@ -0,0 +1,16 @@ +see http://permalink.gmane.org/gmane.comp.clustering.open-mpi.user/20404, +patch obtained via https://svn.open-mpi.org/trac/ompi/changeset/29762 +Index: /branches/v1.7/ompi/mca/pml/ob1/Makefile.am +=================================================================== +--- /branches/v1.7/ompi/mca/pml/ob1/Makefile.am (revision 29624) ++++ /branches/v1.7/ompi/mca/pml/ob1/Makefile.am (revision 29762) +@@ -68,4 +68,9 @@ + mca_pml_ob1_la_LDFLAGS = -module -avoid-version + ++if OPAL_cuda_support ++mca_pml_ob1_la_LIBADD = \ ++ $(top_ompi_builddir)/ompi/mca/common/cuda/libmca_common_cuda.la ++endif ++ + noinst_LTLIBRARIES = $(component_noinst) + libmca_pml_ob1_la_SOURCES = $(ob1_sources) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb index d9eca98720f24b4e306d24afaa12898be2360994..eeb7c2fe82787a088235bc35b36d73572986987b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb @@ -21,12 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb index fb7afbbd4177f8a113e1305d5a3b49b7b55a2ea8..a47fa4f0f1baf045c981ae93242504db83f386d1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb @@ -21,12 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb index e1057430c2d4bc2d76a603cfb1a0177d6506467d..c6c6f0c9abedef3c520b51107fecf6f6e967bff9 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb @@ -20,12 +20,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic dependencies = [('hwloc', '1.9')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb index f73d19d32c411802545c5a64ac6066066ba5be7a..f5e9417cad30712278bc9b5e87c3d59d6da270cb 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb @@ -11,7 +11,6 @@ toolchain = {'name': 'iccifort', 'version': '2013_sp1.4.211'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] - configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support @@ -22,12 +21,10 @@ dependencies = [('hwloc', '1.9')] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb index 3841ad29d2839ebf49c64c3f6de3824817058f48..2eb439ac3492244154f0a12b22fba050ff2f76f2 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb @@ -21,12 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb index e90682df3be715e07cd59d07f3a5cf02cb49b2ca..e009a632591c41042eb786fb2ec7e91a4870d763 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb @@ -21,12 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb index a3c918320f1477209183bbab43419751d09c2324..780c3c78ba6dfab1b6a0032e5c5567383be30fc6 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb @@ -22,12 +22,10 @@ dependencies = [('hwloc', '1.10.0')] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb index d7df86c8d6abbc91c50a7f612a16a123bd34e98f..ca0afea9dc034c006d7c3a8637f513f221a4b69a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb @@ -23,12 +23,10 @@ dependencies = [('hwloc', '1.10.0')] # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb index 17455567fb9698df7cea211bbf5f8ff2d5d44648..095d22d991eba77e2a9063f2f903e35331f42f1b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb @@ -21,12 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-verbs osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] sanity_check_paths = { 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + - ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..3e69e3901f398b39bfafbf4c6d42b4bf0b6978cf --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.6-GNU-4.9.3-2.25.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.8.6' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +dependencies = [('hwloc', '1.11.0')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..5206425bdfdfb081c87166fe0396fe6730228a94 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.8-GNU-4.9.3-2.25.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.8.8' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +dependencies = [('hwloc', '1.11.0')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6dae1dce8531dbe3c06c2fbc0797ec320d00c25e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'http://code.google.com/p/openpgm/' +description = """OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) + specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol + that enables receivers to detect loss, request retransmission of lost data, or notify an application + of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception responsibility.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [GOOGLECODE_SOURCE] +sources = ['libpgm-%(version)s.tar.gz'] + +configopts = '--with-pic' + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.so', 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6800732437215cd1ea418f5f5ad0b87c94b3f865 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb @@ -0,0 +1,21 @@ +name = 'OpenSSL' +version = '1.0.1p' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = ['OpenSSL-%(version)s_icc-fixes.patch'] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015b.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..080b20377074f93dba8a3a9b5f652394a44c8887 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015b.eb @@ -0,0 +1,21 @@ +name = 'OpenSSL' +version = '1.0.1p' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = ['OpenSSL-%(version)s_icc-fixes.patch'] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..733ddd9ac4e3328e8a6d9fe7229406ccadb08ad2 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +name = 'OpenSSL' +version = '1.0.1p' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9e06d07cee82de9d2b8e5cffdd472f7488a2f4e8 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb @@ -0,0 +1,21 @@ +name = 'OpenSSL' +version = '1.0.1p' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = ['OpenSSL-%(version)s_icc-fixes.patch'] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015b.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..a34f9121d15c438df0e5f87a88c290522454f3da --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015b.eb @@ -0,0 +1,21 @@ +name = 'OpenSSL' +version = '1.0.1p' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = ['OpenSSL-%(version)s_icc-fixes.patch'] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p_icc-fixes.patch b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p_icc-fixes.patch new file mode 100644 index 0000000000000000000000000000000000000000..4609252d6d2b23d2c3e8e54a0f245a4c049e5768 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p_icc-fixes.patch @@ -0,0 +1,100 @@ +diff -ru openssl-1.0.1p.orig/Configure openssl-1.0.1p/Configure +--- openssl-1.0.1p.orig/Configure 2015-07-09 14:21:24.000000000 +0200 ++++ openssl-1.0.1p/Configure 2015-07-11 14:02:52.000000000 +0200 +@@ -351,7 +351,7 @@ + # If you compiler does not, do complement config command line with one! + "linux-armv4", "gcc:-O3 -Wall::-D_REENTRANT::-ldl:BN_LLONG RC4_CHAR RC4_CHUNK DES_INT DES_UNROLL BF_PTR:${armv4_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + #### IA-32 targets... +-"linux-ia32-icc", "icc:-DL_ENDIAN -O2 -no_cpprt::-D_REENTRANT::-ldl:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-KPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", ++"linux-ia32-icc", "icc:-DL_ENDIAN -O2::-D_REENTRANT::-ldl -no_cpprt:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-KPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-elf", "gcc:-DL_ENDIAN -O3 -fomit-frame-pointer -Wall::-D_REENTRANT::-ldl:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-aout", "gcc:-DL_ENDIAN -O3 -fomit-frame-pointer -march=i486 -Wall::(unknown):::BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_asm}:a.out", + #### +@@ -359,8 +359,9 @@ + "linux-ppc64", "gcc:-m64 -DB_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHAR RC4_CHUNK DES_RISC1 DES_UNROLL:${ppc64_asm}:linux64:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + "linux-ia64", "gcc:-DL_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_UNROLL DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-ia64-ecc","ecc:-DL_ENDIAN -O2 -Wall -no_cpprt::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", +-"linux-ia64-icc","icc:-DL_ENDIAN -O2 -Wall -no_cpprt::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_RISC1 DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", ++"linux-ia64-icc","icc:-DL_ENDIAN -O2 -Wall::-D_REENTRANT::-ldl -no_cpprt:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_RISC1 DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-x86_64", "gcc:-m64 -DL_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT DES_UNROLL:${x86_64_asm}:elf:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", ++"linux-x86_64-icc", "icc:-DL_ENDIAN -DTERMIO -O2::-D_REENTRANT::-ldl -no_cpprt:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT DES_UNROLL:${x86_64_asm}:elf:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + "linux64-s390x", "gcc:-m64 -DB_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHAR RC4_CHUNK DES_INT DES_UNROLL:${s390x_asm}:64:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + #### So called "highgprs" target for z/Architecture CPUs + # "Highgprs" is kernel feature first implemented in Linux 2.6.32, see +@@ -1416,6 +1417,7 @@ + } + if ($iccver>=8) + { ++ $cflags=~s/\-KPIC/-fPIC/; + # Eliminate unnecessary dependency from libirc.a. This is + # essential for shared library support, as otherwise + # apps/openssl can end up in endless loop upon startup... +@@ -1423,13 +1425,18 @@ + } + if ($iccver>=9) + { +- $cflags.=" -i-static"; +- $cflags=~s/\-no_cpprt/-no-cpprt/; ++ $lflags.=" -i-static"; ++ $lflags=~s/\-no_cpprt/-no-cpprt/; + } + if ($iccver>=10) + { +- $cflags=~s/\-i\-static/-static-intel/; ++ $lflags=~s/\-i\-static/-static-intel/; + } ++ if ($iccver>=11) ++ { ++ $cflags.=" -no-intel-extensions"; # disable Cilk ++ $lflags=~s/\-no\-cpprt/-no-cxxlib/; ++ } + } + + # Unlike other OSes (like Solaris, Linux, Tru64, IRIX) BSD run-time +diff -ru openssl-1.0.1p.orig/crypto/aes/aes_x86core.c openssl-1.0.1p/crypto/aes/aes_x86core.c +--- openssl-1.0.1p.orig/crypto/aes/aes_x86core.c 2015-07-09 14:21:24.000000000 +0200 ++++ openssl-1.0.1p/crypto/aes/aes_x86core.c 2015-07-11 14:02:52.000000000 +0200 +@@ -89,8 +89,10 @@ + #endif + + #undef ROTATE +-#if defined(_MSC_VER) || defined(__ICC) ++#if defined(_MSC_VER) + # define ROTATE(a,n) _lrotl(a,n) ++#elif defined(__ICC) ++# define ROTATE(a,n) _rotl(a,n) + #elif defined(__GNUC__) && __GNUC__>=2 + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE(a,n) ({ register unsigned int ret; \ +diff -ru openssl-1.0.1p.orig/crypto/des/des_locl.h openssl-1.0.1p/crypto/des/des_locl.h +--- openssl-1.0.1p.orig/crypto/des/des_locl.h 2015-07-09 14:21:24.000000000 +0200 ++++ openssl-1.0.1p/crypto/des/des_locl.h 2015-07-11 14:02:52.000000000 +0200 +@@ -162,8 +162,10 @@ + } \ + } + +-# if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) || defined(__ICC) ++# if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) + # define ROTATE(a,n) (_lrotr(a,n)) ++#elif defined(__ICC) ++#define ROTATE(a,n) (_rotr(a,n)) + # elif defined(__GNUC__) && __GNUC__>=2 && !defined(__STRICT_ANSI__) && !defined(OPENSSL_NO_ASM) && !defined(OPENSSL_NO_INLINE_ASM) && !defined(PEDANTIC) + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE(a,n) ({ register unsigned int ret; \ +diff -ru openssl-1.0.1p.orig/crypto/rc5/rc5_locl.h openssl-1.0.1p/crypto/rc5/rc5_locl.h +--- openssl-1.0.1p.orig/crypto/rc5/rc5_locl.h 2015-07-09 14:21:24.000000000 +0200 ++++ openssl-1.0.1p/crypto/rc5/rc5_locl.h 2015-07-11 14:02:52.000000000 +0200 +@@ -146,9 +146,12 @@ + *((c)++)=(unsigned char)(((l)>> 8L)&0xff), \ + *((c)++)=(unsigned char)(((l) )&0xff)) + +-#if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) || defined(__ICC) ++#if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) + # define ROTATE_l32(a,n) _lrotl(a,n) + # define ROTATE_r32(a,n) _lrotr(a,n) ++#elif defined(__ICC) ++#define ROTATE_l32(a,n) _rotl(a,n) ++#define ROTATE_r32(a,n) _rotr(a,n) + #elif defined(__GNUC__) && __GNUC__>=2 && !defined(__STRICT_ANSI__) && !defined(OPENSSL_NO_ASM) && !defined(OPENSSL_NO_INLINE_ASM) && !defined(PEDANTIC) + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE_l32(a,n) ({ register unsigned int ret; \ diff --git a/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..28dbe78fdb1ead464ece83757eda51c4e127ec1d --- /dev/null +++ b/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'ordereddict' +version = '1.1' + +homepage = 'https://pypi.python.org/pypi/ordereddict' +description = """Drop-in substitute for Py2.7's new collections.OrderedDict. +The recipe has big-oh performance that matches regular dictionaries (amortized +O(1) insertion/deletion/lookup and O(n) iteration/repr/copy/equality_testing).""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://pypi.python.org/packages/source/o/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.3' + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/ordereddict.py' % pyshortver], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..d485c2eb5712568c2707c76737dbc0facb1fd307 --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb @@ -0,0 +1,46 @@ +## +# 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_07-02.html +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '5.2.0' + +homepage = 'http://icl.cs.utk.edu/projects/papi/' +description = """PAPI provides the tool designer and application engineer with a consistent interface and + methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables + software engineers to see, in near real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and software stack.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +# Example download URL, for reference: http://icl.cs.utk.edu/projects/papi/downloads/papi-5.0.0.tar.gz +source_urls = ['http://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] + +start_dir = 'src' + +# parallel build doesn't always work +parallel = 1 + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", "version", + "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..cbf18980bca4811f0997088527ee305a5621c3db --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb @@ -0,0 +1,45 @@ +## +# 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/HPCBIOS_07-02.html +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '5.4.0' + +homepage = 'http://icl.cs.utk.edu/projects/papi/' +description = """PAPI provides the tool designer and application engineer with a consistent interface and + methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables + software engineers to see, in near real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and software stack.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] + +start_dir = 'src' + +# parallel build doesn't always work +parallel = 1 + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", "version", + "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..e0822f5ef30310772f7eebef96341330bffb9f96 --- /dev/null +++ b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-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 +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'PBZIP2' +version = '1.1.8' + +homepage = 'http://compression.ca/pbzip2/' +description = """ PBZIP2 is a parallel implementation of the bzip2 block-sorting file + compressor that uses pthreads and achieves near-linear speedup on SMP machines. The output + of this version is fully compatible with bzip2 v1.0.2 or newer (ie: anything compressed + with pbzip2 can be decompressed with bzip2).""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://compression.ca/pbzip2/'] +sources = [SOURCELOWER_TAR_GZ] + +buildopts = " CC=$CXX" + +parallel = 1 + +files_to_copy = [(["pbzip2"], "bin"), (["pbzip2.1"], "man/man1"), "README", "ChangeLog"] + +sanity_check_paths = { + 'files': ["bin/pbzip2"], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..a1befffbe40b73e286c1feec3f07abf8c3a6c965 --- /dev/null +++ b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.8-ictce-6.2.5.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'PBZIP2' +version = '1.1.8' + +homepage = 'http://compression.ca/pbzip2/' +description = """ PBZIP2 is a parallel implementation of the bzip2 block-sorting file + compressor that uses pthreads and achieves near-linear speedup on SMP machines. The output + of this version is fully compatible with bzip2 v1.0.2 or newer (ie: anything compressed + with pbzip2 can be decompressed with bzip2).""" + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +source_urls = ['http://compression.ca/pbzip2/'] +sources = [SOURCELOWER_TAR_GZ] + +buildopts = " CC=$CXX" + +parallel = 1 + +files_to_copy = [(["pbzip2"], "bin"), (["pbzip2.1"], "man/man1"), "README", "ChangeLog"] + +sanity_check_paths = { + 'files': ["bin/pbzip2"], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb index e95902eec830e5311c8f31fc5cc59e80c3a0f24f..4a9ef5925f14b7d11c1ca601fddf4ecf13978508 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb @@ -4,15 +4,15 @@ name = 'PCRE' version = '8.12' homepage = 'http://www.pcre.org/' -description = """The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax - and semantics as Perl 5.""" +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb index 0f58883e8e531fb7cd723cde2485caf9a0f2e867..5916d698fc1f9082c2cca5747400d90876155684 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb @@ -4,15 +4,15 @@ name = 'PCRE' version = '8.12' homepage = 'http://www.pcre.org/' -description = """The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax -and semantics as Perl 5.""" +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb index ae806687ed93f8f1c9a0bea81b4cda0229ebd9a0..e5f29eb85e583a56a26614919094ca460d342bf8 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb @@ -4,15 +4,15 @@ name = 'PCRE' version = '8.12' homepage = 'http://www.pcre.org/' -description = """The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax - and semantics as Perl 5.""" +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb index 0a2a52870426bb96f8de06b8b3f2901c7c58d222..871d373c07e239c49385a39dba53307b5c9a054b 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb @@ -4,16 +4,15 @@ name = 'PCRE' version = '8.12' homepage = 'http://www.pcre.org/' -description = """The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax - and semantics as Perl 5.""" - +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb index 82e14a704ffdfc1c9618b6f7667328d829bc7717..365ae1e42a966e5feb64cf2d21924e35ca6043e1 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb @@ -4,17 +4,15 @@ name = 'PCRE' version = '8.12' homepage = 'http://www.pcre.org/' -description = """ - The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax - and semantics as Perl 5. -""" +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb index fd30422f0b8be97036316c25b84dec07a39d5188..a4df16eaada18086aca6026c399b45256e24c3a2 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb @@ -4,17 +4,15 @@ name = 'PCRE' version = '8.35' homepage = 'http://www.pcre.org/' -description = """ - The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax - and semantics as Perl 5. -""" +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb index dd7d330b7c526125275240f7226c6390b0877dfb..7881c04da420044f2a9277d589e959b39d66b53b 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb @@ -4,10 +4,8 @@ name = 'PCRE' version = '8.36' homepage = 'http://www.pcre.org/' -description = """ - The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax - and semantics as Perl 5. -""" +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" toolchain = {'name': 'foss', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb index 64ff0ffd54fd326687b25366e944738e980161f7..f2529df084483600e9dc344a55d96031cd95b5c5 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb @@ -4,17 +4,15 @@ name = 'PCRE' version = '8.36' homepage = 'http://www.pcre.org/' -description = """ - The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax - and semantics as Perl 5. -""" +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.37-intel-2015a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.37-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..1218fbc5d1c47fda816cc3f31c3d49b8c81930f5 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.37-intel-2015a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.37' + +homepage = 'http://www.pcre.org/' +description = """The PCRE library is a set of functions that implement regular expression pattern matching using + the same syntax and semantics as Perl 5.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb index a6ab7c41555ced86b01c011319965f6a703b0fc6..eef9a27cd74d3ec567c4ae0d2d72a3d9a96e147f 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb @@ -1,12 +1,14 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## -easyblock = 'ConfigureMake' name = "PDT" version = "3.19" @@ -20,31 +22,11 @@ description = """Program Database Toolkit (PDT) is a framework for analyzing sou toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -# http://tau.uoregon.edu/pdt_releases/pdtoolkit-3.19.tar.gz sources = ['pdtoolkit-%(version)s.tar.gz'] source_urls = ['http://tau.uoregon.edu/pdt_releases/'] -prefix_opt = '-prefix=' - -# notes by Bernd Mohr -# Compiler suite should always be specified -- MUCH quicker and SAVER than autodetect -# -KAI|-KCC|-GNU|-CC|-c++|-cxx|-xlC|-pgCC|-icpc|-ecpc -configopts = '-GNU' - -keeppreviousinstall = True - -# notes by Bernd Mohr -# Use hardcoded x86_64 or "import platform; machine = platform.machine()" here? -sanity_check_paths = { - 'files': ["x86_64/bin/cparse", "x86_64/include/pdb.h", "x86_64/lib/libpdb.a"], - 'dirs': [], -} - -skipsteps = ['build'] - -modextrapaths = { - 'PATH': "x86_64/bin", - 'LD_LIBRARY_PATH': "x86_64/lib", -} +checksums = [ + '5c5e1e6607086aa13bf4b1b9befc5864', # pdtoolkit-3.19.tar.gz +] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb index 7faa216ef2db1a4fc8d1759cbca2eeae3c82620a..f50e7519a2ac13354066b88d16058fc84ae3e9e2 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb @@ -1,12 +1,14 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## -easyblock = 'ConfigureMake' name = "PDT" version = "3.19" @@ -20,31 +22,11 @@ description = """Program Database Toolkit (PDT) is a framework for analyzing sou toolchain = {'name': 'ictce', 'version': '5.3.0'} -# http://tau.uoregon.edu/pdt_releases/pdtoolkit-3.19.tar.gz sources = ['pdtoolkit-%(version)s.tar.gz'] source_urls = ['http://tau.uoregon.edu/pdt_releases/'] -prefix_opt = '-prefix=' - -# notes by Bernd Mohr -# Compiler suite should always be specified -- MUCH quicker and SAVER than autodetect -# -KAI|-KCC|-GNU|-CC|-c++|-cxx|-xlC|-pgCC|-icpc|-ecpc -configopts = '-GNU' - -keeppreviousinstall = True - -# notes by Bernd Mohr -# Use hardcoded x86_64 or "import platform; machine = platform.machine()" here? -sanity_check_paths = { - 'files': ["x86_64/bin/cparse", "x86_64/include/pdb.h", "x86_64/lib/libpdb.a"], - 'dirs': [], -} - -skipsteps = ['build'] - -modextrapaths = { - 'PATH': "x86_64/bin", - 'LD_LIBRARY_PATH': "x86_64/lib", -} +checksums = [ + '5c5e1e6607086aa13bf4b1b9befc5864', # pdtoolkit-3.19.tar.gz +] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4acb86b02182eb26cf833201e8ae3242291af8a0 --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb @@ -0,0 +1,32 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = "PDT" +version = "3.20" + +homepage = 'http://www.cs.uoregon.edu/research/pdt/' +description = """Program Database Toolkit (PDT) is a framework for analyzing source + code written in several programming languages and for making rich program knowledge + accessible to developers of static and dynamic analysis tools. PDT implements a standard + program representation, the program database (PDB), that can be accessed in a uniform way + through a class library supporting common PDB operations.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['pdtoolkit-%(version)s.tar.gz'] +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] + +checksums = [ + 'c3edabe202926abe04552e33cd39672d', # pdtoolkit-3.20.tar.gz +] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..bb1e979e805cd021d8d5d004d8f85da8e6045c3f --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb @@ -0,0 +1,48 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Authors:: Jordi Blasco +# License:: New BSD +# +## + +easyblock = 'ConfigureMake' + +name = "PDT" +version = "3.20" + +homepage = 'http://www.cs.uoregon.edu/research/pdt/' +description = """Program Database Toolkit (PDT) is a framework for analyzing source + code written in several programming languages and for making rich program knowledge + accessible to developers of static and dynamic analysis tools. PDT implements a standard + program representation, the program database (PDB), that can be accessed in a uniform way + through a class library supporting common PDB operations.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +# http://tau.uoregon.edu/pdt_releases/pdtoolkit-3.19.tar.gz +sources = ['pdtoolkit-%(version)s.tar.gz'] +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] + +prefix_opt = '-prefix=' + +# notes by Bernd Mohr +# Compiler suite should always be specified -- MUCH quicker and SAVER than autodetect +# -KAI|-KCC|-GNU|-CC|-c++|-cxx|-xlC|-pgCC|-icpc|-ecpc +configopts = '-GNU' + +keeppreviousinstall = True + +# notes by Bernd Mohr +# Use hardcoded x86_64 or "import platform; machine = platform.machine()" here? +sanity_check_paths = { + 'files': ["x86_64/bin/cparse", "x86_64/include/pdb.h", "x86_64/lib/libpdb.a"], + 'dirs': [], +} + +skipsteps = ['build'] + +modextrapaths = { + 'PATH': "x86_64/bin", + 'LD_LIBRARY_PATH': "x86_64/lib", +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb new file mode 100644 index 0000000000000000000000000000000000000000..50bb76fbb335ca5b24752327a4eac513666913cc --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb @@ -0,0 +1,30 @@ +easyblock = 'PackedBinary' + +name = 'PLINK' +version = '1.07-x86_64' + +homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' +description = 'plink-1.07-src: Whole-genome association analysis toolset' + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(namelower)s-%(version)s.zip'] +source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] + +checksums = ['fd0bafeda42151b20534e4f97b0d97df'] + +files_to_copy = [ + 'plink', + 'gPLINK.jar', + 'test.map', + 'test.ped', + 'COPYING.txt', + 'README.txt', +] + +sanity_check_paths = { + 'files': ['plink', 'gPLINK.jar', 'test.map', 'test.ped', 'COPYING.txt', 'README.txt'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..e6ac2070ea914340d95b3e4dda1cdaee8fd6d4ba --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb @@ -0,0 +1,35 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.0.4' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'ictce', 'version': '7.1.2'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = ['PLUMED-%(version)s_eb-env-vars.patch'] + +skipsteps = ['configure'] + +prebuildopts = " ./configure.sh linux.icc && source sourceme.sh && " +preinstallopts = " export PLUMED_PREFIX=%(installdir)s && " + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.so', 'lib/libplumed.so'], + 'dirs': ['lib/plumed'] +} + +modextrapaths = {'PLUMED_KERNEL': 'lib/libplumedKernel.so'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4_eb-env-vars.patch b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4_eb-env-vars.patch new file mode 100644 index 0000000000000000000000000000000000000000..d3cf60fc92e9778e86d8e4bace6aebca5469f32c --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4_eb-env-vars.patch @@ -0,0 +1,77 @@ +# patch to work around the hideous build system of plumed. We use the values +# EB sets in the build system. +diff -urN plumed-2.0.4.orig/configurations/linux.icc plumed-2.0.4/configurations/linux.icc +--- plumed-2.0.4.orig/configurations/linux.icc 2014-09-15 11:41:47.000000000 +0200 ++++ plumed-2.0.4/configurations/linux.icc 2014-12-01 14:54:42.000000000 +0100 +@@ -2,21 +2,21 @@ + #CHECK_BOUNDARIES=-D_GLIBCXX_DEBUG + +-LIBS=-ldl ++LIBS:=-ldl $(LIBS) +-DYNAMIC_LIBS=-lstdc++ -llapack -lblas ++DYNAMIC_LIBS:=-lstdc++ $(LIBS) $(LIBLAPACK) + DOUBLEPRECISION=-r8 + +-CPPFLAGS=-D__PLUMED_HAS_DLOPEN $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE) +-CXXFLAGS=-O -fPIC -Wall -wd981,383,1418 +-CFLAGS=-O -fPIC -Wall ++CPPFLAGS:=-D__PLUMED_HAS_DLOPEN $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE) $(CPPFLAGS) ++CXXFLAGS:=-O -fPIC -Wall -wd981,383,1418 $(CXXFLAGS) ++CFLAGS:=-O -fPIC -Wall $(CFLAGS) + +-LDFLAGS=-rdynamic ++LDFLAGS:=-rdynamic $(LDFLAGS) + SOEXT=so +-LDSO=icc -shared $(CFLAGS) +-LD=icpc +-LDF90=ifort +-CXX=icpc +-CC=icc +-FC=ifort ++LDSO:=$(CC) -shared $(CFLAGS) ++LD:=$(CXX) ++LDF90:=$(F90) ++CXX:=$(CXX) ++CC:=$(CC) ++FC:=$(F77) + + GCCDEP=g++ + +--- plumed-2.0.4.orig/configurations/linux.mpi.icc 2015-06-30 10:02:14.000000000 +0200 ++++ plumed-2.0.4/configurations/linux.mpi.icc 2015-09-11 16:32:00.543631846 +0200 +@@ -1,22 +1,23 @@ + + #CHECK_BOUNDARIES=-D_GLIBCXX_DEBUG + +-LIBS=-ldl +-DYNAMIC_LIBS=-lstdc++ -llapack -lblas ++ ++LIBS:=-ldl $(LIBS) ++DYNAMIC_LIBS:=-lstdc++ $(LIBS) $(LIBLAPACK) + DOUBLEPRECISION=-r8 + +-CPPFLAGS=-D__PLUMED_HAS_DLOPEN -D__PLUMED_MPI $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE) +-CXXFLAGS=-O -fPIC -Wall -wd981,383,1418 +-CFLAGS=-O -fPIC -Wall ++CPPFLAGS:=-D__PLUMED_HAS_DLOPEN -D__PLUMED_MPI $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE) $(CPPFLAGS) ++CXXFLAGS:=-O -fPIC -Wall -wd981,383,1418 $(CXXFLAGS) ++CFLAGS:=-O -fPIC -Wall $(CFLAGS) + +-LDFLAGS=-rdynamic ++LDFLAGS:=-rdynamic $(LDFLAGS) + SOEXT=so +-LDSO=mpicc -shared $(CFLAGS) +-LD=mpic++ +-LDF90=mpif90 +-CXX=mpic++ +-CC=mpicc +-FC=mpif90 ++LDSO:=$(CC) -shared $(CFLAGS) ++LD:=$(CXX) ++LDF90:=$(F90) ++CXX:=$(CXX) ++CC:=$(CC) ++FC:=$(F77) + + GCCDEP=mpic++ + diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..89a5511e514fa9695c53d198d3fa8f9aeeddc37d --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.1.3-intel-2015a.eb @@ -0,0 +1,36 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.1.3' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = ['PLUMED-2.0.4_eb-env-vars.patch'] + +skipsteps = ['configure'] + +prebuildopts = " ./configure.sh linux.mpi.icc && source sourceme.sh && " +preinstallopts = " export PLUMED_PREFIX=%(installdir)s && " + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.so', 'lib/libplumed.so'], + 'dirs': ['lib/plumed'] +} + +modextrapaths = {'PLUMED_KERNEL': 'lib/libplumedKernel.so'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..2060e3874c7fc694274a63e808fd851725b2d1ec --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '4.8.0' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..427477bf963cc96c4830a83e4901011d9532ffc3 --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '4.8.0' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..e299f3c676f5c7266a37457cfb83564d792bfe38 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b5-intel-2015a-mt-maxam7-Python-2.7.10.eb @@ -0,0 +1,38 @@ +name = 'PSI' +version = '4.0b5' +# 'maxam7': maximum angular momentum increased to 7 via LIBINT_OPT_AM +versionsuffix = '-mt-maxam7' + +homepage = 'http://www.psicode.org/' +description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for + efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform + computations with more than 2500 basis functions running serially or in parallel.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +# not using MPI results in a build relying on multithreaded BLAS solely +toolchainopts = {'usempi': False} + +source_urls = ['http://download.sourceforge.net/psicode/'] +sources = ['%(namelower)s%(version)s.tar.gz'] + +patches = [ + 'PSI-4.0b5-failed-test.patch', # the test works but it segfaults on exit + 'PSI-4.0b5-thread-pool.patch', + 'PSI-4.0b5-new-plugin.patch', + 'PSI-%(version)s_python-config.patch', # workaround for broken python-config due to full path to bin/python being used +] + +python = 'Python' +pyver = '2.7.10' +pysuff = '-%s-%s' % (python, pyver) +versionsuffix += pysuff + +dependencies = [ + (python, pyver), + ('Boost', '1.59.0', pysuff), +] + +# increase maximum angular momentum to 7 +configopts = '--with-max-am-eri=7' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-fix-gitversion.patch b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-fix-gitversion.patch new file mode 100644 index 0000000000000000000000000000000000000000..7f36d862a019f968a1e81e632b6ac0b686cb3828 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-fix-gitversion.patch @@ -0,0 +1,12 @@ +# As we have a git version without the git metadata, we tell it which commit we have used +# by wpoely86@gmail.com +diff -ur psi4public-7baee9b8ff6e30b39a7ee627750a518c39bd84f3.orig/src/bin/psi4/gitversion.py psi4public-7baee9b8ff6e30b39a7ee627750a518c39bd84f3/src/bin/psi4/gitversion.py +--- psi4public-7baee9b8ff6e30b39a7ee627750a518c39bd84f3.orig/src/bin/psi4/gitversion.py 2015-08-14 04:47:54.000000000 +0200 ++++ psi4public-7baee9b8ff6e30b39a7ee627750a518c39bd84f3/src/bin/psi4/gitversion.py 2015-08-14 12:50:26.702794481 +0200 +@@ -80,4 +80,5 @@ + ghash = '' + mmp = '' + +-write_version(branch, mmp, ghash, status) ++#write_version(branch, mmp, ghash, status) ++write_version("master", None, "7baee9b8ff6e30b", "") diff --git a/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7-Python-2.7.10.eb b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..46a224ce66c4a026cbb16f9d26644260978ae08d --- /dev/null +++ b/easybuild/easyconfigs/p/PSI/PSI-4.0b6-20150814-intel-2015a-mt-maxam7-Python-2.7.10.eb @@ -0,0 +1,40 @@ +name = 'PSI' +version = '4.0b6-20150814' +versionsuffix = '-mt-maxam7' + +homepage = 'http://www.psicode.org/' +description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for + efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform + computations with more than 2500 basis functions running serially or in parallel.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': False} + +source_urls = ['https://github.com/psi4/psi4public/archive/'] +sources = ['7baee9b8ff6e30b39a7ee627750a518c39bd84f3.tar.gz'] + +patches = [ + 'PSI-%(version)s-fix-gitversion.patch', +] + +configopts = '-DLIBINT_OPT_AM=7 -DENABLE_PLUGINS=ON -DENABLE_DUMMY_PLUGIN=ON ' + +python = 'Python' +pyver = '2.7.10' +pysuff = '-%s-%s' % (python, pyver) +versionsuffix += pysuff + +dependencies = [ + (python, pyver), + ('Boost', '1.59.0', pysuff), +] + +builddependencies = [ + ('CMake', '3.2.3'), + ('Perl', '5.20.1', '-bare'), # for the test suite +] + +# Execute only the 'quick' tests and run 4 in parallel +runtest = 'ARGS="-V -L quicktests -j 4 -E \'pywrap-freq-e-sowreap|stability1|libefp-qchem-qmefp-puream-sp\'" test' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb index eba092fa74dbff3556a55abdf3f4d868248afbbb..76a476c789260cf72da2998aaf9840fde183c9b7 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb @@ -12,7 +12,7 @@ description = """Pango is a library for laying out and rendering of text, with a toolchain = {'name': 'intel', 'version': '2014b'} -source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/pango/%(version_major_minor)s/'] +source_urls = [FTPGNOME_SOURCE] sources = [SOURCELOWER_TAR_XZ] dependencies = [ @@ -22,6 +22,7 @@ dependencies = [ ('GLib', '2.40.0'), ('HarfBuzz', '0.9.35'), ('GObject-Introspection', '1.42.0'), + ('libXft', '2.3.2'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.37.1-intel-2015a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.37.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6797ad144be855f7a2a37614cd90b442e37ff559 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.37.1-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Pango' +version = '1.37.1' + +homepage = 'http://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLib', '2.41.2'), + ('cairo', '1.14.2'), + ('HarfBuzz', '0.9.41'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb b/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d1b5731cfff4e57495660a5f0342056359f00f8e --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.37.2-intel-2015a.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'Pango' +version = '1.37.2' + +homepage = 'http://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis + on internationalization. Pango can be used anywhere that text layout + is needed, though most of the work on Pango so far has been done in + the context of the GTK+ widget toolkit. Pango forms the core of text + and font handling for GTK+-2.x.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('cairo', '1.14.2'), + ('fontconfig', '2.11.94'), + ('freetype', '2.6'), + ('GLib', '2.44.1'), + ('HarfBuzz', '1.0.1'), + ('GObject-Introspection', '1.44.0'), + ('libXft', '2.3.2', '-libX11-1.6.3-Python-2.7.10'), +] + +builddependencies = [ + ('M4', '1.4.17'), +] + +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.so', 'lib/libpangocairo-1.0.so', + 'lib/libpangoft2-1.0.so', 'lib/libpangoxft-1.0.so'], + 'dirs': [] +} + +modextrapaths = { + 'GI_TYPELIB_PATH': 'share', + 'XDG_DATA_DIRS': 'share', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pangomm/Pangomm-2.36.0-intel-2015a.eb b/easybuild/easyconfigs/p/Pangomm/Pangomm-2.36.0-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..044fc1c671029a286e109155c513ae22d59f7496 --- /dev/null +++ b/easybuild/easyconfigs/p/Pangomm/Pangomm-2.36.0-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Pangomm' +version = '2.36.0' + +homepage = 'http://www.pango.org/' +description = """ The Pangomm package provides a C++ interface to Pango. """ + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('GLibmm', '2.41.2'), + ('cairomm', '1.10.0'), + ('Pango', '1.37.1'), +] + + +sanity_check_paths = { + 'files': ['lib/libpangomm-1.4.so'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..973a23b9d22f0c778b92ff6004a230fe1d24b4bf --- /dev/null +++ b/easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli +# License:: MIT/GPL +# +## + +easyblock = 'PerlModule' + +name = 'Parallel-ForkManager' +version = '1.06' + +homepage = 'http://search.cpan.org/~szabgab/Parallel-ForkManager-1.06/lib/Parallel/ForkManager.pm' +description = """A simple parallel processing fork manager""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://search.cpan.org/CPAN/authors/id/S/SZ/SZABGAB/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver) +] + +options = {'modulename': 'Parallel::ForkManager'} + +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/Parallel/ForkManager.pm' % (perlmajver, perlver)], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/Paraview/Paraview-4.1.0-intel-2014b.eb b/easybuild/easyconfigs/p/Paraview/Paraview-4.1.0-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..2f704c2b24fe560c93bd75fa5c066e894dbea016 --- /dev/null +++ b/easybuild/easyconfigs/p/Paraview/Paraview-4.1.0-intel-2014b.eb @@ -0,0 +1,22 @@ +easyblock = 'CMakeMake' + +name = 'Paraview' +version = '4.1.0' + +homepage = "http://www.paraview.org" +description = "Paraview is a scientific parallel visualizer" + +toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'usempi': False, 'pic': True} + +download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] +sources = ["ParaView-v%(version)s-source.tar.gz"] + +dependencies = [('Qt','4.8.6')] + +builddependencies = [('CMake', '3.0.0')] + +separate_build_dir = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..0a7acf4ed3d0cf069e0cea33394e1c39e2537bfc --- /dev/null +++ b/easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb @@ -0,0 +1,34 @@ +# 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 = 'MakeCp' + +name = "PeakSeq" +version = "1.3" + +homepage = 'http://info.gersteinlab.org/PeakSeq' +description = """ PeakSeq is a program for identifying and ranking peak regions in ChIP-Seq + experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from + a control experiment and outputs a file with peak regions ranked with increasing Q-values.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/'] +sources = ['%(name)s.zip'] + +# as the tarball doesn't contain the version we verify the checksum to be sure +# we don't download a newer version and consider it as 1.3 +checksums = [('md5', '32b4d71b2ec9455c7db69516b1bd4910')] + +buildopts = ' CC="$CXX"' + +files_to_copy = ["bin", "README" ] + +sanity_check_paths = { + 'files': ["bin/PeakSeq"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb index 197f8c762ae811cdaf5876b5fadec37258902c9a..c7d3a27ade6493118e1ff63c2e2c320ef1605b8d 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb @@ -812,6 +812,59 @@ exts_list = [ 'source_tmpl': 'Lingua-EN-PluralToSingular-0.14.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BK/BKB/'], }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAVIDO/'], + }), + ('Text::CSV', '1.32', { + 'source_tmpl': 'Text-CSV-1.32.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MAKAMAKA/'], + }), + ('Number::Format', '1.73', { + 'source_tmpl': 'Number-Format-1.73.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/W/WR/WRW/'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DARREN/'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-1.15.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AN/ANDYA/'], + }), + ('Text::Table', '1.15', { + 'source_tmpl': 'Text-Table-1.130.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/'], + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RI/RIBASUSHI/'], + }), + ('GD::Graph', '1.49', { + 'source_tmpl': 'GDGraph-1.49.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RU/RUZ/'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/'], + }), + ('LWP::Simple', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('Test::Pod', '1.50', { + 'source_tmpl': 'Test-Pod-1.50.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DW/DWHEELER/'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MI/MIROD/'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-0.11.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MI/MIYAGAWA/'], + }), + ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2015a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..657707950801e0d9d3719f08ddf50b86ed3c5d2f --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2015a.eb @@ -0,0 +1,870 @@ +name = 'Perl' +version = '5.20.0' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +exts_list = [ + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL/'], + }), + ('DBI', '1.631', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TI/TIMB/'], + }), + ('Module::Build', '0.4205', { + 'source_tmpl': 'Module-Build-0.4205.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT/'], + }), + ('Devel::StackTrace', '1.32', { + 'source_tmpl': 'Devel-StackTrace-1.32.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM/'], + }), + ('Exception::Class', '1.38', { + 'source_tmpl': 'Exception-Class-1.38.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Test::Tester', '0.109', { + 'source_tmpl': 'Test-Tester-0.109.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FD/FDALY/'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('Test::Deep', '0.112', { + 'source_tmpl': 'Test-Deep-0.112.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Algorithm::Diff', '1.15', { + 'source_tmpl': 'Algorithm-Diff-1.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/N/NE/NEDKONZ/'], + }), + ('Text::Diff', '1.41', { + 'source_tmpl': 'Text-Diff-1.41.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], + }), + ('Test::Differences', '0.61', { + 'source_tmpl': 'Test-Differences-0.61.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], + }), + ('Sub::Uplevel', '0.24', { + 'source_tmpl': 'Sub-Uplevel-0.24.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/'], + }), + ('Test::Exception', '0.32', { + 'source_tmpl': 'Test-Exception-0.32.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADIE/'], + }), + ('Test::Warn', '0.30', { + 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY/'], + }), + ('Test::Most', '0.33', { + 'source_tmpl': 'Test-Most-0.33.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], + }), + ('File::Slurp::Tiny', '0.003', { + 'source_tmpl': 'File-Slurp-Tiny-0.003.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Tree::DAG_Node', '1.22', { + 'source_tmpl': 'Tree-DAG_Node-1.22.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE/'], + }), + ('Try::Tiny', '0.20', { + 'source_tmpl': 'Try-Tiny-0.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], + }), + ('Test::Fatal', '0.013', { + 'source_tmpl': 'Test-Fatal-0.013.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Test::Requires', '0.07', { + 'source_tmpl': 'Test-Requires-0.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM/'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('Sub::Install', '0.927', { + 'source_tmpl': 'Sub-Install-0.927.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Data::OptList', '0.109', { + 'source_tmpl': 'Data-OptList-0.109.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-0.987.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Capture::Tiny', '0.24', { + 'source_tmpl': 'Capture-Tiny-0.24.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/'], + }), + ('Test::Output', '1.03', { + 'source_tmpl': 'Test-Output-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BD/BDFOY/'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM/'], + }), + ('Module::Implementation', '0.07', { + 'source_tmpl': 'Module-Implementation-0.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('List::MoreUtils', '0.33', { + 'source_tmpl': 'List-MoreUtils-0.33.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('Package::DeprecationManager', '0.13', { + 'source_tmpl': 'Package-DeprecationManager-0.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], + }), + ('Package::Stash', '0.36', { + 'source_tmpl': 'Package-Stash-0.36.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], + }), + ('TAP::Harness::Env', '3.30', { + 'source_tmpl': 'Test-Harness-3.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT/'], + }), + ('ExtUtils::Helpers', '0.022', { + 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.007', { + 'source_tmpl': 'ExtUtils-Config-0.007.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::InstallPaths', '0.010', { + 'source_tmpl': 'ExtUtils-InstallPaths-0.010.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.036', { + 'source_tmpl': 'Module-Build-Tiny-0.036.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT/'], + }), + ('Class::Load', '0.21', { + 'source_tmpl': 'Class-Load-0.21.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BO/BOBTFISH/'], + }), + ('Sub::Name', '0.05', { + 'source_tmpl': 'Sub-Name-0.05.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FL/FLORA/'], + }), + ('Eval::Closure', '0.11', { + 'source_tmpl': 'Eval-Closure-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], + }), + ('Sub::Exporter::Progressive', '0.001011', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW/'], + }), + ('Devel::GlobalDestruction', '0.12', { + 'source_tmpl': 'Devel-GlobalDestruction-0.12.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('boolean', '0.32', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/I/IN/INGY/'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY/'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], + }), + ('Class::Load::XS', '0.08', { + 'source_tmpl': 'Class-Load-XS-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], + }), + ('Moose', '2.1208', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], + }), + ('Params::Validate', '1.10', { + 'source_tmpl': 'Params-Validate-1.10.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('DateTime::Locale', '0.45', { + 'source_tmpl': 'DateTime-Locale-0.45.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Class::Singleton', '1.4', { + 'source_tmpl': 'Class-Singleton-1.4.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW/'], + }), + ('DateTime::TimeZone', '1.70', { + 'source_tmpl': 'DateTime-TimeZone-1.70.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Test::Warnings', '0.014', { + 'source_tmpl': 'Test-Warnings-0.014.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], + }), + ('DateTime', '1.10', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DW/DWHEELER/'], + }), + ('DateTime::Tiny', '1.04', { + 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/U/UR/URI/'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('IO::HTML', '1.00', { + 'source_tmpl': 'IO-HTML-1.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJM/'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('URI', '1.60', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('Encode::Locale', '1.03', { + 'source_tmpl': 'Encode-Locale-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('HTTP::Request', '6.06', { + 'source_tmpl': 'HTTP-Message-6.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PETDANCE/'], + }), + ('HTML::Entities', '3.71', { + 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('AnyEvent', '7.07', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/'], + }), + ('Devel::CheckCompiler', '0.05', { + 'source_tmpl': 'Devel-CheckCompiler-0.05.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DM/DMUEY/'], + }), + ('Cwd::Guard', '0.04', { + 'source_tmpl': 'Cwd-Guard-0.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Module::Build::XSUtil', '0.10', { + 'source_tmpl': 'Module-Build-XSUtil-0.10.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO/'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-0.004.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], + }), + ('aliased', '0.31', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID/'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-0.003.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], + }), + ('Exporter::Declare', '0.113', { + 'source_tmpl': 'Exporter-Declare-0.113.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], + }), + ('Mock::Quick', '1.107', { + 'source_tmpl': 'Mock-Quick-1.107.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], + }), + ('Test::Exception::LessClever', '0.006', { + 'source_tmpl': 'Test-Exception-LessClever-0.006.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], + }), + ('Test::LeakTrace', '0.14', { + 'source_tmpl': 'Test-LeakTrace-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GF/GFUJI/'], + }), + ('Mouse', '2.3.0', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GF/GFUJI/'], + }), + ('XML::NamespaceSupport', '1.11', { + 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/'], + }), + ('XML::SAX::Base', '1.08', { + 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM/'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM/'], + }), + ('Clone', '0.37', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Config::General', '2.56', { + 'source_tmpl': 'Config-General-2.56.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('Font::TTF', '1.04', { + 'source_tmpl': 'Font-TTF-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MH/MHOSKEN'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Math::Round', '0.06', { + 'source_tmpl': 'Math-Round-0.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Readonly', '1.04', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SA/SANKO/'], + }), + ('Regexp::Common', '2013031301', { + 'source_tmpl': 'Regexp-Common-2013031301.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('Text::Format', '0.59', { + 'source_tmpl': 'Text-Format-0.59.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Crypt::Rijndael', '1.12', { + 'source_tmpl': 'Crypt-Rijndael-1.12.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BD/BDFOY/'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-2.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DP/DPARIS/'], + }), + ('Net::SNMP', '6.0.1', { + 'source_tmpl': 'Net-SNMP-v6.0.1.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DT/DTOWN/'], + }), + ('List::AllUtils', '0.08', { + 'source_tmpl': 'List-AllUtils-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('AnyData', '0.11', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SD/SDOWIDEIT/'], + }), + ('Test::Simple', '1.001003', { + 'source_tmpl': 'Test-Simple-1.001003.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], + }), + ('Getopt::Long', '2.42', { + 'source_tmpl': 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['http://search.cpan.org/CPAN/authors/id/D/DA/DAVIDO/'], + }), + ('Text::CSV', '1.32', { + 'source_tmpl': 'Text-CSV-1.32.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MAKAMAKA/'], + }), + ('Number::Format', '1.73', { + 'source_tmpl': 'Number-Format-1.73.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/W/WR/WRW/'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DARREN/'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-1.15.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AN/ANDYA/'], + }), + ('Text::Table', '1.15', { + 'source_tmpl': 'Text-Table-1.130.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/'], + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RI/RIBASUSHI/'], + }), + ('GD::Graph', '1.49', { + 'source_tmpl': 'GDGraph-1.49.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RU/RUZ/'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/'], + }), + ('LWP::Simple', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('Test::Pod', '1.50', { + 'source_tmpl': 'Test-Pod-1.50.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DW/DWHEELER/'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MI/MIROD/'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-0.11.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MI/MIYAGAWA/'], + }), + +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.2-foss-2015b-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.2-foss-2015b-bare.eb new file mode 100644 index 0000000000000000000000000000000000000000..429d35babf0668308aec9f6659f3d9a5cbb56a4a --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.2-foss-2015b-bare.eb @@ -0,0 +1,17 @@ +name = 'Perl' +version = '5.20.2' +versionsuffix = '-bare' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +# bare, no extensions +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.2-intel-2015b-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.2-intel-2015b-bare.eb new file mode 100644 index 0000000000000000000000000000000000000000..82afea03f3b164418e59c761c805d08cb61c2d79 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.2-intel-2015b-bare.eb @@ -0,0 +1,17 @@ +name = 'Perl' +version = '5.20.2' +versionsuffix = '-bare' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +# bare, no extensions +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ab7a8379bf378ce3f948bc51075280f384d11823 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.3-intel-2015b.eb @@ -0,0 +1,909 @@ +name = 'Perl' +version = '5.20.3' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +exts_list = [ + ('Config::General', '2.58', { + 'source_tmpl': 'Config-General-2.58.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-6.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-0.011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Helpers', '0.022', { + 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('TAP::Harness::Env', '3.35', { + 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-0.008.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-0.039.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Text::Glob', '0.09', { + 'source_tmpl': 'Text-Glob-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('Regexp::Common', '2013031301', { + 'source_tmpl': 'Regexp-Common-2013031301.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-0.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-5.2.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warnings', '0.021', { + 'source_tmpl': 'Test-Warnings-0.021.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('DateTime::Locale', '0.46', { + 'source_tmpl': 'DateTime-Locale-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('DateTime::TimeZone', '1.93', { + 'source_tmpl': 'DateTime-TimeZone-1.93.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + }), + ('Try::Tiny', '0.22', { + 'source_tmpl': 'Try-Tiny-0.22.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Params::Validate', '1.21', { + 'source_tmpl': 'Params-Validate-1.21.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('List::MoreUtils', '0.413', { + 'source_tmpl': 'List-MoreUtils-0.413.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Exporter::Tiny', '0.042', { + 'source_tmpl': 'Exporter-Tiny-0.042.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TOBYINK'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-1.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('DateTime', '1.20', { + 'source_tmpl': 'DateTime-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Module::Build', '0.4214', { + 'source_tmpl': 'Module-Build-0.4214.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Readonly', '2.00', { + 'source_tmpl': 'Readonly-2.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SA/SANKO'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-0.41.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + }), + ('Tree::DAG_Node', '1.27', { + 'source_tmpl': 'Tree-DAG_Node-1.27.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-2.26.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], + }), + ('DBI', '1.634', { + 'source_tmpl': 'DBI-1.634.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.48', { + 'source_tmpl': 'DBD-SQLite-1.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Archive::Extract', '0.76', { + 'source_tmpl': 'Archive-Extract-0.76.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/J/JU/JUERD'], + }), + ('Shell', '0.72', { + 'source_tmpl': 'Shell-0.72.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + }), + ('File::Spec', '3.47', { + 'source_tmpl': 'PathTools-3.47.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('ExtUtils::MakeMaker', '7.10', { + 'source_tmpl': 'ExtUtils-MakeMaker-7.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Simple', '1.001014', { + 'source_tmpl': 'Test-Simple-1.001014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVIDO'], + }), + ('IO::WrapTie', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Encode::Locale', '1.05', { + 'source_tmpl': 'Encode-Locale-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::SAX::Base', '1.08', { + 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('XML::NamespaceSupport', '1.11', { + 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Test::LeakTrace', '0.15', { + 'source_tmpl': 'Test-LeakTrace-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GF/GFUJI'], + }), + ('Test::Exception', '0.40', { + 'source_tmpl': 'Test-Exception-0.40.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::Table', '1.130', { + 'source_tmpl': 'Text-Table-1.130.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('MIME::Types', '2.11', { + 'source_tmpl': 'MIME-Types-2.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), + ('Module::Build::XSUtil', '0.16', { + 'source_tmpl': 'Module-Build-XSUtil-0.16.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HI/HIDEAKIO'], + }), + ('Tie::Function', '0.02', { + 'source_tmpl': 'Tie-Function-0.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAVIDNICO/handy_tied_functions'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DARREN'], + }), + ('HTML::Parser', '3.71', { + 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Handler', '1.2', { + 'source_tmpl': 'Date-Handler-1.2.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BB/BBEAUSEJ'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('IO::HTML', '1.001', { + 'source_tmpl': 'IO-HTML-1.001.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Data::Grove', '0.08', { + 'source_tmpl': 'libxml-perl-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KM/KMACLEOD'], + }), + ('Class::ISA', '0.36', { + 'source_tmpl': 'Class-ISA-0.36.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SM/SMUELLER'], + }), + ('URI', '1.69', { + 'source_tmpl': 'URI-1.69.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Ima::DBI', '0.35', { + 'source_tmpl': 'Ima-DBI-0.35.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERRIN'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('GO', '0.04', { + 'source_tmpl': 'go-db-perl-0.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SJ/SJCARBON'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Pod::POM', '2.00', { + 'source_tmpl': 'Pod-POM-2.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Math::Round', '0.07', { + 'source_tmpl': 'Math-Round-0.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GROMMEL'], + }), + ('Text::Diff', '1.43', { + 'source_tmpl': 'Text-Diff-1.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Log::Message::Simple', '0.10', { + 'source_tmpl': 'Log-Message-Simple-0.10.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Socket::SSL', '2.020', { + 'source_tmpl': 'IO-Socket-SSL-2.020.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-0.004.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAGOLDEN/'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-0.003.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-0.114.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('IO::Stringy', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Getopt::Long', '2.47', { + 'source_tmpl': 'Getopt-Long-2.47.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Mouse', 'v2.4.5', { + 'source_tmpl': 'Mouse-v2.4.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Test::Version', '2.03', { + 'source_tmpl': 'Test-Version-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('DBIx::Admin::TableInfo', '3.01', { + 'source_tmpl': 'DBIx-Admin-TableInfo-3.01.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Net::HTTP', '6.09', { + 'source_tmpl': 'Net-HTTP-6.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Test::Deep', '0.117', { + 'source_tmpl': 'Test-Deep-0.117.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warn', '0.30', { + 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BO/BOBTFISH'], + }), + ('Moo', '2.000002', { + 'source_tmpl': 'Moo-2.000002.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Hash::Merge', '0.200', { + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/'], + 'source_tmpl': 'Hash-Merge-0.200.tar.gz', + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-6.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('HTML::Entities::Interpolate', '1.05', { + 'source_tmpl': 'HTML-Entities-Interpolate-1.05.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-1.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Test::Most', '0.34', { + 'source_tmpl': 'Test-Most-0.34.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/O/OV/OVID'], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-0.34.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Test::Differences', '0.63', { + 'source_tmpl': 'Test-Differences-0.63.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTTP::Tiny', '0.056', { + 'source_tmpl': 'HTTP-Tiny-0.056.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Package::DeprecationManager', '0.14', { + 'source_tmpl': 'Package-DeprecationManager-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-2.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('version', '0.9912', { + 'source_tmpl': 'version-0.9912.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + # fails: uses 'gcc' + #('XML::Bare', '0.53', { + # 'source_tmpl': 'XML-Bare-0.53.tar.gz', + # 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + #}), + ('Dist::CheckConflicts', '0.11', { + 'source_tmpl': 'Dist-CheckConflicts-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Sub::Name', '0.14', { + 'source_tmpl': 'Sub-Name-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece', '1.30', { + 'source_tmpl': 'Time-Piece-1.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Digest::HMAC', '1.03', { + 'source_tmpl': 'Digest-HMAC-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('HTTP::Negotiate', '6.01', { + 'source_tmpl': 'HTTP-Negotiate-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('MIME::Lite', '3.030', { + 'source_tmpl': 'MIME-Lite-3.030.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Crypt::Rijndael', '1.13', { + 'source_tmpl': 'Crypt-Rijndael-1.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('B::Lint', '1.20', { + 'source_tmpl': 'B-Lint-1.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Canary::Stability', '2006', { + 'source_tmpl': 'Canary-Stability-2006.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('AnyEvent', '7.11', { + 'source_tmpl': 'AnyEvent-7.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-0.48.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-1.221.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-1.51.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-1.71.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Net::SMTP::SSL', '1.03', { + 'source_tmpl': 'Net-SMTP-SSL-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::Tiny', '2.06', { + 'source_tmpl': 'XML-Tiny-2.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + }), + ('HTML::Tree', '5.03', { + 'source_tmpl': 'HTML-Tree-5.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Devel::GlobalDestruction', '0.13', { + 'source_tmpl': 'Devel-GlobalDestruction-0.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Expect', '1.32', { + 'source_tmpl': 'Expect-1.32.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SZ/SZABGAB'], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-v6.0.1.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + }), + ('XML::SAX::Writer', '0.56', { + 'source_tmpl': 'XML-SAX-Writer-0.56.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('Statistics::Descriptive', '3.0609', { + 'source_tmpl': 'Statistics-Descriptive-3.0609.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Class::Load', '0.23', { + 'source_tmpl': 'Class-Load-0.23.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::Simple', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-0.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('GD::Graph', '1.49', { + 'source_tmpl': 'GDGraph-1.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-0.30.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('boolean', '0.45', { + 'source_tmpl': 'boolean-0.45.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-1.75.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Test::Tester', '1.001014', { + 'source_tmpl': 'Test-Simple-1.001014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-2.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + }), + ('Exporter', '5.72', { + 'source_tmpl': 'Exporter-5.72.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Class::Inspector', '1.28', { + 'source_tmpl': 'Class-Inspector-1.28.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Parse::RecDescent', '1.967012', { + 'source_tmpl': 'Parse-RecDescent-1.967012.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + }), + ('Carp', '1.36', { + 'source_tmpl': 'Carp-1.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::XPath', '1.13', { + 'source_tmpl': 'XML-XPath-1.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MS/MSERGEANT'], + }), + ('Capture::Tiny', '0.30', { + 'source_tmpl': 'Capture-Tiny-0.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-2.90.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-0.987.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Class::Load::XS', '0.09', { + 'source_tmpl': 'Class-Load-XS-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-1.15.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + }), + ('Sub::Exporter::Progressive', '0.001011', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('LWP', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Data::Dumper::Concise', '2.022', { + 'source_tmpl': 'Data-Dumper-Concise-2.022.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-1.1903.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-1.7.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('strictures', '2.000001', { + 'source_tmpl': 'strictures-2.000001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-2.17.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('File::Which', '1.19', { + 'source_tmpl': 'File-Which-1.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-1.005.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Error', '0.17024', { + 'source_tmpl': 'Error-0.17024.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Mock::Quick', '1.110', { + 'source_tmpl': 'Mock-Quick-1.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::CSV', '1.33', { + 'source_tmpl': 'Text-CSV-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Test::Output', '1.03', { + 'source_tmpl': 'Test-Output-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + }), + ('Class::DBI', 'v3.0.17', { + 'source_tmpl': 'Class-DBI-v3.0.17.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('List::AllUtils', '0.09', { + 'source_tmpl': 'List-AllUtils-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Exception::Class', '1.39', { + 'source_tmpl': 'Exception-Class-1.39.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-4.42.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-0.61.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + }), + ('Eval::Closure', '0.13', { + 'source_tmpl': 'Eval-Closure-0.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('HTTP::Request', '6.11', { + 'source_tmpl': 'HTTP-Message-6.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::Simple', '2.20', { + 'source_tmpl': 'XML-Simple-2.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-0.928.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('HTTP::Cookies', '6.01', { + 'source_tmpl': 'HTTP-Cookies-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + }), + ('Test::Exception::LessClever', '0.006', { + 'source_tmpl': 'Test-Exception-LessClever-0.006.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Scalar::Util', '1.42', { + 'source_tmpl': 'Scalar-List-Utils-1.42.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-0.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('IO::Scalar', '2.111', { + 'source_tmpl': 'IO-stringy-2.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-6.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::HomeDir', '1.00', { + 'source_tmpl': 'File-HomeDir-1.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-2.16.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-1.002005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('DateTime::Tiny', '1.04', { + 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-0.110.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Format', '0.59', { + 'source_tmpl': 'Text-Format-0.59.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Devel::CheckCompiler', '0.06', { + 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Log::Handler', '0.87', { + 'source_tmpl': 'Log-Handler-0.87.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('HTML::Entities', '3.71', { + 'source_tmpl': 'HTML-Parser-3.71.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Devel::StackTrace', '2.00', { + 'source_tmpl': 'Devel-StackTrace-2.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Term::ReadKey', '2.33', { + 'source_tmpl': 'TermReadKey-2.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('Moose', '2.1603', { + 'source_tmpl': 'Moose-2.1603.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-1.110.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Font::TTF', '1.05', { + 'source_tmpl': 'Font-TTF-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MH/MHOSKEN'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-0.048.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('File::Find::Rule', '0.33', { + 'source_tmpl': 'File-Find-Rule-0.33.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('SQL::Statement', '1.407', { + 'source_tmpl': 'SQL-Statement-1.407.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/U/UR/URI'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-0.37.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Data::OptList', '0.109', { + 'source_tmpl': 'Data-OptList-0.109.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('CPANPLUS', '0.9154', { + 'source_tmpl': 'CPANPLUS-0.9154.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Harness', '3.35', { + 'source_tmpl': 'Test-Harness-3.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-1.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Text::Soundex', '3.04', { + 'source_tmpl': 'Text-Soundex-3.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Lingua::EN::PluralToSingular', '0.14', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-0.14.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BK/BKB'], + }), + ('Want', '0.26', { + 'source_tmpl': 'Want-0.26.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + }), + ('Cwd::Guard', '0.04', { + 'source_tmpl': 'Cwd-Guard-0.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-2.1.9.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + }), + ('Mail::Util', '2.14', { + 'source_tmpl': 'MailTools-2.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-GCC-4.9.2-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-GCC-4.9.2-bare.eb new file mode 100644 index 0000000000000000000000000000000000000000..cff5256c81c7ac98ee14851d8ddb495b5771ec4a --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-GCC-4.9.2-bare.eb @@ -0,0 +1,17 @@ +name = 'Perl' +version = '5.22.0' +versionsuffix = '-bare' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +# bare, no extensions +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015b-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015b-bare.eb new file mode 100644 index 0000000000000000000000000000000000000000..57a07e49a5d6e0f25a0388819673e9d6eb33256e --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-foss-2015b-bare.eb @@ -0,0 +1,17 @@ +name = 'Perl' +version = '5.22.0' +versionsuffix = '-bare' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +# bare, no extensions +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.22.0-intel-2015b-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-intel-2015b-bare.eb new file mode 100644 index 0000000000000000000000000000000000000000..4eeb6cf7a02a3b7798bbe94dda0cc3000a7262a5 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.0-intel-2015b-bare.eb @@ -0,0 +1,17 @@ +name = 'Perl' +version = '5.22.0' +versionsuffix = '-bare' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +# bare, no extensions +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..524dd9ba3d66e30769478b0dd7d5c993f7e2cab5 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '2.8.1' + +homepage = 'http://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..04c7f0efa3cf824724db3ccf6669ee49e194a57c --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '2.8.1' + +homepage = 'http://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-2.9.0-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/Pillow/Pillow-2.9.0-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..c3113a66838aa8171a10931889c1c8ab5ca41846 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-2.9.0-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '2.9.0' + +homepage = 'http://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-2.9.0-intel-2015b-Python-3.5.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-2.9.0-intel-2015b-Python-3.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..9e482ed565fa5715b6f815d164edcb6b00ee330c --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-2.9.0-intel-2015b-Python-3.5.0.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '2.9.0' + +homepage = 'http://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '3.5.0' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..65d0c45c59d1130cd39a00d9e14b219d489fe854 --- /dev/null +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb @@ -0,0 +1,47 @@ +# 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 = 'CmdCp' + +name = 'Pindel' +version = '0.2.5a7' + +homepage = 'http://gmt.genome.wustl.edu/packages/pindel/' +description = """ Pindel can detect breakpoints of large deletions, medium sized + insertions, inversions, tandem duplications and other structural variants at single-based + resolution from next-gen sequence data. It uses a pattern growth approach to identify the + breakpoints of these variants from paired-end short reads. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/genome/pindel/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = ['pindel-perl-path.patch'] + +dependencies = [ + ('SAMtools', '0.1.19'), + ('zlib', '1.2.7') +] + +cmds_map = [('.*', "CPATH=$EBROOTSAMTOOLS/include/bam:$CPATH ./INSTALL $EBROOTSAMTOOLS")] + +files_to_copy = [ + (['pindel', 'sam2pindel', 'pindel2vcf', 'bam2pindel.pl', 'Adaptor.pm'], 'bin'), + "demo", + "gmt", + "gmt-web", + "test", + "README.md", + "RELEASE" +] + +sanity_check_paths = { + 'files': ['bin/pindel', 'bin/sam2pindel', 'bin/pindel2vcf', 'bin/bam2pindel.pl'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Pindel/pindel-perl-path.patch b/easybuild/easyconfigs/p/Pindel/pindel-perl-path.patch new file mode 100644 index 0000000000000000000000000000000000000000..db0214c68067c373f7df63d6fabacf7748bdc270 --- /dev/null +++ b/easybuild/easyconfigs/p/Pindel/pindel-perl-path.patch @@ -0,0 +1,9 @@ +diff -ru pindel-0.2.5a7.orig/bam2pindel.pl pindel-0.2.5a7/bam2pindel.pl +--- pindel-0.2.5a7.orig/bam2pindel.pl 2014-09-16 20:53:13.000000000 +0200 ++++ pindel-0.2.5a7/bam2pindel.pl 2015-06-03 21:12:57.775900885 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/env perl + + ######################################################################################################## + # # diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..f0f5501b846be81899908f970ee1dec54dd300a7 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '9.3.5' + +homepage = 'http://www.mysql.com/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +toolchain = {'name': 'intel', 'version': '2014b'} + +osdependencies = [('openssl-devel', 'libssl-dev')] + +java = 'Java' +javaver = '1.7.0_60' + +dependencies = [ + (java, javaver, '', True), + ('libreadline', '6.3'), + ('zlib', '1.2.8'), +# ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons +] + +builddependencies = [ + ('Bison', '3.0.2'), + ('flex', '2.5.39'), + ('Perl', '5.20.0'), +] + +sanity_check_paths = { + 'files': ['bin/psql'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..44847179dbc8290d3e3a879ceb86f0180d86c22d --- /dev/null +++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = 'PyAMG' +version = '2.2.1' + +homepage = 'http://pyamg.org' +description = """PyAMG is a library of Algebraic Multigrid (AMG) solvers with a convenient Python interface.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.8' +pythonshortversion = '.'.join(pythonversion.split('.')[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +options = {'modulename': 'pyamg'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/pyamg' % pythonshortversion], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb index 35c97630e9d63ac118aab8b3720206102c891caf..ef867422c58298b14a4b78701b964c17bd16f0dc 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-goolf-1.5.14-Python-2.7.9.eb @@ -16,7 +16,7 @@ source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version) python = 'Python' pyver = '2.7.9' -pythonshortver = '.'.join(pyver.split('.')[:2]) +pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ @@ -26,11 +26,16 @@ dependencies = [ ] configopts = "configure-ng.py --confirm-license" -configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pythonshortver +configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pyshortver configopts += " --no-sip-files" -options = {'modulename': 'PyQt4'} +options = {'modulename': '%(name)s%(version_major)s'} -modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver} +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s%%(version_major)s' % pyshortver], +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb index aab3898aa9fb2f324b2ba55001a779640d0c5772..48c5bb750a0f6499a905e9d2f60d82fa2f44337f 100644 --- a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.3-intel-2015a-Python-2.7.9.eb @@ -16,7 +16,7 @@ source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version) python = 'Python' pyver = '2.7.9' -pythonshortver = '.'.join(pyver.split('.')[:2]) +pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ @@ -26,11 +26,16 @@ dependencies = [ ] configopts = "configure-ng.py --confirm-license" -configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pythonshortver +configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pyshortver configopts += " --no-sip-files" -options = {'modulename': 'PyQt4'} +options = {'modulename': '%(name)s%(version_major)s'} -modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver} +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s%%(version_major)s' % pyshortver], +} moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..992e13df88a1c506383f269ae1aa70a8d0f6ed40 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt' +version = '4.11.4' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['%(name)s-x11-gpl-%(version)s.tar.gz'] +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SIP', '4.16.8', versionsuffix), + ('Qt', '4.8.6'), +] + +configopts = "configure-ng.py --confirm-license" +configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pyshortver +configopts += " --no-sip-files" + +options = {'modulename': '%(name)s%(version_major)s'} + +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s%%(version_major)s' % pyshortver], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..0d39a830f0aac18ec09a311bfe93c2703a75f48f --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt' +version = '4.11.4' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +sources = ['%(name)s-x11-gpl-%(version)s.tar.gz'] +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] + +python = 'Python' +pyver = '2.7.8' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SIP', '4.16.8', versionsuffix), + ('Qt', '4.8.6'), +] + +configopts = "configure-ng.py --confirm-license" +configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pyshortver +configopts += " --no-sip-files" + +options = {'modulename': '%(name)s%(version_major)s'} + +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s%%(version_major)s' % pyshortver], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..f40c0f4c4be6530467713181180ce7e4d5cb2d3e --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'PyQt' +version = '4.11.4' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['%(name)s-x11-gpl-%(version)s.tar.gz'] +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SIP', '4.16.8', versionsuffix), + ('Qt', '4.8.6'), +] + +configopts = "configure-ng.py --confirm-license" +configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pyshortver +configopts += " --no-sip-files" + +options = {'modulename': '%(name)s%(version_major)s'} + +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pyshortver} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s%%(version_major)s' % pyshortver], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQuante/PyQuante-1.6.4-ictce-5.5.0-Python-2.7.5.eb b/easybuild/easyconfigs/p/PyQuante/PyQuante-1.6.4-ictce-5.5.0-Python-2.7.5.eb index a42bb5b4d8be9961e65465c290cae553c81833b9..1c5dde3609d3a7d7aea9e1413150907c9069776a 100644 --- a/easybuild/easyconfigs/p/PyQuante/PyQuante-1.6.4-ictce-5.5.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/p/PyQuante/PyQuante-1.6.4-ictce-5.5.0-Python-2.7.5.eb @@ -18,11 +18,11 @@ sources = [SOURCE_TAR_GZ] patches = ['PyQuante-1.6.4-Libint.patch'] python = 'Python' -pythonver = '2.7.5' -versionsuffix = '-%s-%s' % (python, pythonver) +pyver = '2.7.5' +versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ - (python, pythonver), + (python, pyver), ('numpy', '1.8.0', versionsuffix), ('matplotlib', '1.3.1', versionsuffix), ('Libint', '1.1.4'), @@ -30,4 +30,10 @@ dependencies = [ options = {'modulename': name} +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (pyshortver, pyshortver)], +} + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..c99ae13f38c756e0c4043e05ea0f8ccd7a0791ae --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '3.11' + +homepage = "https://pypi.python.org/pypi/PyYAML/" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.10' +py_short_ver = '.'.join(pythonversion.split('.')[0:2]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('libyaml', '0.1.6'), +] + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/yaml' % py_short_ver], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-foss-2015a-Python-2.7.9-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-foss-2015a-Python-2.7.9-zmq3.eb new file mode 100644 index 0000000000000000000000000000000000000000..fca9d5270f1ccb81d9fa54919ff1f98b9de7063a --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-foss-2015a-Python-2.7.9-zmq3.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '14.7.0' + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) +zmqversion = '3.2.5' + +versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) + +dependencies = [ + (python, pythonversion), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pyshortver], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-intel-2015a-Python-2.7.10-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-intel-2015a-Python-2.7.10-zmq4.eb new file mode 100644 index 0000000000000000000000000000000000000000..0c0220478e9dd8c0724354d774735af9da80a512 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-intel-2015a-Python-2.7.10-zmq4.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '14.7.0' + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.10' +pyshortver = '.'.join(pythonversion.split('.')[:2]) +zmqversion = '4.1.3' + +versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) + +dependencies = [ + (python, pythonversion), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pyshortver], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-intel-2015a-Python-2.7.9-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-intel-2015a-Python-2.7.9-zmq3.eb new file mode 100644 index 0000000000000000000000000000000000000000..0986a01c066bcb50dce5cc9cb5408a3bef5ccb57 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-intel-2015a-Python-2.7.9-zmq3.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '14.7.0' + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) +zmqversion = '3.2.5' + +versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) + +dependencies = [ + (python, pythonversion), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pyshortver], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..103bb389984d984835204c8c461891a1f7f74388 --- /dev/null +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'Pygments' +version = '2.0.2' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +description = """Python http for humans""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +sanity_check_paths = { + 'files': ['bin/pygmentize'], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s.egg' % (pyshortver, pyshortver)], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..d24209c2d988b9aab061fb20ebcef8c85cdb4a5b --- /dev/null +++ b/easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'Pyke' +version = '1.1.1' + +homepage = 'http://sourceforge.net/projects/pyke/' +description = """Pyke introduces a form of Logic Programming (inspired by Prolog) +to the Python community by providing a knowledge-based inference engine +(expert system) written in 100% Python.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_ZIP] + +python = 'Python' +pyver = '2.7.3' + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), + ('numpy','1.6.2', versionsuffix), + ('scipy', '0.11.0', versionsuffix), +] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/pyke' % pyshortver], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb index a0f450f70fd5da0bba44ca3a55826d5390443d6a..43ff3feba7790c36001122a64fc7d70826fec35f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb index 53b60641322ae403d2d35d672c4cc6a584d31b39..f825fd87bd2b9a40df2c89c63725d9351cc179ac 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb index ed1944c3f288728538d3c4d81fb226e0f309fa84..18d0d4a8df4ba5018da9e938ead4ad9836e072fb 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb index d9118da1063fb338ac6992dbfbe30fe3e4433440..23ddabe854a26e4f7d5889e51b683eb310c2161d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb @@ -11,7 +11,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] -patches = ['python_libffi_int128_icc.patch'] +patches = [ + 'python_libffi_int128_icc.patch', + 'Python-%(version)s_svnversion-cmd.patch', +] dependencies = [ ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb index da9bd1c2a45d9767c7cb9fbb6f27a87554f0ab93..f747214b5c04de81ef7d934c297ae4e88c91fd55 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb @@ -11,7 +11,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] -patches = ['python_libffi_int128_icc.patch'] +patches = [ + 'python_libffi_int128_icc.patch', + 'Python-%(version)s_svnversion-cmd.patch', +] dependencies = [ ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb index ae0e9d0e0895a947a110a64b56929455ff32819b..0228eae5bec85243ecadf62db0050da407306ff8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb index 6d976f526fe56e3370000393ca7ab00b09231d06..fc44c37e78ed1f71580f531eaf88776d834d9af1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch b/easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch new file mode 100644 index 0000000000000000000000000000000000000000..ba79adb02e019dc4eb4548603fb52e16fd86d3a8 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch @@ -0,0 +1,14 @@ +replace svnversion call with mimiced output for non-SVN tarballs for older versions of svnversion, i.e 'exported' +author: Kenneth Hoste (Ghent University) +--- Python-2.5.6/configure.orig 2015-04-29 10:40:05.254502098 +0200 ++++ Python-2.5.6/configure 2015-04-29 10:42:01.739388944 +0200 +@@ -4242,7 +4242,8 @@ + + if test $SVNVERSION = found + then +- SVNVERSION="svnversion \$(srcdir)" ++ #SVNVERSION="svnversion \$(srcdir)" ++ SVNVERSION="echo exported" + else + SVNVERSION="echo exported" + fi diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb new file mode 100644 index 0000000000000000000000000000000000000000..6ce1637771012306e96d91ebe5290fc989d0bc83 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-GNU-4.9.3-2.25-bare.eb @@ -0,0 +1,31 @@ +name = 'Python' +version = '2.7.10' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8', '', ('GCC', '4.9.3-binutils-2.25')), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.10.2'), + ('Tk', '8.6.4', '-no-X11'), +# ('OpenSSL', '1.0.1k'), # 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 +] + +osdependencies = [('openssl-devel', 'libssl-dev')] + +# bare installation: no extensions included +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8e4cfabe9d4b2e41d247f5a137f6a22eda9f154d --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -0,0 +1,122 @@ +name = 'Python' +version = '2.7.10' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.2' +scipyversion = '0.15.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.10.2'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), # required for pycrypto +# ('OpenSSL', '1.0.1m'), # 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 +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.22', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.2', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.14', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..45878617c62869a77b5253ce14fd90b4bc19c777 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015b.eb @@ -0,0 +1,122 @@ +name = 'Python' +version = '2.7.10' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.2' +scipyversion = '0.15.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.10.2'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.0.0a', '', ('GNU', '4.9.3-2.25')), # required for pycrypto +# ('OpenSSL', '1.0.1m'), # 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 +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.22', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.2', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.14', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..66bb207792660d2f60d0f0ec3332b240b72fa943 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.4.10.eb @@ -0,0 +1,122 @@ +name = 'Python' +version = '2.7.10' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.2' +scipyversion = '0.15.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.10.2'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.0.0a', '', ('GCC', '4.7.2')), # required for pycrypto +# ('OpenSSL', '1.0.1m'), # 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 +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.22', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.2', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.14', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..e5f6c7aacced28f0598bd5a0b8ad90eff0dd7f3b --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-goolf-1.7.20.eb @@ -0,0 +1,122 @@ +name = 'Python' +version = '2.7.10' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.2' +scipyversion = '0.15.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.10.2'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.0.0a', '', ('GCC', '4.8.4')), # required for pycrypto +# ('OpenSSL', '1.0.1m'), # 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 +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.22', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.2', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.14', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f5c2309ea848d322c318295c93ffcb02fb1ccccd --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -0,0 +1,122 @@ +name = 'Python' +version = '2.7.10' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.2' +scipyversion = '0.15.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.10.2'), + ('Tk', '8.6.4', '-no-X11'), + ('GMP', '6.0.0a', '', ('GCC', '4.9.2')), # required for pycrypto +# ('OpenSSL', '1.0.1m'), # 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 +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.22', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.2', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.14', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..a5115dc2be096bf024fe6ee931c6096c2baca5d2 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015b.eb @@ -0,0 +1,121 @@ +name = 'Python' +version = '2.7.10' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.2' +scipyversion = '0.15.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.10.2'), + ('Tk', '8.6.4', '-no-X11'), +# ('OpenSSL', '1.0.1m'), # 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 +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.22', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.2', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.14', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb index 8bf00ee94a88e256af85fb3c2ff893fa79752b6b..b447f3f5c56fd2e47691d2c592643a6c91b818fd 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb index 2ade7ad4f1c25f234c63c1f6a83da66a5c46ae8e..3b9b9b0071c316fa3fe06218d68bf14614ce8525 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -65,7 +65,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb index a73fef035d5a7b0a33883a7b68950d7529073641..e9411a98a07021ce56ce98dd659466ea3fabd664 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb index 2af2f0c18115f09e613210010dc70c2ca9229293..9d81cee86be481950aecd7b7cd7177b15061ad19 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -65,7 +65,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb index 0218dcafbddc2e3d668ba61aeb79233037473bcd..b7dfb64df9b022f6ee658b86b4a939eb89230cd7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb index 342b19c101b5e276a0f8ce3f803af85b0348de29..5eb4c88938f924fa0a64e6ef4a9473c64461dc4a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb index b883b3a7a75814974a90f152fa949cdbfdd61e16..878951cc6e476ff20a71f61cae0f90c4c87951dc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb index 53fb8ff2924857614742f01c1aacafe8d97af5f9..957d719fbd04d9e4a5f8b3b4013515b0f7e2330e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb index c2cc52183eedc74fbf505557e3cc76d2de18cb8c..49da1ce96f947abec5e8960eb4c7843f940bb27e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.4.10.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb index 994f20889f1be9b667597d6a9320972f6fabcd1e..ff029a2234b253e799e285d736c993318aab0490 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goolf-1.5.14.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb index 459199e8c52ebaead2eb657385e83dde6e7c82a3..2ef8f9fc886b0c840beb8606ddd784e6dc44c807 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb index 3e4b4f03f3a83a7b57ef96fb2710706d9d634931..b5075a6a9a6b213bb75c831b9e13cc8944b748b9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb index 2e8be6d925b81fbde8ac654713d2c133e31d4a03..e1bc68f6d19e46a49866fb09dbcefbdf7cd67a93 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.2.0.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -65,7 +65,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb index c6d6010f0e9003963ec9b8544608ccdc5f1dd1dc..1f6678ca7318f61796fe2f8a1f41f82f6c4c34b9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-5.3.0.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -65,7 +65,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb index 2da448273b470bc224672e64ad970150f6c3cae3..bcc80770f8f66f12972c6de62e95d72a7e4f6db6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-intel-2015a.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -65,7 +65,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb index b7849aec58a2448a7459d20e99865457b492b0e8..262801c6c11f6379519725f54257f4cd766edc65 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb index c17df2cb09c661bde9393b25b6006b7c2e8e35a2..7713f868794252a35e8ed9367d982ca37a95195f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb @@ -55,7 +55,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -71,7 +71,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb index 9f5cd7d95fb26800a4e2c149749ae36c3fcc0e11..0acac864f5d5fbbd256bc084da5ef05aeac5eecd 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb @@ -49,7 +49,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -65,7 +65,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb index a24d0b3e6e0ef1ac1a72a123ac59260709f3d515..b8e12d524c621f9a7c70eeb390ce3a616a008923 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goolf-1.4.10.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb index cee2b8e18970609115847019d139399236f11477..9fda7777e647ec648efc6a1847c7c6b49aeec6ee 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb @@ -54,7 +54,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -70,7 +70,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb index 751a48399467c682c09fe9042f1a613c0929b16d..6f7edf431ee89ec321ee2d9fe7e68be3451ffc67 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.3.0.eb @@ -52,7 +52,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -68,7 +68,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb index 8b46b16cd303677d3213936e71a423c9481d0347..3c2a47e51e8e3f9beb52133219152d1cf1e89fad 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-5.5.0.eb @@ -52,7 +52,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -68,7 +68,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb index ed13d9428541a6c2c705fb1fbbb5a72d2d5d17f0..c8797b36e9be938d5a2c3dd5973165470445b453 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb @@ -56,7 +56,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -72,7 +72,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb index 8e7a62f6da2a3084bef852a56cc7220a9bb01d73..de11eaf35665adcb3e69194ac8576d31c5301c91 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-goolf-1.4.10.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb index aaba09ba094a0eb8fc69c41b54d05a4ac9dcbc36..b8f2f71c1298a2e06a92f29c7f861226b4c8ffce 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb @@ -54,7 +54,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -70,7 +70,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb index d9f7ad0b7767f7f962fb18207334d61e71c804ae..be1053a62d683f0385756f0b3478ca21b2bbf9a6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-5.5.0.eb @@ -54,7 +54,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -70,7 +70,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb index 6e042b928df66a04ad5d2f9fc589be8b5547157e..caf05b2cc7ffaef59b1e10abb4068850df96ce40 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-foss-2014b.eb @@ -51,7 +51,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -67,7 +67,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb index 09dc45c1e6460374adaa45226b189af1021eb9d6..5c19bcd953243787c7508def9cf5a974e6dca284 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-goolf-1.5.14.eb @@ -60,7 +60,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb index 383b7d978bf8015232c0bcd03a8743d8cbb9ae63..f1ec579fbec9c3a7b1921495625b9a9fe82a8768 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-ictce-7.1.2.eb @@ -61,7 +61,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb index 18aa12a4b8f2516abd580a72efa62e92bb357d49..b6208992739be2617df8f408dead087b982bb260 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb index 787f5ecab186304c7709b9f7e6280bbaa84c9d3d..1ae3ec0c5f68a8a57c9dece5f47ad8fbc7a256db 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014b.eb @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb index 16a9eea25ffc65a690bb5efe2e53845569a113ac..60923e701c5052fa8a481553de1671add9450089 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2015a.eb @@ -57,7 +57,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb index 2ec3cb1dc82da49324c191a27f3970493011764d..5c84059a20ec16c4d4fde4364365fa1d4c2edd28 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb @@ -21,11 +21,19 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] # bare installation: no extensions included exts_list = [] buildopts = 'LINKCC="$CC -dynamic"' +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb index fdb44db0d0f61fcdd3359bd577d645a75a5c5c18..2e085966c758de3a5210a92427e332cdcbe089d1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb @@ -23,7 +23,7 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] buildopts = 'LINKCC="$CC -dynamic"' @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.10.2', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -104,4 +104,12 @@ exts_list = [ }), ] +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb index 09917d502571da702132c267394c4ada9a18e6cc..1e9572eb837c8293f7b1806493415e91e16564e7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb @@ -21,11 +21,19 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] # bare installation: no extensions included exts_list = [] buildopts = 'LINKCC="$CC -dynamic"' +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb index bb0be0ac851d627f2b4924cf49fda8f654ed5972..0c1b139dda1b53898424010860b9a0faa7ce969b 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb @@ -23,7 +23,7 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] buildopts = 'LINKCC="$CC -dynamic"' @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.10.2', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -104,4 +104,12 @@ exts_list = [ }), ] +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb index 10c6659238a6134bfd2d10a0bf323f0b050a5a8d..3fafaaa920caee5a5d3baca1e7a7db3b6b600aed 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb @@ -21,11 +21,19 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] # bare installation: no extensions included exts_list = [] buildopts = 'LINKCC="$CC -dynamic"' +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb index 3950c920d4b550b992c28c3b1d2ee6598eab23d1..186e5f94df6d0b1b73da88e9499b5d89613f3df1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb @@ -23,7 +23,7 @@ dependencies = [ # nice to have an up to date openssl for security reasons ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel'), 'tk-devel'] buildopts = 'LINKCC="$CC -dynamic"' @@ -58,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.10.2', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -104,4 +104,12 @@ exts_list = [ }), ] +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb index 3974b6e842cc2e8f426b4c3cc523eeddf32b2863..7f438347a5a4904fab5f7963107845601804365c 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-GCC-4.9.2-bare.eb @@ -18,6 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # 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 ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..abb705a349eff8e55418d662e9496d829061fe0a --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -0,0 +1,116 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'https://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), +# ('OpenSSL', '1.0.1k'), # 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 +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('https://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + }), + ('scipy', scipyversion, { + 'source_urls': [('https://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '0.10.8', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['https://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2014.10', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb index 669c54c38def38ad20ea465ba06ed10f72c93a7f..dc26dc666bfb39985b0054631347a2f9838c65f7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a-bare.eb @@ -18,6 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # 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 ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb index 3273aa03998caa0ead3d1f8a70d10825b6357d80..bb297e5eb8f68b2d2e970f14b84b1ec274cdb0f8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015a.eb @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # 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 ] @@ -54,7 +55,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '0.10.8', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb index e206b78e2281315e6393f95bb337007c7a1b61dd..ad2c37f79adb5bd9c619d6a67fe1f88a565f3bbb 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-gompi-1.5.16-bare.eb @@ -17,6 +17,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # 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 ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb index 9a1f9af5fcd3daff282eabff8b25ebd77a49eb4c..27281d943cfd6eb641909c9b57adfafa60f61f65 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.5.14.eb @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # 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 ] @@ -54,7 +55,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '0.10.8', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..c011298dc9c62f9feb9698ce0bfd77041e9b7a7f --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb @@ -0,0 +1,117 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'https://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), + #('OpenSSL', '1.0.1k'), # 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 +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('https://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + }), + ('scipy', scipyversion, { + 'source_urls': [('https://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/ '], + }), + ('pbr', '0.10.8', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['https://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2014.10', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb index d2c02867a99986b1654a7b3135f9f887745381cb..d6a4eb1b3cb4883decd61523e54d63b252e278d8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a-bare.eb @@ -18,6 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # 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 ] diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb index 95f4d38205981f8ac460211990b20063e289fee7..2c04d1e9a7f0df30f246722274fcc90c2ef4f67a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-intel-2015a.eb @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), # ('OpenSSL', '1.0.1k'), # 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 ] @@ -57,7 +58,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '0.10.8', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb index 033d18310541548527018e90769abd4cafbd9bf7..ddf1d2d85390d0b5008ba7ad9c9c0430af53978d 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb @@ -49,13 +49,13 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('Cython', '0.19.1', { 'source_urls': ['http://www.cython.org/release/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb index c928dc3ca333668a2eab3463ec2aa3f25e1c5148..86066e4a5eb3c5b8aee0fd1ac75d70b0338099d7 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goolf-1.4.10.eb @@ -49,13 +49,13 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('Cython', '0.19.1', { 'source_urls': ['http://www.cython.org/release/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb index f523509a1d4497a2e814d9530964403c8d7fc239..b01168b83e9499e9210ad557aaaf0aa49d6bbc61 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb @@ -51,13 +51,13 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('Cython', '0.19.1', { 'source_urls': ['http://www.cython.org/release/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb index a47ee809f5c1451b59fc471bca743063b9c4d09d..de9617eacf2ef57da0be8ee59774497069f65761 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-5.3.0.eb @@ -49,13 +49,13 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('Cython', '0.19.1', { 'source_urls': ['http://www.cython.org/release/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb index 07f56943210458966fcc8ee65a13bc695d0721c4..b7690d84fc789d268975ed57c180e3a805a710ff 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2014b.eb @@ -56,9 +56,12 @@ exts_list = [ }), ('paycheck', '1.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -77,6 +80,9 @@ exts_list = [ }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.1_setup-open-README-utf8.patch', + ], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb index ba75d726f90b7d94dbf0ffe7a228c2c72849f70a..91935078a9cf5e99aa877a2ed58a34f89ad551bc 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -56,9 +56,12 @@ exts_list = [ }), ('paycheck', '1.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -77,6 +80,9 @@ exts_list = [ }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.1_setup-open-README-utf8.patch', + ], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb index c5e5b4ddcbb03a666da74c0d19f95c47a7c6111d..5741325e74448e20da59427ab0e27a4f42546422 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -27,7 +27,6 @@ osdependencies = [('openssl-devel', 'libssl-dev')] # order is important! # package versions updated Jan 19th 2015 -exts_filter = ('PYTHONPATH="%(installdir)s:$PYTHONPATH python -c "import %(ext_name)s"', '') exts_list = [ ('setuptools', '15.2', { 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], @@ -55,6 +54,9 @@ exts_list = [ }), ('paycheck', '1.0.2', { 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], }), ('argparse', '1.3.0', { 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], @@ -78,6 +80,9 @@ exts_list = [ ('deap', '1.0.2', { 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.2_setup-open-README-utf8.patch', + ], }), ('decorator', '3.4.2', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], @@ -106,3 +111,5 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], }), ] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..088e6f96d905601e35a3180543576d882f623a6a --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.5.0-intel-2015b.eb @@ -0,0 +1,115 @@ +name = 'Python' +version = '3.5.0' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.3' +scipyversion = '0.16.0' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1p'), # 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 +] + +osdependencies = [('openssl-devel', 'libssl-dev')] + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '18.3.2', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], + 'patches': [ + 'numpy-1.8.0-mkl.patch', # % numpyversion, + ], + }), + ('scipy', scipyversion, { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('argparse', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.23.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('decorator', '4.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/deap-1.0.1_setup-open-README-utf8.patch b/easybuild/easyconfigs/p/Python/deap-1.0.1_setup-open-README-utf8.patch new file mode 100644 index 0000000000000000000000000000000000000000..b7c896999f7e9f9aac6bd383cc831c140705a95f --- /dev/null +++ b/easybuild/easyconfigs/p/Python/deap-1.0.1_setup-open-README-utf8.patch @@ -0,0 +1,17 @@ +--- deap-1.0.1.orig/setup.py 2014-04-08 15:49:52.000000000 +0200 ++++ deap-1.0.1/setup.py 2015-05-21 22:25:37.345008000 +0200 +@@ -1,4 +1,5 @@ + #!/usr/bin/env python ++import codecs + import sys + from distutils.core import setup + try: +@@ -11,7 +12,7 @@ + setup(name='deap', + version=deap.__revision__, + description='Distributed Evolutionary Algorithms in Python', +- long_description=open('README.txt').read(), ++ long_description=codecs.open('README.txt', encoding='utf-8').read(), + author='deap Development Team', + author_email='deap-users@googlegroups.com', + url='http://deap.googlecode.com', diff --git a/easybuild/easyconfigs/p/Python/deap-1.0.2_setup-open-README-utf8.patch b/easybuild/easyconfigs/p/Python/deap-1.0.2_setup-open-README-utf8.patch new file mode 100644 index 0000000000000000000000000000000000000000..6dece6f5d82227b12b2e097eb186bbed8e93c95e --- /dev/null +++ b/easybuild/easyconfigs/p/Python/deap-1.0.2_setup-open-README-utf8.patch @@ -0,0 +1,17 @@ +--- deap-1.0.2.orig/setup.py 2015-05-12 04:06:49.000000000 +0200 ++++ deap-1.0.2/setup.py 2015-05-21 19:06:03.792820042 +0200 +@@ -1,4 +1,5 @@ + #!/usr/bin/env python ++import codecs + import sys + from distutils.core import setup + try: +@@ -10,7 +11,7 @@ + from pypandoc import convert + except ImportError: + print("warning: pypandoc module not found, could not convert Markdown to RST") +- read_md = lambda f: open(f, 'r').read() ++ read_md = lambda f: codecs.open(f, encoding='utf-8').read() + else: + read_md = lambda f: convert(f, 'rst') + diff --git a/easybuild/easyconfigs/p/Python/paycheck-1.0.2_setup-open-README-utf8.patch b/easybuild/easyconfigs/p/Python/paycheck-1.0.2_setup-open-README-utf8.patch new file mode 100644 index 0000000000000000000000000000000000000000..193336def433c6c3acab7bb88054dedea320425e --- /dev/null +++ b/easybuild/easyconfigs/p/Python/paycheck-1.0.2_setup-open-README-utf8.patch @@ -0,0 +1,22 @@ +open README file with utf-8 encoding, to avoid error like: +UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 577: ordinal not in range(128) +author: Kenneth Hoste (HPC-UGent) +--- paycheck-1.0.2/setup.py.orig 2015-05-21 16:09:24.300074046 +0200 ++++ paycheck-1.0.2/setup.py 2015-05-21 16:11:43.503945542 +0200 +@@ -1,6 +1,7 @@ + from distutils.cmd import Command + from distutils.core import setup + ++import codecs + import sys + if sys.version_info >= (3, 0): + try: +@@ -24,7 +25,7 @@ + name = 'paycheck', + version ='1.0.2', + description ='A Python QuickCheck implementation', +- long_description = open("README.txt").read(), ++ long_description = codecs.open("README.txt", encoding='utf-8').read(), + author ='Mark Chadwick', + author_email ='mark.chadwick@gmail.com', + maintainer ='Gregory Crosswhite', diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb b/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..aba7c4da3fd5d4576f6cd34984aca5762eb1db6f --- /dev/null +++ b/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1-GCC-4.9.2.eb @@ -0,0 +1,41 @@ +easyblock = 'MakeCp' + +name = 'p7zip' +version = '9.38.1' + +homepage = 'http://p7zip.sourceforge.net/' +description = """p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip) for Unix. + 7-Zip is a file archiver with highest compression ratio.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['p7zip_%(version)s_src_all.tar.bz2'] + +prebuildopts = "cp makefile.linux_amd64 makefile.linux &&" +buildopts = 'all3 CC="$CC" CXX="$CXX" OPTFLAGS="$CFLAGS"' + +files_to_copy = [ + (['bin/7za', 'bin/7zr', 'bin/7zCon.sfx'], 'bin'), # stand-alone binaries + (['bin/7z', 'bin/7z.so', 'bin/Codecs'], 'libexec'), # 7z requires 7z.so plugin in same directory +] + +# put script in place for 7z, since it *must* be called full path, to ensure that 7z.so is found in the same directory +# see also http://sourceforge.net/p/p7zip/discussion/383044/thread/5e4085ab/ +postinstallcmds = [ + "echo '#!/bin/sh\n%(installdir)s/libexec/7z $@' > %(installdir)s/bin/7z", + "chmod +x %(installdir)s/bin/7z", # set execution bits according to current umask +] + +sanity_check_paths = { + 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'libexec/7z', 'libexec/7z.so'], + 'dirs': ['libexec/Codecs'], +} + +# check whether 7z script works +sanity_check_commands = [ + ('7z', '--help'), # print help, exit 0 + ('7z', "x || test $? -gt 0"), # missing argument, exit code > 0 +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1.eb b/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..b709c55a99bb41e02f085b0e8642ececce9bccf0 --- /dev/null +++ b/easybuild/easyconfigs/p/p7zip/p7zip-9.38.1.eb @@ -0,0 +1,41 @@ +easyblock = 'MakeCp' + +name = 'p7zip' +version = '9.38.1' + +homepage = 'http://p7zip.sourceforge.net/' +description = """p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip) for Unix. + 7-Zip is a file archiver with highest compression ratio.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['p7zip_%(version)s_src_all.tar.bz2'] + +prebuildopts = "cp makefile.linux_amd64 makefile.linux &&" +buildopts = 'all3' + +files_to_copy = [ + (['bin/7za', 'bin/7zr', 'bin/7zCon.sfx'], 'bin'), # stand-alone binaries + (['bin/7z', 'bin/7z.so', 'bin/Codecs'], 'libexec'), # 7z requires 7z.so plugin in same directory +] + +# put script in place for 7z, since it *must* be called full path, to ensure that 7z.so is found in the same directory +# see also http://sourceforge.net/p/p7zip/discussion/383044/thread/5e4085ab/ +postinstallcmds = [ + "echo '#!/bin/sh\n%(installdir)s/libexec/7z $@' > %(installdir)s/bin/7z", + "chmod +x %(installdir)s/bin/7z", # set execution bits according to current umask +] + +sanity_check_paths = { + 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'libexec/7z', 'libexec/7z.so'], + 'dirs': ['libexec/Codecs'], +} + +# check whether 7z script works +sanity_check_commands = [ + ('7z', '--help'), # print help, exit 0 + ('7z', "x || test $? -gt 0"), # missing argument, exit code > 0 +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..fa5b729bcb665c94125a32b00bba0743f166fa49 --- /dev/null +++ b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +## +easyblock = "MakeCp" + +name = 'pBWA' +version = '0.5.9_1.21009' + +homepage = 'http://pbwa.sourceforge.net/' +description = "pBWA is a parallel implementation of the popular software BWA." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(name)s_%(version)s.zip'] +source_urls = [('http://sourceforge.net/projects/pbwa/files/latest', 'download')] + +dependencies = [('BWA', '0.7.4')] + +files_to_copy = [(['pBWA','qualfa2fq.pl','solid2fastq.pl' ], 'bin')] + +sanity_check_paths = { + 'files': ['bin/pBWA','bin/qualfa2fq.pl','bin/solid2fastq.pl'], + 'dirs': ['.'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.16.2-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/p/pandas/pandas-0.16.2-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..b006e661ec8f4c96c0fd105fbceece58f3171f79 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.16.2-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.16.2' + +homepage = "https://pypi.python.org/pypi/pandas/" +description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures + and data analysis tools for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +pylibdir = "lib/python%s/site-packages/%s" % (pyshortver, name) + +sanity_check_paths = { + 'files': [("%s-%%(version)s-py%s.egg" % (pylibdir, pyshortver), + "%s-%%(version)s-py%s-linux-x86_64.egg" % (pylibdir, pyshortver))], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/parallel/parallel-20150822-GCC-4.9.2.eb b/easybuild/easyconfigs/p/parallel/parallel-20150822-GCC-4.9.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..cd915dedbc0479b85802910fe22da28b7dd483b1 --- /dev/null +++ b/easybuild/easyconfigs/p/parallel/parallel-20150822-GCC-4.9.2.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'parallel' +version = '20150822' + +homepage = 'http://savannah.gnu.org/projects/parallel/' +description = """parallel: Build and execute shell commands in parallel""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('Perl', '5.22.0', '-bare'), +] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 05e281d1d75ce5ce814470a3e857840dea6e9e57..2d44a2d96bd6760d1021223c6c600d74e5d585f0 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -19,4 +19,10 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/paycheck' % pyshortver], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb index 67f7bc47b5b16626ecd6903a11191ef2bd2cf97a..67abbe4783f69e09f877beeb250d3fb4e5d6f040 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb @@ -18,4 +18,10 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/paycheck' % pyshortver], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb index 0f1fade586e32c6a8dc263b15c40b89285766017..14fdb01611f716ce580281f6f71d7dbf9ec0b4bf 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb @@ -19,4 +19,10 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/paycheck' % pyshortver], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb index 5170a4d2bd316400aba1314bdfb537f2c75bfaf1..9fdde707312cba290df8d7ee6d6e6de93edebf2d 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb @@ -19,4 +19,10 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/paycheck' % pyshortver], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb index f140852405768fee38989e584f22905b8ae66e86..dcddbf5da11ead5deed010c168ebfe2392f193e3 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb @@ -19,4 +19,10 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/paycheck' % pyshortver], +} + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..f3e698bb5f2d9d87f2f673753ca1feb7b37fea1c --- /dev/null +++ b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'pbs_python' +version = '4.6.0' + +homepage = 'https://oss.trac.surfsara.nl/pbs_python' +description = """The pbs_python package is a wrapper class for the Torque C library. With this package you now can + write utilities/extensions in Python instead of C. We developed this package because we want to replace xpbsmon by + an ascii version named pbsmon. PBSQuery is also included in this package. This is a python module build on top of + the pbs python module to simplify querying the batch server, eg: how many jobs, how many nodes, ...""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ftp.sara.nl/pub/outgoing/'] +sources = [SOURCE_TAR_GZ] + +patches = [ + 'pbs_python-%(version)s_CC.patch', + 'pbs_python-%(version)s_remove-printf.patch', +] + +python = 'Python' +pythonver = '2.7.10' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [(python, pythonver)] + +osdependencies = ['torque-devel'] + +# this is needed for setup.py script +configopts = "--datarootdir=%(installdir)s --docdir=%(installdir)s" +prebuildopts = 'export CFLAGS="$CFLAGS -I/usr/include/torque/" && ' +preinstallopts = prebuildopts + +pythonpath = 'lib/python%s/site-packages' % pythonshortver +modextrapaths = {"PYTHONPATH": pythonpath} + +sanity_check_paths = { + 'files': [], + 'dirs': ["%s/pbs" % pythonpath] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.9.eb index 2b1f46d33d4f93d7fde1a264b24ceb29eb283e9e..ab7a722fecabcdaa3c0510bbe0709f645df53559 100644 --- a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.9.eb @@ -14,7 +14,10 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['http://ftp.sara.nl/pub/outgoing/'] sources = [SOURCE_TAR_GZ] -patches = ['pbs_python-%(version)s_CC.patch'] +patches = [ + 'pbs_python-%(version)s_CC.patch', + 'pbs_python-%(version)s_remove-printf.patch', +] python = 'Python' pythonver = '2.7.9' diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0_remove-printf.patch b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0_remove-printf.patch new file mode 100644 index 0000000000000000000000000000000000000000..9ac2e25c7b693f1a1bfb540e7f66035cd3e90e60 --- /dev/null +++ b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0_remove-printf.patch @@ -0,0 +1,34 @@ +remove printf debug statements +see https://oss.trac.surfsara.nl/pbs_python/ticket/46 +author: Ewan Higgs (Ghent University) +Index: src/C++/pbs_wrap.cxx +=================================================================== +--- src/C++/pbs_wrap.cxx (revision 342) ++++ src/C++/pbs_wrap.cxx (working copy) +@@ -3015,7 +3015,7 @@ + allocate memory as a one block is handy for Python scripts + and fill in the next fields so it also works for the C-library + */ +- printf("basje \n"); ++ //printf("basje \n"); + ptr = (struct attrl *) malloc(number * sizeof(struct attrl)); + + prev = NULL; +@@ -3022,7 +3022,7 @@ + current = ptr + (number - 1); + for (i=0; i < number; i++) + { +- printf("constructor called\n"); ++ //printf("constructor called\n"); + current->name = (char *) malloc(MAXNAMLEN * sizeof(char)); + current->resource = (char *) malloc(MAXNAMLEN * sizeof(char)); + current->value = (char *) malloc(MAXNAMLEN * sizeof(char)); +@@ -3059,7 +3059,7 @@ + current = ptr + (number - 1); + for (i=0; i < number; i++) + { +- printf("constructor called\n"); ++ //printf("constructor called\n"); + current->name = (char *) malloc(MAXNAMLEN * sizeof(char)); + current->resource = (char *) malloc(MAXNAMLEN * sizeof(char)); + current->value = (char *) malloc(MAXNAMLEN * sizeof(char)); diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-1.9.6-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/phonopy/phonopy-1.9.6-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..3007b29a1b80763b0f9c89a4c7952c4143718dcb --- /dev/null +++ b/easybuild/easyconfigs/p/phonopy/phonopy-1.9.6-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'phonopy' +version = '1.9.6' + +homepage = 'http://phonopy.sourceforge.net/' +description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.10' +pythonshortversion = '.'.join(pythonversion.split('.')[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.4.3', versionsuffix), + ('lxml', '3.4.4', versionsuffix), + ('PyYAML', '3.11', versionsuffix), +] + +pylibdir = "lib/python%s/site-packages/%%(name)s" % pythonshortversion + +sanity_check_paths = { + 'files': [], + 'dirs': [('%s-%%(version)s-py%s.egg' % (pylibdir, pythonshortversion), pylibdir)], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-1.9.6.2-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/p/phonopy/phonopy-1.9.6.2-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..47381e3887609b329e2788740cb6fe974630815c --- /dev/null +++ b/easybuild/easyconfigs/p/phonopy/phonopy-1.9.6.2-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'phonopy' +version = '1.9.6.2' + +homepage = 'http://phonopy.sourceforge.net/' +description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.10' +pythonshortversion = '.'.join(pythonversion.split('.')[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.4.3', versionsuffix), + ('lxml', '3.4.4', versionsuffix), + ('PyYAML', '3.11', versionsuffix), +] + +pylibdir = "lib/python%s/site-packages/%%(name)s" % pythonshortversion + +sanity_check_paths = { + 'files': [], + 'dirs': [('%s-%%(version)s-py%s.egg' % (pylibdir, pythonshortversion), pylibdir)], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/picard/picard-1.109.eb b/easybuild/easyconfigs/p/picard/picard-1.109.eb new file mode 100644 index 0000000000000000000000000000000000000000..b02c4dfde3bc59612325564d3d90cc1b3e535b8e --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-1.109.eb @@ -0,0 +1,14 @@ +name = 'picard' +version = '1.109' + +homepage = 'http://sourceforge.net/projects/picard' +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 = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-tools-%(version)s.zip'] + +dependencies = [('Java', '1.7.0_10')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/picard/picard-1.119-Java-1.7.0_80.eb b/easybuild/easyconfigs/p/picard/picard-1.119-Java-1.7.0_80.eb new file mode 100644 index 0000000000000000000000000000000000000000..a097dca76dd5c335938654a8e6ee894f0a17b74a --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-1.119-Java-1.7.0_80.eb @@ -0,0 +1,17 @@ +name = 'picard' +version = '1.119' + +homepage = 'http://sourceforge.net/projects/picard' +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 = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-tools-%(version)s.zip'] + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.32.6-goolf-1.7.20.eb b/easybuild/easyconfigs/p/pixman/pixman-0.32.6-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..9a915bad5f07f1c75fafd779994dd2c1d9efaacf --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.32.6-goolf-1.7.20.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.32.6' + +homepage = 'http://www.pixman.org/' +description = """Pixman is a low-level software library for pixel manipulation, providing features such as image +compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.so'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.32.6-intel-2015a.eb b/easybuild/easyconfigs/p/pixman/pixman-0.32.6-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..480001289ad988385e94f2c6319de9908c524083 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.32.6-intel-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.32.6' + +homepage = 'http://www.pixman.org/' +description = """Pixman is a low-level software library for pixel manipulation, providing features such as image +compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.so'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-intel-2015a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f5981f1368671b6e0497edaafb918579f99a93da --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-intel-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.28' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +# don't use PAX, it might break. +tar_config_opts = True + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-2.6.1.eb b/easybuild/easyconfigs/p/protobuf/protobuf-2.6.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..e0cb785e1fddaf3a2cb3ffa393925fa68c35c700 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-2.6.1.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'protobuf' +version = '2.6.1' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/google/protobuf/releases/download/v%(version)s/'] + +sanity_check_paths = { + 'files': ['bin/protoc'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pycosat/pycosat-0.6.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/p/pycosat/pycosat-0.6.0-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..0dcfa43ff4743a18d49fab5c1f8ea43de93b1a93 --- /dev/null +++ b/easybuild/easyconfigs/p/pycosat/pycosat-0.6.0-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'pycosat' +version = '0.6.0' + +homepage = 'https://pypi.python.org/pypi/pycosat' +description = """pycosat provides efficient Python bindings to picosat on the C level, i.e. when importing pycosat, + the picosat solver becomes part of the Python process itself.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/pycosat.so' % pyshortver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.3rc2-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.3rc2-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..1804c2f2a8ed17a9ebef5b67d03f69da5aa25099 --- /dev/null +++ b/easybuild/easyconfigs/p/pygraphviz/pygraphviz-1.3rc2-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'pygraphviz' +version = '1.3rc2' + +homepage = 'https://pypi.python.org/pypi/pycosat' +description = """pycosat provides efficient Python bindings to picosat on the C level, i.e. when importing pycosat, + the picosat solver becomes part of the Python process itself.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('Graphviz', '2.38.0', versionsuffix), +] + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/pygraphviz' % pyshortver], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..27ca7fc128c87d64d772124c23f496c83b48b0d2 --- /dev/null +++ b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'pysqlite' +version = '2.6.3' + +homepage = 'https://pypi.python.org/pypi/pysqlite' +description = """pysqlite is an interface to the SQLite 3.x embedded relational database engine. + It is almost fully compliant with the Python database API version 2.0 also exposes the unique features of SQLite.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SQLite', '3.8.8.1'), # also dependency for Python itself +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s%%(version_major)s' % pyshortver], +} + +options = {'modulename': '%(name)s%(version_major)s'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb index dd5a337d1f1e054a3faf4b11e511b2f3e95fc4c4..625317ad022b5ae257eea45986813818f1ee4ba7 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb @@ -15,12 +15,15 @@ toolchain = {'name': 'ictce', 'version': '7.1.2'} sources = ['%(namelower)s-%(version)s-src.tgz'] source_urls = ['http://www.qhull.org/download/'] -patches = ['Qhull-2012.1-intel-fix.patch'] +patches = [ + 'Qhull-2012.1-intel-fix.patch', + 'Qhull_pkgconfig.patch', +] builddependencies = [('CMake', '2.8.12')] sanity_check_paths = { - 'files': ['bin/qhull', 'lib/libqhull.so'], + 'files': ['bin/qhull', 'lib/libqhull.so', 'lib/pkgconfig/qhull.pc'], 'dirs': [], } diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb index 188d2a929cf42ff1542fdc71ba7cda856d2d4797..617a67c44d822dcbaf051b343a83b26b5c14e888 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb @@ -15,12 +15,15 @@ toolchain = {'name': 'intel', 'version': '2014b'} sources = ['%(namelower)s-%(version)s-src.tgz'] source_urls = ['http://www.qhull.org/download/'] -patches = ['Qhull-2012.1-intel-fix.patch'] +patches = [ + 'Qhull-2012.1-intel-fix.patch', + 'Qhull_pkgconfig.patch', +] builddependencies = [('CMake', '2.8.12')] sanity_check_paths = { - 'files': ['bin/qhull', 'lib/libqhull.so'], + 'files': ['bin/qhull', 'lib/libqhull.so', 'lib/pkgconfig/qhull.pc'], 'dirs': [], } diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb index d32af2c6540224508acf563247fcfea61264f422..1488f628fe22f7f0fcab3b1a6e1607a6eaa497a2 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb @@ -15,12 +15,15 @@ toolchain = {'name': 'intel', 'version': '2015a'} sources = ['%(namelower)s-%(version)s-src.tgz'] source_urls = ['http://www.qhull.org/download/'] -patches = ['Qhull-2012.1-intel-fix.patch'] +patches = [ + 'Qhull-2012.1-intel-fix.patch', + 'Qhull_pkgconfig.patch', +] builddependencies = [('CMake', '3.2.1', '', ('GCC', '4.9.2'))] sanity_check_paths = { - 'files': ['bin/qhull', 'lib/libqhull.so'], + 'files': ['bin/qhull', 'lib/libqhull.so', 'lib/pkgconfig/qhull.pc'], 'dirs': [], } diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..8544695ac424bffdea87d314db759609d270c708 --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015b.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2012.1' + +homepage = 'http://www.qhull.org' +description = """ +Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, +furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, +and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. +""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = ['%(namelower)s-%(version)s-src.tgz'] +source_urls = ['http://www.qhull.org/download/'] + +patches = [ + 'Qhull-2012.1-intel-fix.patch', + 'Qhull_pkgconfig.patch', +] + +builddependencies = [('CMake', '3.2.1', '', ('GNU', '4.9.3-2.25'))] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull.so', 'lib/pkgconfig/qhull.pc'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch b/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch new file mode 100644 index 0000000000000000000000000000000000000000..53f43a015db96fdf837b574ffa698248ce8fe6d4 --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull_pkgconfig.patch @@ -0,0 +1,29 @@ +inspired by qhull-2003.1-pkgconfig.patch, available from git://pkgs.fedoraproject.org/qhull +requires making CMake to fill in the gaps via 'configure_file(... @ONLY)' +author: Kenneth Hoste (UGent) +--- qhull/CMakeLists.txt.orig 2015-09-21 15:27:38.424110227 +0200 ++++ qhull/CMakeLists.txt 2015-09-21 15:27:06.403494984 +0200 +@@ -430,3 +430,9 @@ + install(FILES html/rbox.man DESTINATION ${MAN_INSTALL_DIR} RENAME rbox.1) + install(FILES ${doc_FILES} DESTINATION ${DOC_INSTALL_DIR}) + install(DIRECTORY html/ DESTINATION ${DOC_INSTALL_DIR}) ++ ++CONFIGURE_FILE( ++ "${CMAKE_CURRENT_SOURCE_DIR}/qhull.pc.in" ++ "${CMAKE_CURRENT_BINARY_DIR}/qhull.pc" ++) ++INSTALL(FILES "${CMAKE_BINARY_DIR}/qhull.pc" DESTINATION lib/pkgconfig) +--- qhull/qhull.pc.in 1970-01-01 01:00:00.000000000 +0100 ++++ qhull/qhull.pc.in 2012-07-08 08:04:07.795336862 +0200 +@@ -0,0 +1,11 @@ ++prefix=@CMAKE_INSTALL_PREFIX@ ++exec_prefix=${prefix} ++includedir=${prefix}/include ++libdir=${prefix}/lib ++ ++Name: qhull ++Description: General dimension convex hull library ++Version: @qhull_VERSION2@ ++Requires: ++Libs: -L${libdir} -lqhull -lm ++Cflags: -I${includedir} diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb index feb10d4a75d6bb0dda9c1a6efdb1c0ca87c60835..b6405c19b67e256ca1ed16ae9201f9bb2ba07531 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb index e8472dac116c8b9a467210f1980b37d0f16f03c5..54ce3a579116ca6d7177630df94edcc586269834 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb index c489c5aa682dc189801d00ca78badd7605f47344..7ff79c377b5198a587e9dc201c0e58d95c22a62a 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..f353838078f048fb559a78b277cef22c148d331c --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb @@ -0,0 +1,17 @@ +name = 'Qt' +version = '4.8.4' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +dependencies = [('GLib', '2.34.3')] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb index 4a7a10534b010eb44940b5c9b222ccc771571d71..327564fbd37590ead581dacbcb8d8ae43e6b4c91 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb @@ -1,15 +1,15 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'lowopt': True} # use -O1 source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb index a411477c0b4a84ffa9789a5b47ee2c5ea1822563..1bfd983e7ea37100374862fce292afac457e637c 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb index 3c0ae0a9af0e5c4e53a5345aa2721d80a94d6b7c..3644b946c0012a29bf16e5db620a715058efb1bd 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb index 7569a7cd7bfeabf0f8b1b45e509cd00ac2b78270..6abe0d811d8c00c835f93de23f247811415d9769 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.5' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'gmpolf', 'version': '1.4.8'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb index d39e90c9e46e3001311fb5366759aca6da0491b0..7bcfcdfee8aa4c73f770b512c2d457e0df2a0369 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb @@ -1,12 +1,15 @@ name = 'Qt' version = '4.8.5' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goolf', 'version': '1.5.14'} -source_urls = ['http://download.qt-project.org/official_releases/qt/4.8/4.8.5/'] +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] dependencies = [('GLib', '2.34.3')] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb index 312d6b1990967b49de842fb1ab05f316e7b8cd8f..bfd0e1cd2f9a992b5073639f0fd9bf63b809d3ea 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.5' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a-GLib-2.44.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a-GLib-2.44.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..38321434760d58c3dc92925e0b42cf7c9574248a --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a-GLib-2.44.0.eb @@ -0,0 +1,21 @@ +name = 'Qt' +version = '4.8.6' + +homepage = 'http://qt-project.org/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [ + 'http://origin.releases.qt-project.org/qt4/source/', + 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +glib = 'GLib' +glibver = '2.44.0' +versionsuffix = "-%s-%s" % (glib, glibver) + +dependencies = [(glib, glibver)] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0bfab5d015d1905fb336ac9a6d5af9dba426fb6a --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb @@ -0,0 +1,17 @@ +name = 'Qt' +version = '4.8.6' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +dependencies = [('GLib', '2.42.1')] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-goolf-1.5.14.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-goolf-1.5.14.eb index 6435694c00b4b278b079abc8dfe17f99b1088b54..a829af981d63808ed2586e5de22dc5a824b9ee63 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-goolf-1.5.14.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.6' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goolf', 'version': '1.5.14'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb index 1c0c56d935b9a88c00e6de0793f06c3de8ade6d9..61b425c25a0f0433ee83b57b89f57e8a0f21dd17 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.6' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'intel', 'version': '2014b'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a-GLib-2.44.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a-GLib-2.44.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..3c920b2a404f44e2c3e3f0ed878c5cd8521e1ecc --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a-GLib-2.44.0.eb @@ -0,0 +1,23 @@ +name = 'Qt' +version = '4.8.6' + +homepage = 'http://qt-project.org/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'http://origin.releases.qt-project.org/qt4/source/', + 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +patches = ['Qt-4.8.6_icc-qUnused.patch'] + +glib = 'GLib' +glibver = '2.44.0' +versionsuffix = "-%s-%s" % (glib, glibver) + +dependencies = [(glib, glibver)] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a-GLib-2.44.1.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a-GLib-2.44.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..ba0734aff4e3622b19cbcdea7a4d8b9956c83e9d --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a-GLib-2.44.1.eb @@ -0,0 +1,28 @@ +name = 'Qt' +version = '4.8.6' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [ + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' +] +sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] + +patches = [ + 'Qt-%(version)s_icc-qUnused.patch', + 'Qt-%(version)s_phonon-export.patch', +] + +glib = 'GLib' +glibver = '2.44.1' +versionsuffix = '-%s-%s' % (glib, glibver) + +dependencies = [ + (glib, glibver), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb index aa253ef5eb61b7029bee2827281a37e20c4ec584..1ab132124a8bd7aea8a1cb8ad1d8504745434a20 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb @@ -1,18 +1,21 @@ name = 'Qt' version = '4.8.6' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'intel', 'version': '2015a'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + 'http://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/', + 'http://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/' ] sources = ['%(namelower)s-everywhere-opensource-src-%(version)s.tar.gz'] -patches = ['Qt-4.8.6_icc-qUnused.patch'] +patches = [ + 'Qt-%(version)s_icc-qUnused.patch', + 'Qt-%(version)s_phonon-export.patch', +] dependencies = [('GLib', '2.40.0')] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6_phonon-export.patch b/easybuild/easyconfigs/q/Qt/Qt-4.8.6_phonon-export.patch new file mode 100644 index 0000000000000000000000000000000000000000..4170411ac114fdf21b10742f9aa496b493a89172 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6_phonon-export.patch @@ -0,0 +1,15 @@ +fixed for error "undefined reference to `vtable for Phonon::ObjectDescriptionModel<(Phonon::ObjectDescriptionType)0>'" +that occurs (only) on some systems (e.g. RHEL6/Sandy Bridge) +based on https://forum.qt.io/topic/35044/build-failure-4-8-5-on-mac-with-phonon/9 +author: Kenneth Hoste (HPC-UGent) +--- qt-everywhere-opensource-src-4.8.6/src/3rdparty/phonon/phonon/objectdescriptionmodel.h.orig 2015-06-22 23:18:54.723573581 +0300 ++++ qt-everywhere-opensource-src-4.8.6/src/3rdparty/phonon/phonon/objectdescriptionmodel.h 2015-06-22 23:19:16.902399019 +0300 +@@ -141,7 +141,7 @@ + + /* Required to ensure template class vtables are exported on both symbian + and existing builds. */ +-#if (defined(Q_OS_SYMBIAN) && defined(Q_CC_RVCT)) || defined(Q_CC_CLANG) ++#if (defined(Q_OS_SYMBIAN) && defined(Q_CC_RVCT)) || defined(Q_CC_CLANG) || defined(Q_CC_INTEL) + // RVCT compiler (2.2.686) requires the export declaration to be on the class to export vtables + // MWC compiler works both ways + // GCCE compiler is unknown (it can't compile QtCore yet) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb index 9409f95fc206cd19a6e196e4177f62b5e4d9200b..d000d6ec7f80957c94aa1346e31e5480b3f1790d 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz - 'http://files.qe-forge.org/index.php?file=', # others ] patches = ['yambo-3.2.5_fix-objects-files.patch'] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb index 4a03ccc94bd4e3b3aaff407cb3c90d8d7e7e0949..a34afc570a3cbd1764e03b523fae1b6489b3b583 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz - 'http://files.qe-forge.org/index.php?file=', # others ] patches = ['yambo-3.2.5_fix-objects-files.patch'] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb index d97dae5c5d8dd5c07024fde7d92ab102129c0b7d..5ef2e6d1b1259e0ff9d2cfaef8185595504f11b2 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz - 'http://files.qe-forge.org/index.php?file=', # others ] patches = ['yambo-3.2.5_fix-objects-files.patch'] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb index d7fb61f42cb35e3be57acdace48cca8609ec54ab..1e036026dae443c9e666fc69773b46cde049838a 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz - 'http://files.qe-forge.org/index.php?file=', # others ] patches = ['yambo-3.2.5_fix-objects-files.patch'] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb index 04f547b28a8e665ed375dcd49da27afa4509a9c4..464f26364720517fb45c03ef4514efdb3d95a354 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz - 'http://files.qe-forge.org/index.php?file=', # others ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb index 479e526fb358b8c079887fe5c8316cf5665d683b..cd0fac60cb1d3a870bf4f02d2a78eb9108afdcfd 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz - 'http://files.qe-forge.org/index.php?file=', # others ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb index 1b9a405ed89847f871fa0c890342dc25af73533c..9533b73dfd3f2bae3abb7e33f8d6eb663cbd2a9e 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz - 'http://files.qe-forge.org/index.php?file=', # others ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb index 5740815aa1c84140baf6e0da8cfaf4a064d38aff..b3212736f0f818b3149ac2340a4fd42cfab244e4 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz - 'http://files.qe-forge.org/index.php?file=', # others ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb index bf87cf39af9adacab29cce8aa61d4f3cd13ccf63..ae347ad0bd17c206cd887e1aa73880c5f050de2e 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz - 'http://files.qe-forge.org/index.php?file=', # others ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb index a341ebad381bd60aae7be259ee6334a7407eda82..2a054ef2d33c93919abe85746ea69a0c1753280f 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz - 'http://files.qe-forge.org/index.php?file=', # others ] patches = [ diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..b172ff01378a04a83d2706c32bb475ee750f3433 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -0,0 +1,145 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.1' +rver = '3.2.0' +versionsuffix = '-R-%s' % rver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [('R', rver)] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +exts_list = [ + ('BiocGenerics', '0.14.0', bioconductor_options), + ('Biobase', '2.28.0', bioconductor_options), + ('S4Vectors', '0.6.3', bioconductor_options), + ('IRanges', '2.2.7', bioconductor_options), + ('GenomeInfoDb', '1.4.2', bioconductor_options), + ('AnnotationDbi', '1.30.1', bioconductor_options), + ('XVector', '0.8.0', bioconductor_options), + ('zlibbioc', '1.14.0', bioconductor_options), + ('Biostrings', '2.36.4', bioconductor_options), + ('GenomicRanges', '1.20.5', bioconductor_options), + ('Rsamtools', '1.20.4', bioconductor_options), + ('lambda.r', '1.1.7', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.1', ext_options), + ('BiocParallel', '1.2.20', bioconductor_options), + ('GenomicAlignments', '1.4.1', bioconductor_options), + ('ShortRead', '1.26.0', bioconductor_options), + ('graph', '1.46.0', bioconductor_options), + ('affyio', '1.36.0', bioconductor_options), + ('BiocInstaller', '1.18.4', bioconductor_options), + ('preprocessCore', '1.30.0', bioconductor_options), + ('affy', '1.46.1', bioconductor_options), + ('GO.db', '3.1.2', bioconductor_options), + ('limma', '3.24.15', bioconductor_options), + ('RBGL', '1.44.0', bioconductor_options), + ('org.Hs.eg.db', '3.1.2', bioconductor_options), + ('AnnotationForge', '1.10.1', bioconductor_options), + ('KEGG.db', '3.1.2', bioconductor_options), + ('annaffy', '1.40.0', bioconductor_options), + ('gcrma', '2.40.0', bioconductor_options), + ('oligoClasses', '1.30.0', bioconductor_options), + ('edgeR', '3.10.2', bioconductor_options), + ('PFAM.db', '3.1.2', bioconductor_options), + ('perm', '1.0-0.0', ext_options), + ('baySeq', '2.2.0', bioconductor_options), + ('qvalue', '2.0.0', bioconductor_options), + ('impute', '1.42.0', bioconductor_options), + ('samr', '2.0', ext_options), + ('DEGseq', '1.22.0', bioconductor_options), + ('hgu133plus2.db', '3.1.3', bioconductor_options), + ('illuminaio', '0.10.0', bioconductor_options), + ('rtracklayer', '1.28.9', bioconductor_options), + ('biomaRt', '2.24.0', bioconductor_options), + ('GenomicFeatures', '1.20.3', bioconductor_options), + ('bumphunter', '1.8.0', bioconductor_options), + ('multtest', '2.24.0', bioconductor_options), + ('siggenes', '1.42.0', bioconductor_options), + ('DynDoc', '1.46.0', bioconductor_options), + ('genoset', '1.22.0', bioconductor_options), + ('NOISeq', '2.14.0', bioconductor_options), + ('Rgraphviz', '2.12.0', bioconductor_options), + ('RNASeqPower', '1.8.0', bioconductor_options), + ('annotate', '1.46.1', bioconductor_options), + ('GSEABase', '1.30.2', bioconductor_options), + ('genefilter', '1.50.0', bioconductor_options), + ('Category', '2.34.2', bioconductor_options), + ('GOstats', '2.34.0', bioconductor_options), + ('BSgenome', '1.36.3', bioconductor_options), + ('VariantAnnotation', '1.14.11', bioconductor_options), + ('biovizBase', '1.16.0', bioconductor_options), + ('OrganismDbi', '1.10.0', bioconductor_options), + ('ggbio', '1.16.1', bioconductor_options), + ('geneplotter', '1.46.0', bioconductor_options), + ('DESeq2', '1.8.1', bioconductor_options), + ('ReportingTools', '2.8.0', bioconductor_options), + ('affycoretools', '1.40.5', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.1.2', bioconductor_options), + ('Homo.sapiens', '1.1.2', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), + ('AgiMicroRna', '2.18.0', bioconductor_options), + ('GenomeGraphs', '1.28.0', bioconductor_options), + ('geneLenDataBase', '1.4.0', bioconductor_options), + ('goseq', '1.20.0', bioconductor_options), + ('KEGGREST', '1.8.0', bioconductor_options), + ('KEGGgraph', '1.26.0', bioconductor_options), + ('KEGGprofile', '1.10.0', bioconductor_options), + ('GEOquery', '2.34.0', bioconductor_options), + ('minfi', '1.14.0', bioconductor_options), + ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options), + ('methylumi', '2.14.0', bioconductor_options), + ('lumi', '2.20.2', bioconductor_options), + ('widgetTools', '1.46.0', bioconductor_options), + ('tkWidgets', '1.46.0', bioconductor_options), + ('Mfuzz', '2.28.0', bioconductor_options), + ('maSigPro', '1.40.0', bioconductor_options), + ('SPIA', '2.20.0', bioconductor_options), + ('Gviz', '1.12.1', bioconductor_options), + ('cummeRbund', '2.10.0', bioconductor_options), + ('GenomicFiles', '1.4.0', bioconductor_options), + ('derfinderHelper', '1.2.0', bioconductor_options), + ('derfinder', '1.2.1', bioconductor_options), + ('polyester', '1.4.0', bioconductor_options), + ('Rsubread', '1.18.0', bioconductor_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..8c43cb0960d428b83d3692bdacfa8715b35aa779 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -0,0 +1,145 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.1' +rver = '3.2.1' +versionsuffix = '-R-%s' % rver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [('R', rver)] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +exts_list = [ + ('BiocGenerics', '0.14.0', bioconductor_options), + ('Biobase', '2.28.0', bioconductor_options), + ('S4Vectors', '0.6.3', bioconductor_options), + ('IRanges', '2.2.7', bioconductor_options), + ('GenomeInfoDb', '1.4.2', bioconductor_options), + ('AnnotationDbi', '1.30.1', bioconductor_options), + ('XVector', '0.8.0', bioconductor_options), + ('zlibbioc', '1.14.0', bioconductor_options), + ('Biostrings', '2.36.4', bioconductor_options), + ('GenomicRanges', '1.20.5', bioconductor_options), + ('Rsamtools', '1.20.4', bioconductor_options), + ('lambda.r', '1.1.7', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.1', ext_options), + ('BiocParallel', '1.2.20', bioconductor_options), + ('GenomicAlignments', '1.4.1', bioconductor_options), + ('ShortRead', '1.26.0', bioconductor_options), + ('graph', '1.46.0', bioconductor_options), + ('affyio', '1.36.0', bioconductor_options), + ('BiocInstaller', '1.18.4', bioconductor_options), + ('preprocessCore', '1.30.0', bioconductor_options), + ('affy', '1.46.1', bioconductor_options), + ('GO.db', '3.1.2', bioconductor_options), + ('limma', '3.24.15', bioconductor_options), + ('RBGL', '1.44.0', bioconductor_options), + ('org.Hs.eg.db', '3.1.2', bioconductor_options), + ('AnnotationForge', '1.10.1', bioconductor_options), + ('KEGG.db', '3.1.2', bioconductor_options), + ('annaffy', '1.40.0', bioconductor_options), + ('gcrma', '2.40.0', bioconductor_options), + ('oligoClasses', '1.30.0', bioconductor_options), + ('edgeR', '3.10.2', bioconductor_options), + ('PFAM.db', '3.1.2', bioconductor_options), + ('perm', '1.0-0.0', ext_options), + ('baySeq', '2.2.0', bioconductor_options), + ('qvalue', '2.0.0', bioconductor_options), + ('impute', '1.42.0', bioconductor_options), + ('samr', '2.0', ext_options), + ('DEGseq', '1.22.0', bioconductor_options), + ('hgu133plus2.db', '3.1.3', bioconductor_options), + ('illuminaio', '0.10.0', bioconductor_options), + ('rtracklayer', '1.28.9', bioconductor_options), + ('biomaRt', '2.24.0', bioconductor_options), + ('GenomicFeatures', '1.20.3', bioconductor_options), + ('bumphunter', '1.8.0', bioconductor_options), + ('multtest', '2.24.0', bioconductor_options), + ('siggenes', '1.42.0', bioconductor_options), + ('DynDoc', '1.46.0', bioconductor_options), + ('genoset', '1.22.0', bioconductor_options), + ('NOISeq', '2.14.0', bioconductor_options), + ('Rgraphviz', '2.12.0', bioconductor_options), + ('RNASeqPower', '1.8.0', bioconductor_options), + ('annotate', '1.46.1', bioconductor_options), + ('GSEABase', '1.30.2', bioconductor_options), + ('genefilter', '1.50.0', bioconductor_options), + ('Category', '2.34.2', bioconductor_options), + ('GOstats', '2.34.0', bioconductor_options), + ('BSgenome', '1.36.3', bioconductor_options), + ('VariantAnnotation', '1.14.11', bioconductor_options), + ('biovizBase', '1.16.0', bioconductor_options), + ('OrganismDbi', '1.10.0', bioconductor_options), + ('ggbio', '1.16.1', bioconductor_options), + ('geneplotter', '1.46.0', bioconductor_options), + ('DESeq2', '1.8.1', bioconductor_options), + ('ReportingTools', '2.8.0', bioconductor_options), + ('affycoretools', '1.40.5', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.1.2', bioconductor_options), + ('Homo.sapiens', '1.1.2', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), + ('AgiMicroRna', '2.18.0', bioconductor_options), + ('GenomeGraphs', '1.28.0', bioconductor_options), + ('geneLenDataBase', '1.4.0', bioconductor_options), + ('goseq', '1.20.0', bioconductor_options), + ('KEGGREST', '1.8.0', bioconductor_options), + ('KEGGgraph', '1.26.0', bioconductor_options), + ('KEGGprofile', '1.10.0', bioconductor_options), + ('GEOquery', '2.34.0', bioconductor_options), + ('minfi', '1.14.0', bioconductor_options), + ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options), + ('methylumi', '2.14.0', bioconductor_options), + ('lumi', '2.20.2', bioconductor_options), + ('widgetTools', '1.46.0', bioconductor_options), + ('tkWidgets', '1.46.0', bioconductor_options), + ('Mfuzz', '2.28.0', bioconductor_options), + ('maSigPro', '1.40.0', bioconductor_options), + ('SPIA', '2.20.0', bioconductor_options), + ('Gviz', '1.12.1', bioconductor_options), + ('cummeRbund', '2.10.0', bioconductor_options), + ('GenomicFiles', '1.4.0', bioconductor_options), + ('derfinderHelper', '1.2.0', bioconductor_options), + ('derfinder', '1.2.1', bioconductor_options), + ('polyester', '1.4.0', bioconductor_options), + ('Rsubread', '1.18.0', bioconductor_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..aa48ed3b8142fba4c91dd7a6b160279657cd6de6 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb @@ -0,0 +1,49 @@ +easyblock = 'Bundle' + +name = 'R-bundle-devtools' +version = '20150520' +rver = '3.1.3' +versionsuffix = '-R-%s' % rver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [ + ('R', rver), + ('R-bundle-extra', '20150323', '-R-%s' % rver), +] + +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +# !! order of packages is important !! +exts_list = [ + ('memoise', '0.2.1', ext_options), + ('whisker', '0.3-2', ext_options), + ('rstudioapi', '0.3.1', ext_options), + ('roxygen2', '4.1.1', ext_options), + ('git2r', '0.10.1', ext_options), + ('rversions', '1.0.0', ext_options), + ('devtools', '1.8.0', ext_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['devtools'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..1bde4e9f5d00a790d810f00df655a78076d4c28e --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb @@ -0,0 +1,100 @@ +easyblock = 'Bundle' + +name = 'R-bundle-extra' +version = '20150323' +rver = '3.1.3' +versionsuffix = '-R-%s' % rver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [ + ('R', rver), + ('cURL', '7.41.0'), + ('libxml2', '2.9.2'), +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} +# Bioconductor packages have a different download url +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +exts_list = [ + ('RCurl', '1.95-4.5', ext_options), # requires cURL + ('XML', '3.98-1.1', ext_options), # requires libxml2 + # extensions below require one or more extensions that have an external dependency listed above + ('picante', '1.6-2', ext_options), + ('spacodiR', '0.13.0115', ext_options), + ('picante', '1.6-2', ext_options), + ('httr', '0.6.1', ext_options), + ('tkWidgets', '1.44.0', bioconductor_options), + ('Mfuzz', '2.26.0', bioconductor_options), + ('maSigPro', '1.38.0', bioconductor_options), + ('rtracklayer', '1.26.3', bioconductor_options), + ('BSgenome', '1.34.1', bioconductor_options), + ('GEOquery', '2.32.0', bioconductor_options), + ('biomaRt', '2.22.0', bioconductor_options), + ('annotate', '1.44.0', bioconductor_options), + ('GSEABase', '1.28.0', bioconductor_options), + ('genefilter', '1.48.1', bioconductor_options), + ('Category', '2.32.0', bioconductor_options), + ('GOstats', '2.32.0', bioconductor_options), + ('geneplotter', '1.44.0', bioconductor_options), + ('DESeq2', '1.6.3', bioconductor_options), + ('GenomicFeatures', '1.18.7', bioconductor_options), + ('VariantAnnotation', '1.12.9', bioconductor_options), + ('biovizBase', '1.14.1', bioconductor_options), + ('OrganismDbi', '1.8.1', bioconductor_options), + ('ggbio', '1.14.0', bioconductor_options), + ('ReportingTools', '2.6.0', bioconductor_options), + ('affycoretools', '1.38.0', bioconductor_options), + ('AgiMicroRna', '2.16.0', bioconductor_options), + ('DESeq', '1.18.0', bioconductor_options), + ('GenomeGraphs', '1.26.0', bioconductor_options), + ('geneLenDataBase', '1.1.1', bioconductor_options), + ('goseq', '1.18.0', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.0.0', bioconductor_options), + ('Homo.sapiens', '1.1.2', bioconductor_options), + ('KEGGgraph', '1.24.0', bioconductor_options), + ('KEGGREST', '1.6.4', bioconductor_options), + ('KEGGprofile', '1.8.2', bioconductor_options), + ('minfi', '1.12.0', bioconductor_options), + ('methylumi', '2.12.0', bioconductor_options), + ('lumi', '2.18.0', bioconductor_options), + ('Gviz', '1.10.11', bioconductor_options), + ('methyAnalysis', '1.8.0', bioconductor_options), + ('pathview', '1.6.0', bioconductor_options), + ('SPIA', '2.18.0', bioconductor_options), + ('cummeRbund', '2.8.2', bioconductor_options), + ('spliceR', '1.8.0', bioconductor_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['RCurl', 'XML', 'spliceR'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..dd2dee5fb47b0b515cc7cff2c35bd95bfdffbd0c --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb @@ -0,0 +1,49 @@ +easyblock = 'Bundle' + +name = 'R-bundle-pbd' +version = '20150605' +rver = '3.1.3' +versionsuffix = '-R-%s' % rver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [ + ('R', rver), +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +exts_list = [ + ('pbdMPI', '0.2-5', ext_options), + ('pbdSLAP', '0.2-0', ext_options), + ('pbdBASE', '0.2-3', dict(ext_options.items() + [('patches', ['pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch'])])), + ('pbdDMAT', '0.2-3', ext_options), + ('pbdDEMO', '0.2-0', ext_options), + ('pmclust', '0.1-6', ext_options), + ('EMCluster', '0.2-4', ext_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['EMCluster', 'pbdBASE', 'pbdDEMO', 'pbdDMAT', 'pbdMPI', 'pbdSLAP', 'pmclust'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R-bundle-pbd/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch b/easybuild/easyconfigs/r/R-bundle-pbd/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch new file mode 100644 index 0000000000000000000000000000000000000000..34eaf4da137f5c6683481e276bfdfb569dd2d5f8 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-pbd/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch @@ -0,0 +1,45 @@ +# Add support for intel mpi by removing references to BI_COMM_WORLD +# BI_COMM_WORLD just appears to shadow MPI_COMM_WORLD. +--- pbdBASE.orig/src/export_blacs/pkg_tools.c 2015-06-02 15:25:57.705288000 +0200 ++++ pbdBASE/src/export_blacs/pkg_tools.c 2015-06-02 15:25:29.470539000 +0200 +@@ -25,7 +25,9 @@ + BLACS_APTS.BI_AuxBuff = &BI_AuxBuff; + BLACS_APTS.BI_MyContxts = BI_MyContxts; + BLACS_APTS.BI_SysContxts = BI_SysContxts; ++#ifndef __INTEL_COMPILER + BLACS_APTS.BI_COMM_WORLD = BI_COMM_WORLD; ++#endif + BLACS_APTS.BI_Stats = BI_Stats; + + #if (BLACS_APTS_DEBUG & 1) == 1 +@@ -44,7 +46,9 @@ + BI_AuxBuff.nAops, BI_AuxBuff.N); + REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, + &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); ++#ifndef __INTEL_COMPILER + REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, ++#endif + BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); + REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, + BI_Stats); +@@ -89,7 +93,9 @@ + + BI_MyContxts = (BLACSCONTEXT**) BLACS_APTS_ptr->BI_MyContxts; + BI_SysContxts = (MPI_Comm*) BLACS_APTS_ptr->BI_SysContxts; ++#ifndef __INTEL_COMPILER + BI_COMM_WORLD = (int*) BLACS_APTS_ptr->BI_COMM_WORLD; ++#endif + BI_Stats = (MPI_Status*) BLACS_APTS_ptr->BI_Stats; + + #if (BLACS_APTS_DEBUG & 1) == 1 +@@ -109,7 +115,9 @@ + REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, + &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); + REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, ++#ifndef __INTEL_COMPILER + BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); ++#endif + REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, + BI_Stats); + } + diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb index 5d7d661a1f248144cbf742d79620820b747434aa..d82c3b8db250e2ae6d88b27bc4bd1401e27cd7cd 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -47,7 +47,7 @@ bioconductor_options = { } # !! order of packages is important !! -# packages updated on January 8th 2015 +# packages updated on January 8th 2015 (last change for Bioconductor: June 25th 2015) exts_list = [ # default libraries, only here to sanity check their presence 'base', @@ -224,7 +224,7 @@ exts_list = [ ('Biobase', '2.26.0', bioconductor_options), ('S4Vectors', '0.4.0', bioconductor_options), ('IRanges', '2.0.1', bioconductor_options), - ('GenomeInfoDb', '1.2.4', bioconductor_options), + ('GenomeInfoDb', '1.2.5', bioconductor_options), ('AnnotationDbi', '1.28.2', bioconductor_options), ('XVector', '0.6.0', bioconductor_options), ('zlibbioc', '1.12.0', bioconductor_options), @@ -313,7 +313,7 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('affyio', '1.34.0', bioconductor_options), - ('BiocInstaller', '1.16.2', bioconductor_options), + ('BiocInstaller', '1.16.5', bioconductor_options), ('preprocessCore', '1.28.0', bioconductor_options), ('affy', '1.44.0', bioconductor_options), ('GO.db', '3.0.0', bioconductor_options), @@ -380,7 +380,12 @@ exts_list = [ ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), ('Rsubread', '1.16.1', bioconductor_options), + ('vegan', '2.2-1', ext_options), # requires Tcl/Tk + ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk + ('forecast', '6.1', ext_options), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), ] moduleclass = 'lang' - diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index fefd97519c25995f75b0bfc5f161050447f64412..53bd4b075109ffc77b6119b2495460fcea2e8ba0 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -47,7 +47,7 @@ bioconductor_options = { } # !! order of packages is important !! -# packages updated on January 8th 2015 +# packages updated on January 8th 2015 (last change for Bioconductor: June 25th 2015) exts_list = [ # default libraries, only here to sanity check their presence 'base', @@ -224,7 +224,7 @@ exts_list = [ ('Biobase', '2.26.0', bioconductor_options), ('S4Vectors', '0.4.0', bioconductor_options), ('IRanges', '2.0.1', bioconductor_options), - ('GenomeInfoDb', '1.2.4', bioconductor_options), + ('GenomeInfoDb', '1.2.5', bioconductor_options), ('AnnotationDbi', '1.28.2', bioconductor_options), ('XVector', '0.6.0', bioconductor_options), ('zlibbioc', '1.12.0', bioconductor_options), @@ -313,7 +313,7 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('affyio', '1.34.0', bioconductor_options), - ('BiocInstaller', '1.16.2', bioconductor_options), + ('BiocInstaller', '1.16.5', bioconductor_options), ('preprocessCore', '1.28.0', bioconductor_options), ('affy', '1.44.0', bioconductor_options), ('GO.db', '3.0.0', bioconductor_options), @@ -380,6 +380,12 @@ exts_list = [ ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), ('Rsubread', '1.16.1', bioconductor_options), + ('vegan', '2.2-1', ext_options), # requires Tcl/Tk + ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk + ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..37f178514d9137b6c8cd7cdbcd41fa96b53ad9cc --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -0,0 +1,353 @@ +name = 'R' +version = '3.2.0' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk + ('cURL', '7.43.0'), # for RCurl + ('libxml2', '2.9.2'), # for XML +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + + +# !! order of packages is important !! +# packages updated on January 8th 2015 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + # Rmpi segfaults (on some systems) when built with goolf/1.7.20? + #('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + ('abind', '1.4-3', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-5', ext_options), + ('bit', '1.1-12', ext_options), + ('filehash', '2.2-2', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '3.7.1', ext_options), + ('bootstrap', '2015.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.14', ext_options), + ('formatR', '1.2', ext_options), + ('gtools', '3.4.2', ext_options), + ('gdata', '2.13.3', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.5', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-20', ext_options), + ('mime', '0.3', ext_options), + ('markdown', '0.7.7', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-6', ext_options), + ('mclust', '5.0.1', ext_options), + ('RANN', '2.5', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.1', ext_options), + ('som', '0.3-5', ext_options), + ('SuppDists', '1.1-9.1', ext_options), + ('stabledist', '0.6-6', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-16', ext_options), + ('timeDate', '3012.100', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.7-2', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-2', ext_options), + ('BH', '1.55.0-3', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.7', ext_options), + ('longitudinal', '1.1.11', ext_options), + ('checkmate', '1.5.2', ext_options), + ('cubature', '1.1-2', ext_options), + ('DEoptimR', '1.0-2', ext_options), + ('digest', '0.6.8', ext_options), + ('fastmatch', '1.0-4', ext_options), + ('ffbase', '0.11.3', ext_options), + ('iterators', '1.0.7', ext_options), + ('maps', '2.3-9', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.0-1', ext_options), + ('subplex', '1.1-4', ext_options), + ('stringr', '0.6.2', ext_options), + ('evaluate', '0.7', ext_options), + ('logspline', '2.1.5', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.8-3', ext_options), + ('plotrix', '3.5-11', ext_options), + ('randomForest', '4.6-10', ext_options), + ('scatterplot3d', '0.3-35', ext_options), + ('SparseM', '1.6', ext_options), + ('tripack', '1.3-6', ext_options), + ('irace', '1.06', ext_options), + ('rJava', '0.9-6', ext_options), + ('lattice', '0.20-31', ext_options), + ('RColorBrewer', '1.1-2', ext_options), + ('latticeExtra', '0.6-26', ext_options), + ('Matrix', '1.2-0', ext_options), + ('png', '0.1-7', ext_options), + ('Rcpp', '0.11.5', ext_options), + ('RcppArmadillo', '0.5.000.0', ext_options), + ('plyr', '1.8.2', ext_options), + ('pROC', '1.7.3', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2014.10-1', ext_options), + ('BBmisc', '1.9', ext_options), + ('fail', '1.2', ext_options), + ('rlecuyer', '0.3-3', ext_options), + ('snow', '0.3-13', ext_options), + ('MASS', '7.3-40', ext_options), + ('tree', '1.0-35', ext_options), + ('pls', '2.4-3', ext_options), + ('class', '7.3-12', ext_options), + ('e1071', '1.6-4', ext_options), + ('nnet', '7.3-9', ext_options), + ('nlme', '3.1-120', ext_options), + ('minqa', '1.2.4', ext_options), + ('RcppEigen', '0.3.2.4.0', ext_options), + ('quantreg', '5.11', ext_options), + ('mgcv', '1.8-6', ext_options), + ('colorspace', '1.2-6', ext_options), + ('robustbase', '0.92-3', ext_options), + ('sp', '1.1-0', ext_options), + ('vcd', '1.3-2', ext_options), + ('snowfall', '1.84-6', ext_options), + ('rpart', '4.1-9', ext_options), + ('mice', '2.22', ext_options), + ('urca', '1.2-8', ext_options), + ('fracdiff', '1.4-2', ext_options), + ('logistf', '1.21', ext_options), + ('akima', '0.5-11', ext_options), + ('bitops', '1.0-6', ext_options), + ('boot', '1.3-15', ext_options), + ('mixtools', '1.0.3', ext_options), + ('cluster', '2.0.1', ext_options), + ('gclus', '1.3.1', ext_options), + ('coda', '0.17-1', ext_options), + ('codetools', '0.2-11', ext_options), + ('foreach', '1.4.2', ext_options), + ('doMC', '1.3.3', ext_options), + ('DBI', '0.3.1', ext_options), + ('foreign', '0.8-63', ext_options), + ('survival', '2.38-1', ext_options), + ('gam', '1.09.1', ext_options), + ('gamlss.data', '4.2-7', ext_options), + ('gamlss.dist', '4.3-4', ext_options), + ('hwriter', '1.3.2', ext_options), + ('KernSmooth', '2.23-14', ext_options), + ('zoo', '1.7-12', ext_options), + ('xts', '0.9-7', ext_options), + ('TTR', '0.22-0', ext_options), + ('quantmod', '0.4-4', ext_options), + ('lmtest', '0.9-33', ext_options), + ('mnormt', '1.5-2', ext_options), + ('mvtnorm', '1.0-2', ext_options), + ('pcaPP', '1.9-60', ext_options), + ('numDeriv', '2012.9-1', ext_options), + ('lava', '1.4.0', ext_options), + ('prodlim', '1.5.1', ext_options), + ('pscl', '1.4.9', ext_options), + ('RSQLite', '1.0.0', ext_options), + ('BatchJobs', '1.6', ext_options), + ('sandwich', '2.3-3', ext_options), + ('sfsmisc', '1.0-27', ext_options), + ('spatial', '7.3-9', ext_options), + ('VGAM', '0.9-7', ext_options), + ('waveslim', '1.7.5', ext_options), + ('xtable', '1.7-4', ext_options), + ('profileModel', '0.5-9', ext_options), + ('brglm', '0.5-9', ext_options), + ('deSolve', '1.11', ext_options), + ('tseriesChaos', '0.1-13', ext_options), + ('tseries', '0.10-34', ext_options), + ('fastICA', '1.2-0', ext_options), + ('R.methodsS3', '1.7.0', ext_options), + ('R.oo', '1.19.0', ext_options), + ('cgdsr', '1.1.33', ext_options), + ('R.utils', '2.0.1', ext_options), + ('R.matlab', '3.2.0', ext_options), + ('gbm', '2.1.1', ext_options), + ('dichromat', '2.0-0', ext_options), + ('Formula', '1.2-1', ext_options), + ('acepack', '1.3-3.3', ext_options), + ('reshape2', '1.4.1', ext_options), + ('gtable', '0.1.2', ext_options), + ('munsell', '0.4.2', ext_options), + ('labeling', '0.3', ext_options), + ('scales', '0.2.4', ext_options), + ('proto', '0.3-10', ext_options), + ('ggplot2', '1.0.1', ext_options), + ('Hmisc', '3.15-0', ext_options), + ('fastcluster', '1.1.16', ext_options), + ('chron', '2.3-45', ext_options), + ('data.table', '1.9.4', ext_options), + ('igraph', '0.7.1', ext_options), + ('GeneNet', '1.2.12', ext_options), + ('ape', '3.2', ext_options), + ('htmltools', '0.2.6', ext_options), + ('RJSONIO', '1.3-0', ext_options), + ('caTools', '1.17.1', ext_options), + ('gplots', '2.16.0', ext_options), + ('ROCR', '1.0-7', ext_options), + ('httpuv', '1.3.2', ext_options), + ('R6', '2.0.1', ext_options), + ('shiny', '0.11.1', ext_options), + ('adegenet', '1.4-2', ext_options), + ('phylobase', '0.6.8', ext_options), + ('adephylo', '1.1-6', ext_options), + ('animation', '2.3', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), + ('bigmemory', '4.4.6', ext_options), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.3-40', ext_options), + ('dismo', '1.0-12', ext_options), + ('expm', '0.99-1.1', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.3', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '8.2-1', ext_options), + ('shapefiles', '0.7', ext_options), + ('fossil', '0.3.7', ext_options), + ('geiger', '2.0.3', ext_options), + ('glmnet', '2.0-2', ext_options), + ('labdsv', '1.6-1', ext_options), + ('MatrixModels', '0.4-0', ext_options), + ('stabs', '0.5-1', ext_options), + ('mboost', '2.4-2', ext_options), + ('msm', '1.5', ext_options), + ('nor1mix', '1.2-0', ext_options), + ('np', '0.60-2', ext_options), + ('polynom', '1.3-8', ext_options), + ('quantreg', '5.11', ext_options), + ('polspline', '1.1.9', ext_options), + ('TH.data', '1.0-6', ext_options), + ('multcomp', '1.4-0', ext_options), + ('gridExtra', '0.9.1', ext_options), + ('rms', '4.3-0', ext_options), + ('RWekajars', '3.7.12-1', ext_options), + ('RWeka', '0.4-24', ext_options), + ('slam', '0.1-32', ext_options), + ('tm', '0.6', ext_options), + ('TraMineR', '1.8-9', ext_options), + ('chemometrics', '1.3.9', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-4', ext_options), + ('yaml', '2.1.13', ext_options), + ('knitr', '1.10', ext_options), + ('statmod', '1.4.21', ext_options), + ('miscTools', '0.6-16', ext_options), + ('maxLik', '1.2-4', ext_options), + ('mlogit', '0.2-4', ext_options), + ('getopt', '1.20.0', ext_options), + ('gsalib', '2.1', ext_options), + ('reshape', '0.8.5', ext_options), + ('optparse', '1.3.0', ext_options), + ('klaR', '0.6-12', ext_options), + ('neuRosim', '0.2-12', ext_options), + ('locfit', '1.5-9.1', ext_options), + ('GGally', '0.5.0', ext_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('matrixStats', '0.14.0', ext_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '2.9', ext_options), + ('nloptr', '1.0.4', ext_options), + ('lme4', '1.1-8', ext_options), + ('pbkrtest', '0.4-2', ext_options), + ('car', '2.0-25', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.29', ext_options), + ('modeltools', '0.2-21', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', '2.3-13', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-6', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-9', ext_options), + ('BiasedUrn', '1.06.1', ext_options), + ('TeachingDemos', '2.9', ext_options), + ('jsonlite', '0.9.16', ext_options), + ('kohonen', '2.0.18', ext_options), + ('base64', '1.1', ext_options), + ('registry', '0.2', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doRNG', '1.6', ext_options), + ('nleqslv', '2.7', ext_options), + ('RGCCA', '2.0', ext_options), + ('pheatmap', '1.0.2', ext_options), + ('openxlsx', '2.4.0', ext_options), + ('pvclust', '1.3-2', ext_options), + ('RCircos', '1.1.2', ext_options), + ('VennDiagram', '1.6.9', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('vegan', '2.3-0', ext_options), + ('forecast', '6.1', ext_options), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), + ('XML', '3.98-1.1', ext_options), + ('memoise', '0.2.1', ext_options), + ('crayon', '1.3.1', ext_options), + ('testthat', '0.10.0', ext_options), + ('rmarkdown', '0.7', ext_options), + ('curl', '0.9.1', ext_options), + ('RCurl', '1.95-4.7', ext_options), + ('httr', '0.6.1', ext_options), + ('maptools', '0.8-36', ext_options), + ('deldir', '0.1-9', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.3-0', ext_options), + ('goftest', '1.0-2', ext_options), + ('spatstat', '1.41-1', ext_options), + ('gdalUtils', '0.3.1', ext_options), + ('pracma', '1.8.3', ext_options), + ('bio3d', '2.2-2', ext_options), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb new file mode 100644 index 0000000000000000000000000000000000000000..fb021535855eab46b5739ba0527c953ab5721cc7 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb @@ -0,0 +1,29 @@ +name = 'R' +version = '3.2.0' +versionsuffix = '-bare' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk +] + +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b-bare.eb new file mode 100644 index 0000000000000000000000000000000000000000..a09dbc1a665b7c9a320823513c0a81a47a7f7588 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b-bare.eb @@ -0,0 +1,27 @@ +name = 'R' +version = '3.2.1' +versionsuffix = '-bare' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.1'), # for plottting in R + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it +] + +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..e61ba5e9a56d889cdebf5f6e3d97f2807e93839d --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.1-foss-2015b.eb @@ -0,0 +1,369 @@ +name = 'R' +version = '3.2.1' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.1'), # for plottting in R + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk + ('cURL', '7.43.0'), # for RCurl + ('libxml2', '2.9.2'), # for XML +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + + +# !! order of packages is important !! +# packages updated on January 8th 2015 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-5', ext_options), + ('abind', '1.4-3', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-5', ext_options), + ('bit', '1.1-12', ext_options), + ('filehash', '2.2-2', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '3.8.1', ext_options), + ('bootstrap', '2015.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.15', ext_options), + ('formatR', '1.2', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.5', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-20', ext_options), + ('mime', '0.3', ext_options), + ('markdown', '0.7.7', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-8', ext_options), + ('mclust', '5.0.2', ext_options), + ('RANN', '2.5', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.1', ext_options), + ('som', '0.3-5', ext_options), + ('SuppDists', '1.1-9.1', ext_options), + ('stabledist', '0.7-0', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-17', ext_options), + ('timeDate', '3012.100', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.7-2', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-2', ext_options), + ('BH', '1.58.0-1', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.8', ext_options), + ('longitudinal', '1.1.12', ext_options), + ('checkmate', '1.6.0', ext_options), + ('cubature', '1.1-2', ext_options), + ('DEoptimR', '1.0-2', ext_options), + ('digest', '0.6.8', ext_options), + ('fastmatch', '1.0-4', ext_options), + ('ffbase', '0.12.1', ext_options), + ('iterators', '1.0.7', ext_options), + ('maps', '2.3-10', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.0-1', ext_options), + ('subplex', '1.1-6', ext_options), + ('stringi', '0.5-5', ext_options), + ('magrittr', '1.5', ext_options), + ('stringr', '1.0.0', ext_options), + ('evaluate', '0.7', ext_options), + ('logspline', '2.1.8', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.8-4', ext_options), + ('plotrix', '3.5-12', ext_options), + ('randomForest', '4.6-10', ext_options), + ('scatterplot3d', '0.3-35', ext_options), + ('SparseM', '1.6', ext_options), + ('tripack', '1.3-6', ext_options), + ('irace', '1.06', ext_options), + ('rJava', '0.9-6', ext_options), + ('lattice', '0.20-31', ext_options), + ('RColorBrewer', '1.1-2', ext_options), + ('latticeExtra', '0.6-26', ext_options), + ('Matrix', '1.2-2', ext_options), + ('png', '0.1-7', ext_options), + ('Rcpp', '0.11.6', ext_options), + ('RcppArmadillo', '0.5.200.1.0', ext_options), + ('plyr', '1.8.3', ext_options), + ('pROC', '1.8', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2014.10-1', ext_options), + ('BBmisc', '1.9', ext_options), + ('fail', '1.2', ext_options), + ('rlecuyer', '0.3-3', ext_options), + ('snow', '0.3-13', ext_options), + ('MASS', '7.3-42', ext_options), + ('tree', '1.0-36', ext_options), + ('pls', '2.4-3', ext_options), + ('class', '7.3-13', ext_options), + ('e1071', '1.6-4', ext_options), + ('nnet', '7.3-10', ext_options), + ('nlme', '3.1-121', ext_options), + ('minqa', '1.2.4', ext_options), + ('RcppEigen', '0.3.2.4.0', ext_options), + ('quantreg', '5.11', ext_options), + ('mgcv', '1.8-6', ext_options), + ('colorspace', '1.2-6', ext_options), + ('robustbase', '0.92-4', ext_options), + ('sp', '1.1-1', ext_options), + ('zoo', '1.7-12', ext_options), + ('lmtest', '0.9-34', ext_options), + ('vcd', '1.4-1', ext_options), + ('snowfall', '1.84-6', ext_options), + ('rpart', '4.1-10', ext_options), + ('mice', '2.22', ext_options), + ('urca', '1.2-8', ext_options), + ('fracdiff', '1.4-2', ext_options), + ('logistf', '1.21', ext_options), + ('akima', '0.5-11', ext_options), + ('bitops', '1.0-6', ext_options), + ('boot', '1.3-17', ext_options), + ('mixtools', '1.0.3', ext_options), + ('cluster', '2.0.2', ext_options), + ('gclus', '1.3.1', ext_options), + ('coda', '0.17-1', ext_options), + ('codetools', '0.2-11', ext_options), + ('foreach', '1.4.2', ext_options), + ('doMC', '1.3.3', ext_options), + ('DBI', '0.3.1', ext_options), + ('foreign', '0.8-65', ext_options), + ('survival', '2.38-3', ext_options), + ('gam', '1.12', ext_options), + ('gamlss.data', '4.2-7', ext_options), + ('gamlss.dist', '4.3-4', ext_options), + ('hwriter', '1.3.2', ext_options), + ('KernSmooth', '2.23-15', ext_options), + ('xts', '0.9-7', ext_options), + ('TTR', '0.23-0', ext_options), + ('quantmod', '0.4-4', ext_options), + ('mnormt', '1.5-3', ext_options), + ('mvtnorm', '1.0-2', ext_options), + ('pcaPP', '1.9-60', ext_options), + ('numDeriv', '2014.2-1', ext_options), + ('lava', '1.4.1', ext_options), + ('prodlim', '1.5.1', ext_options), + ('pscl', '1.4.9', ext_options), + ('RSQLite', '1.0.0', ext_options), + ('BatchJobs', '1.6', ext_options), + ('sandwich', '2.3-3', ext_options), + ('sfsmisc', '1.0-27', ext_options), + ('spatial', '7.3-10', ext_options), + ('VGAM', '0.9-8', ext_options), + ('waveslim', '1.7.5', ext_options), + ('xtable', '1.7-4', ext_options), + ('profileModel', '0.5-9', ext_options), + ('brglm', '0.5-9', ext_options), + ('deSolve', '1.12', ext_options), + ('tseriesChaos', '0.1-13', ext_options), + ('tseries', '0.10-34', ext_options), + ('fastICA', '1.2-0', ext_options), + ('R.methodsS3', '1.7.0', ext_options), + ('R.oo', '1.19.0', 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'1.0.1', ext_options), + ('GeneNet', '1.2.12', ext_options), + ('ape', '3.3', ext_options), + ('htmltools', '0.2.6', ext_options), + ('RJSONIO', '1.3-0', ext_options), + ('caTools', '1.17.1', ext_options), + ('gplots', '2.17.0', ext_options), + ('ROCR', '1.0-7', ext_options), + ('httpuv', '1.3.2', ext_options), + ('R6', '2.1.0', ext_options), + ('jsonlite', '0.9.16', ext_options), + ('shiny', '0.12.1', ext_options), + ('seqinr', '3.1-3', ext_options), + ('LearnBayes', '2.15', ext_options), + ('deldir', '0.1-9', ext_options), + ('spdep', '0.5-88', ext_options), + ('assertthat', '0.1', ext_options), + ('lazyeval', '0.1.10', ext_options), + ('dplyr', '0.4.2', ext_options), + ('adegenet', '2.0.0', ext_options), + ('phylobase', '0.6.8', ext_options), + ('adephylo', '1.1-6', ext_options), + ('animation', '2.3', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), + ('bigmemory', '4.4.6', ext_options), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.4-15', ext_options), + ('dismo', '1.0-12', ext_options), + ('expm', '0.99-1.1', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.3', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '8.2-1', ext_options), + ('shapefiles', '0.7', ext_options), + ('fossil', '0.3.7', ext_options), + ('geiger', '2.0.3', ext_options), + ('glmnet', '2.0-2', ext_options), + ('rgl', '0.95.1247', ext_options), + ('labdsv', '1.7-0', ext_options), + ('MatrixModels', '0.4-0', ext_options), + ('stabs', '0.5-1', ext_options), + ('mboost', '2.4-2', ext_options), + ('msm', '1.5', ext_options), + ('nor1mix', '1.2-0', ext_options), + ('np', '0.60-2', ext_options), + ('polynom', '1.3-8', ext_options), + ('quantreg', '5.11', ext_options), + ('polspline', '1.1.11', ext_options), + ('TH.data', '1.0-6', ext_options), + ('multcomp', '1.4-0', ext_options), + ('rms', '4.3-1', ext_options), + ('RWekajars', '3.7.12-1', ext_options), + ('RWeka', '0.4-24', ext_options), + ('slam', '0.1-32', ext_options), + ('tm', '0.6-2', ext_options), + ('TraMineR', '1.8-9', ext_options), + ('chemometrics', '1.3.9', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-4', ext_options), + ('yaml', '2.1.13', ext_options), + ('knitr', '1.10.5', ext_options), + ('statmod', '1.4.21', ext_options), + ('miscTools', '0.6-16', ext_options), + ('maxLik', '1.2-4', ext_options), + ('mlogit', '0.2-4', ext_options), + ('getopt', '1.20.0', ext_options), + ('gsalib', '2.1', ext_options), + ('reshape', '0.8.5', ext_options), + ('optparse', '1.3.0', ext_options), + ('klaR', '0.6-12', ext_options), + ('neuRosim', '0.2-12', ext_options), + ('locfit', '1.5-9.1', ext_options), + ('GGally', '0.5.0', ext_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('matrixStats', '0.14.2', ext_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '2.9', ext_options), + ('nloptr', '1.0.4', ext_options), + ('lme4', '1.1-8', ext_options), + ('pbkrtest', '0.4-2', ext_options), + ('car', '2.0-25', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.31.3', ext_options), + ('modeltools', '0.2-21', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', '2.3-13', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-7', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-9', ext_options), + ('BiasedUrn', '1.06.1', ext_options), + ('TeachingDemos', '2.9', ext_options), + ('jsonlite', '0.9.16', ext_options), + ('kohonen', '2.0.18', ext_options), + ('base64', '1.1', ext_options), + ('doRNG', '1.6', ext_options), + ('nleqslv', '2.8', ext_options), + ('RGCCA', '2.0', ext_options), + ('pheatmap', '1.0.7', ext_options), + ('openxlsx', '3.0.0', ext_options), + ('pvclust', '1.3-2', ext_options), + ('RCircos', '1.1.2', ext_options), + ('VennDiagram', '1.6.9', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('vegan', '2.3-0', ext_options), + ('forecast', '6.1', ext_options), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), + ('XML', '3.98-1.3', ext_options), + ('memoise', '0.2.1', ext_options), + ('crayon', '1.3.1', ext_options), + ('testthat', '0.10.0', ext_options), + ('rmarkdown', '0.7', ext_options), + ('curl', '0.9.1', ext_options), + ('httr', '1.0.0', ext_options), + ('maptools', '0.8-36', ext_options), + ('deldir', '0.1-9', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.3-2', ext_options), + ('goftest', '1.0-3', ext_options), + ('spatstat', '1.42-2', ext_options), + ('gdalUtils', '0.3.1', ext_options), + ('pracma', '1.8.3', ext_options), + ('RCurl', '1.95-4.7', ext_options), + ('bio3d', '2.2-2', ext_options), + ('AUC', '0.3.0', ext_options), + ('interpretR', '0.2.3', ext_options), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..2c0d70505808d7cc3335941f74568ad6e4ceb8cb --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -0,0 +1,369 @@ +name = 'R' +version = '3.2.1' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.1'), # for plottting in R + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk + ('cURL', '7.43.0'), # for RCurl + ('libxml2', '2.9.2'), # for XML +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + + +# !! order of packages is important !! +# packages updated on January 8th 2015 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + ('abind', '1.4-3', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-5', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), + ('bit', '1.1-12', ext_options), + ('filehash', '2.2-2', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '3.8.1', ext_options), + ('bootstrap', '2015.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.15', ext_options), + ('formatR', '1.2', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.5', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-20', ext_options), + ('mime', '0.3', ext_options), + ('markdown', '0.7.7', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-8', ext_options), + ('mclust', '5.0.2', ext_options), + ('RANN', '2.5', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.1', ext_options), + ('som', '0.3-5', ext_options), + ('SuppDists', '1.1-9.1', ext_options), + ('stabledist', '0.7-0', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-17', ext_options), + ('timeDate', '3012.100', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.7-2', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-2', ext_options), + ('BH', '1.58.0-1', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.8', ext_options), + ('longitudinal', '1.1.12', ext_options), + ('checkmate', '1.6.0', ext_options), + ('cubature', '1.1-2', ext_options), + ('DEoptimR', '1.0-2', ext_options), + ('digest', '0.6.8', ext_options), + ('fastmatch', '1.0-4', ext_options), + ('ffbase', '0.12.1', ext_options), + ('iterators', '1.0.7', ext_options), + ('maps', '2.3-10', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.0-1', ext_options), + ('subplex', '1.1-6', ext_options), + ('stringi', '0.5-5', ext_options), + ('magrittr', '1.5', ext_options), + ('stringr', '1.0.0', ext_options), + ('evaluate', '0.7', ext_options), + ('logspline', '2.1.8', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.8-4', ext_options), + ('plotrix', '3.5-12', ext_options), + ('randomForest', '4.6-10', ext_options), + ('scatterplot3d', '0.3-35', ext_options), + ('SparseM', '1.6', ext_options), + ('tripack', '1.3-6', ext_options), + ('irace', '1.06', ext_options), + ('rJava', '0.9-6', ext_options), + ('lattice', '0.20-31', ext_options), + ('RColorBrewer', '1.1-2', ext_options), + ('latticeExtra', '0.6-26', ext_options), + ('Matrix', '1.2-2', ext_options), + ('png', '0.1-7', ext_options), + ('Rcpp', '0.11.6', ext_options), + ('RcppArmadillo', '0.5.200.1.0', ext_options), + ('plyr', '1.8.3', ext_options), + ('pROC', '1.8', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2014.10-1', ext_options), + ('BBmisc', '1.9', ext_options), + ('fail', '1.2', ext_options), + ('rlecuyer', '0.3-3', ext_options), + ('snow', '0.3-13', ext_options), + ('MASS', '7.3-42', ext_options), + ('tree', '1.0-36', ext_options), + ('pls', '2.4-3', ext_options), + ('class', '7.3-13', ext_options), + ('e1071', '1.6-4', ext_options), + ('nnet', '7.3-10', ext_options), + ('nlme', '3.1-121', ext_options), + ('minqa', '1.2.4', ext_options), + ('RcppEigen', '0.3.2.4.0', ext_options), + ('quantreg', '5.11', ext_options), + ('mgcv', '1.8-6', ext_options), + ('colorspace', '1.2-6', ext_options), + ('robustbase', '0.92-4', ext_options), + ('sp', '1.1-1', ext_options), + ('zoo', '1.7-12', ext_options), + ('lmtest', '0.9-34', ext_options), + ('vcd', '1.4-1', ext_options), + ('snowfall', '1.84-6', ext_options), + ('rpart', '4.1-10', ext_options), + ('mice', '2.22', ext_options), + ('urca', '1.2-8', ext_options), + ('fracdiff', '1.4-2', ext_options), + ('logistf', '1.21', ext_options), + ('akima', '0.5-11', ext_options), + ('bitops', '1.0-6', ext_options), + ('boot', '1.3-17', ext_options), + ('mixtools', '1.0.3', ext_options), + ('cluster', '2.0.2', ext_options), + ('gclus', '1.3.1', ext_options), + ('coda', '0.17-1', ext_options), + ('codetools', '0.2-11', ext_options), + ('foreach', '1.4.2', ext_options), + ('doMC', '1.3.3', ext_options), + ('DBI', '0.3.1', ext_options), + ('foreign', '0.8-65', ext_options), + ('survival', '2.38-3', ext_options), + ('gam', '1.12', ext_options), + ('gamlss.data', '4.2-7', ext_options), + ('gamlss.dist', '4.3-4', ext_options), + ('hwriter', '1.3.2', ext_options), + ('KernSmooth', '2.23-15', ext_options), + ('xts', '0.9-7', ext_options), + ('TTR', '0.23-0', ext_options), + ('quantmod', '0.4-4', ext_options), + ('mnormt', '1.5-3', ext_options), + ('mvtnorm', '1.0-2', ext_options), + ('pcaPP', '1.9-60', ext_options), + ('numDeriv', '2014.2-1', ext_options), + ('lava', '1.4.1', ext_options), + ('prodlim', '1.5.1', ext_options), + ('pscl', '1.4.9', ext_options), + ('RSQLite', '1.0.0', ext_options), + ('BatchJobs', '1.6', ext_options), + ('sandwich', '2.3-3', ext_options), + ('sfsmisc', '1.0-27', ext_options), + ('spatial', '7.3-10', ext_options), + ('VGAM', '0.9-8', ext_options), + ('waveslim', '1.7.5', ext_options), + ('xtable', '1.7-4', ext_options), + ('profileModel', '0.5-9', ext_options), + ('brglm', '0.5-9', ext_options), + ('deSolve', '1.12', ext_options), + ('tseriesChaos', '0.1-13', ext_options), + ('tseries', '0.10-34', ext_options), + ('fastICA', '1.2-0', ext_options), + ('R.methodsS3', '1.7.0', ext_options), + ('R.oo', '1.19.0', ext_options), + ('cgdsr', '1.1.33', ext_options), + ('R.utils', '2.1.0', ext_options), + ('R.matlab', '3.2.0', ext_options), + ('gbm', '2.1.1', ext_options), + ('dichromat', '2.0-0', 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'1.17.1', ext_options), + ('gplots', '2.17.0', ext_options), + ('ROCR', '1.0-7', ext_options), + ('httpuv', '1.3.2', ext_options), + ('R6', '2.1.0', ext_options), + ('jsonlite', '0.9.16', ext_options), + ('shiny', '0.12.1', ext_options), + ('seqinr', '3.1-3', ext_options), + ('LearnBayes', '2.15', ext_options), + ('deldir', '0.1-9', ext_options), + ('spdep', '0.5-88', ext_options), + ('assertthat', '0.1', ext_options), + ('lazyeval', '0.1.10', ext_options), + ('dplyr', '0.4.2', ext_options), + ('adegenet', '2.0.0', ext_options), + ('phylobase', '0.6.8', ext_options), + ('adephylo', '1.1-6', ext_options), + ('animation', '2.3', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), + ('bigmemory', '4.4.6', ext_options), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.4-15', ext_options), + ('dismo', '1.0-12', ext_options), + ('expm', '0.99-1.1', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.3', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '8.2-1', ext_options), + ('shapefiles', '0.7', ext_options), + ('fossil', '0.3.7', ext_options), + ('geiger', '2.0.3', ext_options), + ('glmnet', '2.0-2', ext_options), + ('rgl', '0.95.1247', ext_options), + ('labdsv', '1.7-0', ext_options), + ('MatrixModels', '0.4-0', ext_options), + ('stabs', '0.5-1', ext_options), + ('mboost', '2.4-2', ext_options), + ('msm', '1.5', ext_options), + ('nor1mix', '1.2-0', ext_options), + ('np', '0.60-2', ext_options), + ('polynom', '1.3-8', ext_options), + ('quantreg', '5.11', ext_options), + ('polspline', '1.1.11', ext_options), + ('TH.data', '1.0-6', ext_options), + ('multcomp', '1.4-0', ext_options), + ('rms', '4.3-1', ext_options), + ('RWekajars', '3.7.12-1', ext_options), + ('RWeka', '0.4-24', ext_options), + ('slam', '0.1-32', ext_options), + ('tm', '0.6-2', ext_options), + ('TraMineR', '1.8-9', ext_options), + ('chemometrics', '1.3.9', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-4', ext_options), + ('yaml', '2.1.13', ext_options), + ('knitr', '1.10.5', ext_options), + ('statmod', '1.4.21', ext_options), + ('miscTools', '0.6-16', ext_options), + ('maxLik', '1.2-4', ext_options), + ('mlogit', '0.2-4', ext_options), + ('getopt', '1.20.0', ext_options), + ('gsalib', '2.1', ext_options), + ('reshape', '0.8.5', ext_options), + ('optparse', '1.3.0', ext_options), + ('klaR', '0.6-12', ext_options), + ('neuRosim', '0.2-12', ext_options), + ('locfit', '1.5-9.1', ext_options), + ('GGally', '0.5.0', ext_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('matrixStats', '0.14.2', ext_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '2.9', ext_options), + ('nloptr', '1.0.4', ext_options), + ('lme4', '1.1-8', ext_options), + ('pbkrtest', '0.4-2', ext_options), + ('car', '2.0-25', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.31.3', ext_options), + ('modeltools', '0.2-21', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', '2.3-13', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-7', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-9', ext_options), + ('BiasedUrn', '1.06.1', ext_options), + ('TeachingDemos', '2.9', ext_options), + ('jsonlite', '0.9.16', ext_options), + ('kohonen', '2.0.18', ext_options), + ('base64', '1.1', ext_options), + ('doRNG', '1.6', ext_options), + ('nleqslv', '2.8', ext_options), + ('RGCCA', '2.0', ext_options), + ('pheatmap', '1.0.7', ext_options), + ('openxlsx', '3.0.0', ext_options), + ('pvclust', '1.3-2', ext_options), + ('RCircos', '1.1.2', ext_options), + ('VennDiagram', '1.6.9', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('vegan', '2.3-0', ext_options), + ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), + ('XML', '3.98-1.3', ext_options), + ('memoise', '0.2.1', ext_options), + ('crayon', '1.3.1', ext_options), + ('testthat', '0.10.0', ext_options), + ('rmarkdown', '0.7', ext_options), + ('curl', '0.9.1', ext_options), + ('httr', '1.0.0', ext_options), + ('maptools', '0.8-36', ext_options), + ('deldir', '0.1-9', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.3-2', ext_options), + ('goftest', '1.0-3', ext_options), + ('spatstat', '1.42-2', ext_options), + ('gdalUtils', '0.3.1', ext_options), + ('pracma', '1.8.3', ext_options), + ('RCurl', '1.95-4.7', ext_options), + ('bio3d', '2.2-2', ext_options), + ('AUC', '0.3.0', ext_options), + ('interpretR', '0.2.3', ext_options), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b-bare.eb new file mode 100644 index 0000000000000000000000000000000000000000..427432ba537dd035374b99c74b6fcdee95989bb1 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b-bare.eb @@ -0,0 +1,27 @@ +name = 'R' +version = '3.2.1' +versionsuffix = '-bare' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.1'), # for plottting in R + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it +] + +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..f9b3e10876332c40b4c7d603b7280638c5698b62 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015b.eb @@ -0,0 +1,369 @@ +name = 'R' +version = '3.2.1' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.1'), # for plottting in R + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk + ('cURL', '7.43.0'), # for RCurl + ('libxml2', '2.9.2'), # for XML +] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + + +# !! order of packages is important !! +# packages updated on January 8th 2015 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + ('abind', '1.4-3', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-5', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), + ('bit', '1.1-12', ext_options), + ('filehash', '2.2-2', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '3.8.1', ext_options), + ('bootstrap', '2015.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.15', ext_options), + ('formatR', '1.2', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.5', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-20', ext_options), + ('mime', '0.3', ext_options), + ('markdown', '0.7.7', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-8', ext_options), + ('mclust', '5.0.2', ext_options), + ('RANN', '2.5', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.1', ext_options), + ('som', '0.3-5', ext_options), + ('SuppDists', '1.1-9.1', ext_options), + ('stabledist', '0.7-0', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-17', ext_options), + ('timeDate', '3012.100', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.7-2', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-2', ext_options), + ('BH', '1.58.0-1', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.8', ext_options), + ('longitudinal', '1.1.12', ext_options), + ('checkmate', '1.6.0', ext_options), + ('cubature', '1.1-2', ext_options), + ('DEoptimR', '1.0-2', ext_options), + ('digest', '0.6.8', ext_options), + ('fastmatch', '1.0-4', ext_options), + ('ffbase', '0.12.1', ext_options), + ('iterators', '1.0.7', ext_options), + ('maps', '2.3-10', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.0-1', ext_options), + ('subplex', '1.1-6', ext_options), + ('stringi', '0.5-5', ext_options), + ('magrittr', '1.5', ext_options), + ('stringr', '1.0.0', ext_options), + ('evaluate', '0.7', ext_options), + ('logspline', '2.1.8', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.8-4', ext_options), + ('plotrix', '3.5-12', ext_options), + ('randomForest', '4.6-10', ext_options), + ('scatterplot3d', '0.3-35', ext_options), + ('SparseM', '1.6', ext_options), + ('tripack', '1.3-6', ext_options), + ('irace', '1.06', ext_options), + ('rJava', '0.9-6', ext_options), + ('lattice', '0.20-31', ext_options), + ('RColorBrewer', '1.1-2', ext_options), + ('latticeExtra', '0.6-26', ext_options), + ('Matrix', '1.2-2', ext_options), + ('png', '0.1-7', ext_options), + ('Rcpp', '0.11.6', ext_options), + ('RcppArmadillo', '0.5.200.1.0', ext_options), + ('plyr', '1.8.3', ext_options), + ('pROC', '1.8', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2014.10-1', ext_options), + ('BBmisc', '1.9', ext_options), + ('fail', '1.2', ext_options), + ('rlecuyer', '0.3-3', ext_options), + ('snow', '0.3-13', ext_options), + ('MASS', '7.3-42', ext_options), + ('tree', '1.0-36', ext_options), + ('pls', '2.4-3', ext_options), + ('class', '7.3-13', ext_options), + ('e1071', '1.6-4', ext_options), + ('nnet', '7.3-10', ext_options), + ('nlme', '3.1-121', ext_options), + ('minqa', '1.2.4', ext_options), + ('RcppEigen', '0.3.2.4.0', ext_options), + ('quantreg', '5.11', ext_options), + ('mgcv', '1.8-6', ext_options), + ('colorspace', '1.2-6', ext_options), + ('robustbase', '0.92-4', ext_options), + ('sp', '1.1-1', ext_options), + ('zoo', '1.7-12', ext_options), + ('lmtest', '0.9-34', ext_options), + ('vcd', '1.4-1', ext_options), + ('snowfall', '1.84-6', ext_options), + ('rpart', '4.1-10', ext_options), + ('mice', '2.22', ext_options), + ('urca', '1.2-8', ext_options), + ('fracdiff', '1.4-2', ext_options), + ('logistf', '1.21', ext_options), + ('akima', '0.5-11', ext_options), + ('bitops', '1.0-6', ext_options), + ('boot', '1.3-17', ext_options), + ('mixtools', '1.0.3', ext_options), + ('cluster', '2.0.2', ext_options), + ('gclus', '1.3.1', ext_options), + ('coda', '0.17-1', ext_options), + ('codetools', '0.2-11', ext_options), + ('foreach', '1.4.2', ext_options), + ('doMC', '1.3.3', ext_options), + ('DBI', '0.3.1', ext_options), + ('foreign', '0.8-65', ext_options), + ('survival', '2.38-3', ext_options), + ('gam', '1.12', ext_options), + ('gamlss.data', '4.2-7', ext_options), + ('gamlss.dist', '4.3-4', ext_options), + ('hwriter', '1.3.2', ext_options), + ('KernSmooth', '2.23-15', ext_options), + ('xts', '0.9-7', ext_options), + ('TTR', '0.23-0', ext_options), + ('quantmod', '0.4-4', ext_options), + ('mnormt', '1.5-3', ext_options), + ('mvtnorm', '1.0-2', ext_options), + ('pcaPP', '1.9-60', ext_options), + ('numDeriv', '2014.2-1', ext_options), + ('lava', '1.4.1', ext_options), + ('prodlim', '1.5.1', ext_options), + ('pscl', '1.4.9', ext_options), + ('RSQLite', '1.0.0', ext_options), + ('BatchJobs', '1.6', ext_options), + ('sandwich', '2.3-3', ext_options), + ('sfsmisc', '1.0-27', ext_options), + ('spatial', '7.3-10', ext_options), + ('VGAM', '0.9-8', ext_options), + ('waveslim', '1.7.5', ext_options), + ('xtable', '1.7-4', ext_options), + ('profileModel', '0.5-9', ext_options), + ('brglm', '0.5-9', ext_options), + ('deSolve', '1.12', ext_options), + ('tseriesChaos', '0.1-13', ext_options), + ('tseries', '0.10-34', ext_options), + ('fastICA', '1.2-0', ext_options), + ('R.methodsS3', '1.7.0', ext_options), + ('R.oo', '1.19.0', ext_options), + ('cgdsr', '1.1.33', ext_options), + ('R.utils', '2.1.0', ext_options), + ('R.matlab', '3.2.0', ext_options), + ('gbm', '2.1.1', ext_options), + ('dichromat', '2.0-0', ext_options), + ('Formula', '1.2-1', ext_options), + ('acepack', '1.3-3.3', ext_options), + ('reshape2', '1.4.1', ext_options), + ('gtable', '0.1.2', ext_options), + ('munsell', '0.4.2', ext_options), + ('labeling', '0.3', ext_options), + ('scales', '0.2.5', ext_options), + ('proto', '0.3-10', ext_options), + ('ggplot2', '1.0.1', ext_options), + ('gridExtra', '0.9.1', ext_options), + ('Hmisc', '3.16-0', ext_options), + ('fastcluster', '1.1.16', ext_options), + ('chron', '2.3-47', ext_options), + ('data.table', '1.9.4', ext_options), + ('registry', '0.3', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doParallel', '1.0.8', ext_options), + ('gridBase', '0.4-7', ext_options), + ('NMF', '0.20.6', ext_options), + ('irlba', '1.0.3', ext_options), + ('igraph', '1.0.1', ext_options), + ('GeneNet', '1.2.12', ext_options), + ('ape', '3.3', ext_options), + ('htmltools', '0.2.6', ext_options), + ('RJSONIO', '1.3-0', ext_options), + ('caTools', '1.17.1', ext_options), + ('gplots', '2.17.0', ext_options), + ('ROCR', '1.0-7', ext_options), + ('httpuv', '1.3.2', ext_options), + ('R6', '2.1.0', ext_options), + ('jsonlite', '0.9.16', ext_options), + ('shiny', '0.12.1', ext_options), + ('seqinr', '3.1-3', ext_options), + ('LearnBayes', '2.15', ext_options), + ('deldir', '0.1-9', ext_options), + ('spdep', '0.5-88', ext_options), + ('assertthat', '0.1', ext_options), + ('lazyeval', '0.1.10', ext_options), + ('dplyr', '0.4.2', ext_options), + ('adegenet', '2.0.0', ext_options), + ('phylobase', '0.6.8', ext_options), + ('adephylo', '1.1-6', ext_options), + ('animation', '2.3', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), + ('bigmemory', '4.4.6', ext_options), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.4-15', ext_options), + ('dismo', 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ext_options), + ('TraMineR', '1.8-9', ext_options), + ('chemometrics', '1.3.9', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-4', ext_options), + ('yaml', '2.1.13', ext_options), + ('knitr', '1.10.5', ext_options), + ('statmod', '1.4.21', ext_options), + ('miscTools', '0.6-16', ext_options), + ('maxLik', '1.2-4', ext_options), + ('mlogit', '0.2-4', ext_options), + ('getopt', '1.20.0', ext_options), + ('gsalib', '2.1', ext_options), + ('reshape', '0.8.5', ext_options), + ('optparse', '1.3.0', ext_options), + ('klaR', '0.6-12', ext_options), + ('neuRosim', '0.2-12', ext_options), + ('locfit', '1.5-9.1', ext_options), + ('GGally', '0.5.0', ext_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('matrixStats', '0.14.2', ext_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '2.9', ext_options), + ('nloptr', '1.0.4', ext_options), + ('lme4', '1.1-8', ext_options), + ('pbkrtest', '0.4-2', ext_options), + ('car', '2.0-25', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.31.3', ext_options), + ('modeltools', '0.2-21', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', '2.3-13', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-7', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-9', ext_options), + ('BiasedUrn', '1.06.1', ext_options), + ('TeachingDemos', '2.9', ext_options), + ('jsonlite', '0.9.16', ext_options), + ('kohonen', '2.0.18', ext_options), + ('base64', '1.1', ext_options), + ('doRNG', '1.6', ext_options), + ('nleqslv', '2.8', ext_options), + ('RGCCA', '2.0', ext_options), + ('pheatmap', '1.0.7', ext_options), + ('openxlsx', '3.0.0', ext_options), + ('pvclust', '1.3-2', ext_options), + ('RCircos', '1.1.2', ext_options), + ('VennDiagram', '1.6.9', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('vegan', '2.3-0', ext_options), + ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), + ('XML', '3.98-1.3', ext_options), + ('memoise', '0.2.1', ext_options), + ('crayon', '1.3.1', ext_options), + ('testthat', '0.10.0', ext_options), + ('rmarkdown', '0.7', ext_options), + ('curl', '0.9.1', ext_options), + ('httr', '1.0.0', ext_options), + ('maptools', '0.8-36', ext_options), + ('deldir', '0.1-9', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.3-2', ext_options), + ('goftest', '1.0-3', ext_options), + ('spatstat', '1.42-2', ext_options), + ('gdalUtils', '0.3.1', ext_options), + ('pracma', '1.8.3', ext_options), + ('RCurl', '1.95-4.7', ext_options), + ('bio3d', '2.2-2', ext_options), + ('AUC', '0.3.0', ext_options), + ('interpretR', '0.2.3', ext_options), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/forecast-6.1_icpc-wd308.patch b/easybuild/easyconfigs/r/R/forecast-6.1_icpc-wd308.patch new file mode 100644 index 0000000000000000000000000000000000000000..8582ea93aeaac9b2adab311e43a9f8c6eb115d04 --- /dev/null +++ b/easybuild/easyconfigs/r/R/forecast-6.1_icpc-wd308.patch @@ -0,0 +1,9 @@ +ignore warning/error when building with Intel C++ compiler by including -wd308 flag in $CXXFLAGS +author: Kenneth Hoste (HPC-UGent) +--- forecast/src/Makevars.orig 2015-05-12 11:56:10.000000000 +0200 ++++ forecast/src/Makevars 2015-05-28 10:53:13.878100139 +0200 +@@ -1,2 +1,4 @@ + ## Use the R_HOME indirection to support installations of multiple R version + PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-avx.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-avx.eb new file mode 100644 index 0000000000000000000000000000000000000000..34e93e35d82c4b518c5ed37a487d0829daca87c7 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-avx.eb @@ -0,0 +1,29 @@ +# 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 = 'MakeCp' + +name = 'RAxML' +version = '8.1.1' +versionsuffix ='-mpi-avx' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] +sources = ['v%(version)s.zip'] + +buildopts = ' -f Makefile.AVX.MPI.gcc' + +files_to_copy = [(["raxmlHPC-MPI-AVX"], "bin"), "usefulScripts", "README", "manual"] + +sanity_check_paths = { + 'files': ["bin/raxmlHPC-MPI-AVX"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-sse3.eb new file mode 100644 index 0000000000000000000000000000000000000000..42ce2e4fdd0c6599bcd8ca3e2b67cfaad282c915 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mpi-sse3.eb @@ -0,0 +1,29 @@ +# 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 = 'MakeCp' + +name = 'RAxML' +version = '8.1.1' +versionsuffix ='-mpi-sse3' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] +sources = ['v%(version)s.zip'] + +buildopts = ' -f Makefile.SSE3.MPI.gcc' + +files_to_copy = [(["raxmlHPC-MPI-SSE3"], "bin"), "usefulScripts", "README", "manual"] + +sanity_check_paths = { + 'files': ["bin/raxmlHPC-MPI-SSE3"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-avx.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-avx.eb new file mode 100644 index 0000000000000000000000000000000000000000..09ffafe613b2e55941c21e0b7243b13ef76e1e10 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-avx.eb @@ -0,0 +1,29 @@ +# 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 = 'MakeCp' + +name = 'RAxML' +version = '8.1.1' +versionsuffix ='-mt-avx' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] +sources = ['v%(version)s.zip'] + +buildopts = '-f Makefile.AVX.PTHREADS.gcc' + +files_to_copy = [(["raxmlHPC-PTHREADS-AVX"], "bin"), "usefulScripts", "README", "manual"] + +sanity_check_paths = { + 'files': ["bin/raxmlHPC-PTHREADS-AVX"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-sse3.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-sse3.eb new file mode 100644 index 0000000000000000000000000000000000000000..305c9c94a640a137e4fa53ec7c66c53194891c21 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.1.1-goolf-1.4.10-mt-sse3.eb @@ -0,0 +1,29 @@ +# 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 = 'MakeCp' + +name = 'RAxML' +version = '8.1.1' +versionsuffix ='-mt-sse3' + +homepage = 'https://github.com/stamatak/standard-RAxML' +description = "RAxML search algorithm for maximum likelihood based inference of phylogenetic trees." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/stamatak/standard-RAxML/archive/'] +sources = ['v%(version)s.zip'] + +buildopts = '-f Makefile.SSE3.PTHREADS.gcc' + +files_to_copy = [(["raxmlHPC-PTHREADS-SSE3"], "bin"), "usefulScripts", "README", "manual"] + +sanity_check_paths = { + 'files': ["bin/raxmlHPC-PTHREADS-SSE3"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RELION/RELION-1.3-foss-2014b.eb b/easybuild/easyconfigs/r/RELION/RELION-1.3-foss-2014b.eb index 5101540bd39ba4e272aeb9e2269aea6438dca0d6..0ad7f07069a17f142675d597d13b84b38fc422ff 100644 --- a/easybuild/easyconfigs/r/RELION/RELION-1.3-foss-2014b.eb +++ b/easybuild/easyconfigs/r/RELION/RELION-1.3-foss-2014b.eb @@ -32,7 +32,7 @@ dependencies = [ # RELION expects FLTK to be in external/fltk-1.3.0 configopts = ['--enable-mpi --enable-openmp && ln -s $EBROOTFLTK/include external/fltk-1.3.0'] buildopts = 'LIBS="-lfftw3_threads -lfftw3 -lm -lpthread -lfltk -lX11 -lXft -lfontconfig -lXext -lXinerama" ' -installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/relion " +installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/%(namelower)s " sanity_check_paths = { 'files': ['bin/relion'], diff --git a/easybuild/easyconfigs/r/RELION/RELION-1.3-intel-2014b.eb b/easybuild/easyconfigs/r/RELION/RELION-1.3-intel-2014b.eb index 7b003f1cbf188be766c193f8b77f15077203d1ec..25abcbdcb90c23421ab7a3b6b631747aba5d6213 100644 --- a/easybuild/easyconfigs/r/RELION/RELION-1.3-intel-2014b.eb +++ b/easybuild/easyconfigs/r/RELION/RELION-1.3-intel-2014b.eb @@ -34,7 +34,7 @@ dependencies = [ configopts = ['--enable-mpi --enable-openmp && ln -s $EBROOTFLTK/include external/fltk-1.3.0'] buildopts = 'LIBS="-lfftw3_threads -lfftw3 -lm -lpthread -lfltk -lX11 -lXft -lfontconfig -lXext -lXinerama" ' # users expect the maingui binary to be called relion -installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/relion " +installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/%(namelower)s " moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Rosetta/Rosetta-2015.31.58019-intel-2015a.eb b/easybuild/easyconfigs/r/Rosetta/Rosetta-2015.31.58019-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..10b2a8fd9cf6106fa3492a12934a14b6af9c7b84 --- /dev/null +++ b/easybuild/easyconfigs/r/Rosetta/Rosetta-2015.31.58019-intel-2015a.eb @@ -0,0 +1,20 @@ +name = 'Rosetta' +version = '2015.31.58019' + +homepage = 'https://www.rosettacommons.org' +description = """Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, +multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and +nucleic acids.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +sources = ['%(namelower)s_src_%(version)s_bundle.tgz'] + +builddependencies = [('SCons', '2.3.6', '-Python-2.7.9')] + +modextravars = { + 'ROSETTA3_DB': '$root/database', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b1d493612160c91e60b7fcce5028a0979d756d47 --- /dev/null +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'renderproto' +version = '0.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrender protocol and ancillary headers" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files' : ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], + 'dirs' : [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/requests/requests-2.7.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/r/requests/requests-2.7.0-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..d4e3a34ddb4077bba27fd17eea91ca0003d17631 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.7.0-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.7.0' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +description = """Python http for humans""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/requests-%s-py%s.egg' % (pyshortver, version, pyshortver)], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/requests/requests-2.7.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/r/requests/requests-2.7.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..f8a41a318c69b51939836fd182a23f118206f411 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.7.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.7.0' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +description = """Python http for humans""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/requests-%s-py%s.egg' % (pyshortver, version, pyshortver)], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/rjags/rjags-3-13-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/r/rjags/rjags-3-13-intel-2014b-R-3.1.1.eb index 20b52d9cdae742f84292a7d5807b1ba38ff80cc6..8ed75f2aca836a0c994e355cdd99daf12a9ddbbc 100644 --- a/easybuild/easyconfigs/r/rjags/rjags-3-13-intel-2014b-R-3.1.1.eb +++ b/easybuild/easyconfigs/r/rjags/rjags-3-13-intel-2014b-R-3.1.1.eb @@ -20,7 +20,12 @@ versionsuffix = '-%s-%s' % (r, rver) dependencies = [ (r, rver), - ("JAGS", "3.4.0"), + ('JAGS', '3.4.0'), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['rjags'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..463de39baadc9e3a3b3320449d899e95d8732faa --- /dev/null +++ b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'rpy2' +version = '2.4.3' + +homepage = 'http://rpy.sourceforge.net/' +description = """rpy2 is a redesign and rewrite of rpy. It is providing a low-level +interface to R from Python, a proposed high-level interface, including wrappers to +graphical libraries, as well as R-like structures and functions. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://pypi.python.org/packages/source/r/%(name)s'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.3' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('R', '2.15.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (pyshortver, pyshortver)], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..5287791d7cab1724223d2e7175245647c4bb5b53 --- /dev/null +++ b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'rpy2' +version = '2.4.3' + +homepage = 'http://rpy.sourceforge.net/' +description = """rpy2 is a redesign and rewrite of rpy. It is providing a low-level +interface to R from Python, a proposed high-level interface, including wrappers to +graphical libraries, as well as R-like structures and functions. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://pypi.python.org/packages/source/r/%(name)s'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '3.2.3' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('R', '2.15.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % (pyshortver, pyshortver)], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/r/runjags/runjags-1.2.1-0-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/r/runjags/runjags-1.2.1-0-intel-2014b-R-3.1.1.eb index 23eb06777144c0c548561835d629283c934cdcd5..f7c90f5eff6a25836d95e1613ef124c8c0d06d81 100644 --- a/easybuild/easyconfigs/r/runjags/runjags-1.2.1-0-intel-2014b-R-3.1.1.eb +++ b/easybuild/easyconfigs/r/runjags/runjags-1.2.1-0-intel-2014b-R-3.1.1.eb @@ -20,7 +20,12 @@ versionsuffix = '-%s-%s' % (r, rver) dependencies = [ (r, rver), - ("JAGS", "3.4.0"), + ('JAGS', '3.4.0'), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['runjags'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c7a055062ea6d5e726004229a88aaec1fcd2320c --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2015a.eb @@ -0,0 +1,21 @@ +name = 'SAMtools' +version = '0.1.19' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [('http://sourceforge.net/projects/samtools/files/%(namelower)s/%(version)s', 'download')] + +patches = ['SAMtools-%(version)s_Makefile-ncurses.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..cb7232a3fb1298973ce3fdb7def4ba575588775d --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb @@ -0,0 +1,22 @@ +name = 'SAMtools' +version = '0.1.19' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [('http://sourceforge.net/projects/samtools/files/%(namelower)s/%(version)s', 'download')] + +checksums = ['ff8b46e6096cfb452003b1ec5091d86a'] + +patches = ['SAMtools-%(version)s_Makefile-ncurses.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..91e58c27f084775489ef7213be45f4e4df14f20a --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.eb @@ -0,0 +1,35 @@ +## +# 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 +## + +name = 'SAMtools' +version = '1.1' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = ['SAMtools-1.1_Makefile.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..695f8c6b45dd56a582adb2f1b0dfbbaee8e29bf9 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.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:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## + +name = 'SAMtools' +version = '1.2' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] + +patches = ['SAMtools-1.1_Makefile.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-intel-2015b-HTSlib-1.2.1.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-intel-2015b-HTSlib-1.2.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..739c632246bcd9469d420af8af445945179efe52 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-intel-2015b-HTSlib-1.2.1.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## + +name = 'SAMtools' +version = '1.2' + +homepage = 'http://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + SAMtools - Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format""" + +toolchain = {'name': 'intel', 'version': '2015b'} +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'] + +htslib = 'HTSlib' +htsver = '1.2.1' +versionsuffix = '-%s-%s' % (htslib, htsver) + +dependencies = [ + (htslib, htsver), + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..88fe827b030bb2923ea49a7f9d70f5cb87edfeef --- /dev/null +++ b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,43 @@ +# 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 = 'PerlModule' + +name = 'SCANMS' +version = '2.02' + +homepage = 'http://compbio.ucmerced.edu/ardell/software/scanms/' +description = """SCANMS is an open source utility written in Perl that works in + conjunction with Richard Hudson’s coalescent simulator MS to do parametric + bootstrapping of a sliding window analysis of neutrality test statistics. + Currently supported statistics are Tajima’s D and Fu and Li’s D* and F*. + Its output of a joint distribution of window minima and maxima may then be + used to correct for multiple comparisons in such analyses.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://compbio.ucmerced.edu/'] +sources = [SOURCELOWER_TAR_GZ] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), +] + +# override the default sanity check for perl packages which tries to load Perl module +exts_filter = ('scanms -v 2>&1 | grep version', "") + +sanity_check_paths = { + 'files': ["bin/scanms"], + 'dirs': [] +} + +# copy all the documentation provided in the tarball to install directory +postinstallcmds = ["cp -r %(builddir)s/*/{README,SCANMS.pdf,scanms.doc.html} %(installdir)s"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..f5bdd9828b42f190729fe1fb0bdf05f2b1156633 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb @@ -0,0 +1,14 @@ +name = 'SCOTCH' +version = '6.0.4' + +homepage = 'http://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True} + +source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..3f65d37408d342312805a3efce1be9c93bbaf502 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015b.eb @@ -0,0 +1,14 @@ +name = 'SCOTCH' +version = '6.0.4' + +homepage = 'http://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..34df491afde567145705a81dc709f9904116220b --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-intel-2015b.eb @@ -0,0 +1,14 @@ +name = 'SCOTCH' +version = '6.0.4' + +homepage = 'http://gforge.inria.fr/projects/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = ['http://gforge.inria.fr/frs/download.php/file/34618/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.3.6-foss-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/s/SCons/SCons-2.3.6-foss-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..6056720861b0a9f3ba78c2905e30034d274ae172 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.3.6-foss-2015a-Python-2.7.10.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.3.6' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [(python, pyver)] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s-%(version)s/%(name)s'], +} + +options = {'modulename': False} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.3.6-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SCons/SCons-2.3.6-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..862d3382aceb57a8c25a6fad1434f8659dab3df0 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.3.6-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.3.6' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [(python, pyver)] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s-%(version)s/%(name)s'], +} + +options = {'modulename': False} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.3.6-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/s/SCons/SCons-2.3.6-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..ffd4f194b16c9b431a8e6fb6028226b8077702bc --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.3.6-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.3.6' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [(python, pyver)] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s-%(version)s/%(name)s'], +} + +options = {'modulename': False} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SCons/SCons-2.3.6-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SCons/SCons-2.3.6-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..eaa34798de048693e3a6538075c8fd2069e7393f --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-2.3.6-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '2.3.6' + +homepage = 'http://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [(python, pyver)] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': ['lib/%(namelower)s-%(version)s/%(name)s'], +} + +options = {'modulename': False} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb index 20ee0d6828287dd62cd29076424bdede86128276..2c2c1d2e6afa0cd35c5820862b885bb61d3278ab 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-goolf-1.5.14-Python-2.7.9.eb @@ -20,6 +20,14 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] -configopts = "configure.py" +pyshortver = '.'.join(pyver.split('.')[:2]) +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " +configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortver + +sanity_check_paths = { + 'files': ['bin/sip', 'include/sip.h'] + + ['lib/python%s/site-packages/%s' % (pyshortver, x) for x in ['sip.so', 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb index 2de546ee642538fb3e6828a41463cd078b3a516c..db47a517caf321cc1739273ad1f3e8b39ee9221e 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.4-intel-2015a-Python-2.7.9.eb @@ -20,6 +20,14 @@ versionsuffix = '-%s-%s' % (python, pyver) dependencies = [(python, pyver)] -configopts = "configure.py" +pyshortver = '.'.join(pyver.split('.')[:2]) +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " +configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortver + +sanity_check_paths = { + 'files': ['bin/sip', 'include/sip.h'] + + ['lib/python%s/site-packages/%s' % (pyshortver, x) for x in ['sip.so', 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..c03c93c847b615b55e879e7fbe3fdf9400bd04ff --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'SIP' +version = '4.16.8' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " +configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortver + +sanity_check_paths = { + 'files': ['bin/sip', 'include/sip.h'] + + ['lib/python%s/site-packages/%s' % (pyshortver, x) for x in ['sip.so', 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..d266d5f8e0f8b5e3736e7ff661248f8b731c9c3b --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'SIP' +version = '4.16.8' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +python = 'Python' +pyver = '2.7.8' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " +configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortver + +sanity_check_paths = { + 'files': ['bin/sip', 'include/sip.h'] + + ['lib/python%s/site-packages/%s' % (pyshortver, x) for x in ['sip.so', 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..4fb9048408c8829413b88e106df5276d6d4ee4d0 --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +easyblock = 'ConfigureMakePythonPackage' + +name = 'SIP' +version = '4.16.8' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[:2]) +configopts = "configure.py --bindir %(installdir)s/bin --incdir %(installdir)s/include " +configopts += "--destdir %%(installdir)s/lib/python%s/site-packages" % pyshortver + +sanity_check_paths = { + 'files': ['bin/sip', 'include/sip.h'] + + ['lib/python%s/site-packages/%s' % (pyshortver, x) for x in ['sip.so', 'sipconfig.py', 'sipdistutils.py']], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015a.eb b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..1761063fd76ef1b21d3fd27e373709897cc467bd --- /dev/null +++ b/easybuild/easyconfigs/s/SOAPdenovo2/SOAPdenovo2-r240-intel-2015a.eb @@ -0,0 +1,40 @@ +# With <3 for EasyBuild +# +# EasyConfig for SOAPdenovo2: +# ---------------------------------------------------------------------------- +# Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Petar Forai +# ---------------------------------------------------------------------------- + +easyblock = "MakeCp" + +name = 'SOAPdenovo2' +version = 'r240' + +homepage = 'http://soap.genomics.org.cn/index.html' +description = """SOAPdenovo is a novel short-read assembly method that can build a + de novo draft assembly for human-sized genomes. The program is specially designed to + assemble Illumina short reads. It creates new opportunities for building reference + sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. + SOAPdenovo2 is the successor of SOAPdenovo.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-src-%(version)s.tgz'] + +patches = ['SOAPdenovo2-fix-unistd-includes.patch'] + +# parallel build is broken +maxparallel = 1 + +files_to_copy = [(['SOAPdenovo-127mer','SOAPdenovo-63mer'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/SOAPdenovo-63mer', 'bin/SOAPdenovo-127mer'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SOBAcl/SOBAcl-r18-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/s/SOBAcl/SOBAcl-r18-intel-2014b-Perl-5.20.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..cf5f1f9a0218e2231721bd10da6ef43a791b05b5 --- /dev/null +++ b/easybuild/easyconfigs/s/SOBAcl/SOBAcl-r18-intel-2014b-Perl-5.20.0.eb @@ -0,0 +1,27 @@ +easyblock = "Tarball" + +name = 'SOBAcl' +version = 'r18' + +homepage = 'http://www.sequenceontology.org/software/sobacl.html' +description = """SOBAcl is a command line tool for analyzing GFF3 annotations. +GFF3 is a standard file format for genomic annotation data. SOBAcl gathers +statistics from GFF3 files and can generate a wide variety of tables +and graphs.""" + +toolchain = {'name': 'intel', 'version': '2014b'} +sources = [('SOBA_%s.tar.gz' % (version))] +source_urls = ['http://www.sequenceontology.org/software/SOBA_Code/'] + +perl = 'Perl' +perlver = '5.20.0' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [('GraphViz', '2.18', versionsuffix)] + +sanity_check_paths = { + 'files': ['bin/SOBAcl', 'bin/so_tree', 'lib/Bundle/SOBA.pm', 'lib/SOBA/Base.pm', 'lib/SOBA/Run.pm'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-foss-2015a.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..31a4eb409aa8870a08588b24ae192ac81239e16c --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-foss-2015a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'SPIDER' +version = '22.10' + +homepage = 'http://spider.wadsworth.org/spider_doc/spider/docs/spider.html' +description = """SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is + an image processing system for electron microscopy.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'static': True} + +source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] +sources = ['spiderweb.%(version)s.tar.gz'] + +patches = [ + 'SPIDER-%(version)s_fix-syntax-ifort.patch', + 'SPIDER-%(version)s_gfortran49.patch', +] + +start_dir = 'spider/src' + +buildininstalldir = True + +parallel = 1 + +skipsteps = ['configure', 'install'] + +prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " +buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_GFORTRAN -cpp -dM -c" LF="$F90FLAGS"' + +modextrapaths = {'PATH': ['spider/bin']} + +sanity_check_paths = { + 'files': ['spider/bin/spider'], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb new file mode 100644 index 0000000000000000000000000000000000000000..cdcacc46310bdf3fb79cbe27197742c00658f2a6 --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'SPIDER' +version = '22.10' +versionsuffix = '-mpi' + +homepage = 'http://spider.wadsworth.org/spider_doc/spider/docs/spider.html' +description = """SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is + an image processing system for electron microscopy.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] +sources = ['spiderweb.%(version)s.tar.gz'] + +patches = ['SPIDER-%(version)s_fix-syntax-ifort.patch'] + +dependencies = [('FFTW', '3.3.4')] + +start_dir = 'spider/src' + +buildininstalldir = True + +parallel = 1 + +skipsteps = ['configure', 'install'] + +prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " +buildopts = '-f Makefile_linux_mp COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DUSE_MPI" LF="$F90FLAGS -ldl -lpthread"' + +modextrapaths = {'PATH': ['spider/bin']} + +sanity_check_paths = { + 'files': ['spider/bin/spider'], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb new file mode 100644 index 0000000000000000000000000000000000000000..a747562bcb644866afb681fbfc94d22e88c60531 --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'SPIDER' +version = '22.10' +versionsuffix = '-mt' + +homepage = 'http://spider.wadsworth.org/spider_doc/spider/docs/spider.html' +description = """SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is + an image processing system for electron microscopy.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'static': True, 'openmp': True} + +source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] +sources = ['spiderweb.%(version)s.tar.gz'] + +patches = ['SPIDER-%(version)s_fix-syntax-ifort.patch'] + +dependencies = [('FFTW', '3.3.4')] + +start_dir = 'spider/src' + +buildininstalldir = True + +parallel = 1 + +skipsteps = ['configure', 'install'] + +prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " +buildopts = '-f Makefile_linux_mp COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DSP_MP" LF="$F90FLAGS"' + +modextrapaths = {'PATH': ['spider/bin']} + +sanity_check_paths = { + 'files': ['spider/bin/spider'], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..cf9bac0479914f784a929fd34fe848d4a4f5c112 --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'SPIDER' +version = '22.10' + +homepage = 'http://spider.wadsworth.org/spider_doc/spider/docs/spider.html' +description = """SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is + an image processing system for electron microscopy.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'static': True} + +source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] +sources = ['spiderweb.%(version)s.tar.gz'] + +patches = ['SPIDER-%(version)s_fix-syntax-ifort.patch'] + +dependencies = [('FFTW', '3.3.4')] + +start_dir = 'spider/src' + +buildininstalldir = True + +parallel = 1 + +skipsteps = ['configure', 'install'] + +prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " +buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c" LF="$F90FLAGS"' + +modextrapaths = {'PATH': ['spider/bin']} + +sanity_check_paths = { + 'files': ['spider/bin/spider'], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch new file mode 100644 index 0000000000000000000000000000000000000000..957ed589cf4a903a5545b1be859bbb2dadff78a5 --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch @@ -0,0 +1,202 @@ +fix syntax issues that trip Intel Fortran compiler (ifort) +author: Kenneth Hoste (HPC-UGent) +--- spider/src/copyfromtif.f.orig 2014-11-20 17:31:58.000000000 +0100 ++++ spider/src/copyfromtif.f 2015-05-21 12:04:17.049891641 +0200 +@@ -88,7 +88,7 @@ + INTEGER(KIND=1), ALLOCATABLE :: I1VALS(:) + INTEGER(KIND=4), ALLOCATABLE :: I4VALS(:) + +- CHARACTER(LEN=1), ALLOCATABLE :: CVAL(:) ++ CHARACTER(LEN=:), ALLOCATABLE :: CVAL + + CHARACTER(LEN=24) :: CDATE + +@@ -290,7 +290,7 @@ + IF ( ICOUNT > ICVAL_LEN) THEN + IF (ALLOCATED(CVAL)) DEALLOCATE(CVAL) + ICVAL_LEN = ICOUNT +- ALLOCATE(CVAL(1)(ICVAL_LEN), STAT=IRTFLG) ++ ALLOCATE(CHARACTER(LEN=ICVAL_LEN) :: CVAL, STAT=IRTFLG) + + IF (IRTFLG .NE. 0) THEN + CALL ERRT(46,'COPYFROMTIF; CVAL...',ICVAL_LEN) +@@ -432,9 +432,9 @@ + GOTRESU = .TRUE. + + ELSEIF (ITAG == 306) THEN +- CDATE = CVAL(1)(1:22) ++ CDATE = CVAL(1:22) + c IF (DEBUG) WRITE(NOUT,'(2X,A,1X,200A)')'DATE & TIME:', +-c & CVAL(1)(1:ICOUNT) ++c & CVAL(1:ICOUNT) + GOTDATE = .TRUE. + + ELSE +--- spider/src/copypos.f.orig 2015-05-20 21:21:12.693293000 +0200 ++++ spider/src/copypos.f 2015-05-20 21:21:37.499077116 +0200 +@@ -269,7 +269,7 @@ + ENDIF + + C GREATER OF (0 AND (THE SMALLER OF RVAL AND 255)) +- IVAL = MAX(0,MIN(RVAL, 255.)) ++ IVAL = MAX(0.,MIN(RVAL, 255.)) + + IF (FLIP) THEN + IVAL = 255 - IVAL +--- spider/src/hisd.f.orig 2015-05-20 21:30:04.788208000 +0200 ++++ spider/src/hisd.f 2015-05-20 21:30:29.848221000 +0200 +@@ -146,9 +146,7 @@ + & 'OUTPUT DOC FILE (OR * IF NONE)',ISOLD,APPEND,MESSAGE, + & NEWFILE,IRTFLG) + +- WANTDOC = (IRTFLG == 0) +- +- IF (WANTDOC) THEN ++ IF (IRTFLG == 0) THEN + C OUTPUT TO DOC FILE + + C 123456789 123456789 123456789 123456789 123456789 +--- spider/src/star2doc.f.orig 2015-05-20 21:41:24.588241000 +0200 ++++ spider/src/star2doc.f 2015-05-20 21:41:50.069338858 +0200 +@@ -82,6 +82,7 @@ + CHARACTER(LEN=1) :: CDUM + INTEGER :: LUNDOCT,ILOC,IT,NLIST,ILAST + INTEGER :: IHI,I,IKEY,IRTFLG,LENREC,IVAR,ITOK ++ INTEGER :: NSPI + + LOGICAL :: ISOPEN,EX,CALLERRT,ASKNAM + LOGICAL :: ADDEXT,GETNAME +--- spider/src/Makebody.inc.orig 2015-05-21 09:53:57.937621000 +0200 ++++ spider/src/Makebody.inc 2015-05-21 09:52:36.558197000 +0200 +@@ -14,4 +14,4 @@ + .f.a: + $(COMP) $(FFLAGS) $< + $(AR) $(AFLAGS) $(LIB) $*.o +- @\rm $*.o ++# @\rm $*.o +--- spider/src/four_fq.f.orig 2015-05-21 10:37:01.109541000 +0200 ++++ spider/src/four_fq.f 2015-05-21 10:36:37.703908871 +0200 +@@ -1028,13 +1028,11 @@ + C BUTTERWORTH ELLIPTIC LOWPASS FILTER ********* + CALL ERRT(101, + & 'OPTION NOT IMPLEMENTED FOR VOLUMES',IOPT) +- RETURN + + ELSEIF (IOPT == 12) THEN + C BUTTERWORTH ELLIPTIC HIGHPASS FILTER ********* + CALL ERRT(101, + & 'OPTION NOT IMPLEMENTED FOR VOLUMES',IOPT) +- RETURN + + + ELSEIF (IOPT == 13) THEN +--- spider/src/spider.f.orig 2015-04-21 15:30:40.000000000 +0200 ++++ spider/src/spider.f 2015-05-21 15:03:36.159704166 +0200 +@@ -195,9 +195,15 @@ + + #ifndef USE_MPI + #ifndef __APPLE__ ++#ifdef SP_IFC ++ isiz1 = kmp_get_stacksize() ++ CALL kmp_set_stacksize(65536) ++ isiz2 = kmp_get_stacksize() ++#else + isiz1 = omp_get_stack_size() + CALL omp_set_stack_size(65536) + isiz2 = omp_get_stack_size() ++#endif + !write(6,*) ' OMP Stack size: ',isiz1,' -->',isiz2 + + #endif +--- spider/src/lundoc.f.orig 2015-03-27 14:08:10.000000000 +0100 ++++ spider/src/lundoc.f 2015-05-21 15:26:30.008871936 +0200 +@@ -1252,7 +1252,7 @@ + INCLUDE 'CMBLOCK.INC' + + INTEGER :: NDOC,MAXKEYT,MAXREGT,KEYSINUSE,IRTFLG +- LOGICAL :: SAYIT ++ LOGICAL :: SAYIT, EOF + + REAL, POINTER :: IPQ(:) + CHARACTER(LEN=80) :: RECLIN ! ONLY NEEDS START +@@ -1319,15 +1319,15 @@ + BACKSPACE(NDOC) ! REREAD LINE + READ(NDOC,*,END=100,IOSTAT=IER) RECLIN + +- ENDFILE = .TRUE. ++ EOF = .TRUE. + READ(NDOC,*,END=100,IOSTAT=IER) NKEY,NREGPLINE +- ENDFILE = .FALSE. ++ EOF = .FALSE. + ENDIF + + +- 100 CALL BCAST_MPI('LUNDOCINFO','ENDFILE',ENDFILE,1,'L',ICOMM) ++ 100 CALL BCAST_MPI('LUNDOCINFO','EOF',EOF,1,'L',ICOMM) + CALL BCAST_MPI('LUNDOCINFO','IER',IER,1,'I',ICOMM) +- IF (ENDFILE) GOTO 799 ++ IF (EOF) GOTO 799 + + CALL BCAST_MPI('LUNDOCINFO','NKEY',NKEY,1,'I',ICOMM) + CALL BCAST_MPI('LUNDOCINFO','NREGPLINE',NREGPLINE,1, +@@ -1434,7 +1434,7 @@ + + REAL :: PLIST(*) + CHARACTER(LEN=180) :: RECLIN +- LOGICAL :: TILLEND ++ LOGICAL :: TILLEND, EOF, ERRFILE + + CALL SET_MPI(ICOMM,MYPID,MPIERR) ! SETS ICOMM AND MYPID + +@@ -1464,18 +1464,18 @@ + 10 CONTINUE + IF (MYPID == 0) THEN + ERRFILE = .TRUE. +- ENDFILE = .TRUE. ++ EOF = .TRUE. + READ (LUNDOC,81,ERR=100,END=200) RECLIN + 81 FORMAT(A120) + ERRFILE = .FALSE. +- ENDFILE = .FALSE. ++ EOF = .FALSE. + ENDIF + + 100 CALL BCAST_MPI('LUNDOCGETCOM','ERRFILE',ERRFILE,1,'L',ICOMM) + IF (ERRFILE) GOTO 998 + +-200 CALL BCAST_MPI('LUNDOCGETCOM','ENDFILE',ENDFILE,1,'L',ICOMM) +- IF (ENDFILE) GOTO 997 ++200 CALL BCAST_MPI('LUNDOCGETCOM','EOF',EOF,1,'L',ICOMM) ++ IF (EOF) GOTO 997 + + CALL BCAST_MPI('LUNDOCGETCOM','RECLIN',RECLIN,180,'C',ICOMM) + +@@ -1580,7 +1580,7 @@ + CHARACTER *120 RECLIN + #ifdef USE_MPI + include 'mpif.h' +- LOGICAL ENDFILE, ERRFILE ++ LOGICAL EOF, ERRFILE + ICOMM = MPI_COMM_WORLD + CALL MPI_COMM_RANK(ICOMM, MYPID, MPIERR) + #else +@@ -1595,15 +1595,15 @@ + #ifdef USE_MPI + 10 IF (MYPID == 0) THEN + ERRFILE = .TRUE. +- ENDFILE = .TRUE. ++ EOF = .TRUE. + READ (LUNDOC,81,ERR=100,END=100) RECLIN + ERRFILE = .FALSE. +- ENDFILE = .FALSE. ++ EOF = .FALSE. + ENDIF + +-100 CALL BCAST_MPI('LUNDOCSAYHDR','ENDFILE',ENDFILE,1,'L',ICOMM) ++100 CALL BCAST_MPI('LUNDOCSAYHDR','EOF',EOF,1,'L',ICOMM) + CALL BCAST_MPI('LUNDOCSAYHDR','ERRFILE',ERRFILE,1,'L',ICOMM) +- IF (ENDFILE .OR. ERRFILE) GOTO 999 ++ IF (EOF .OR. ERRFILE) GOTO 999 + + CALL BCAST_MPI('LUNDOCSAYHDR','RECLIN',RECLIN,120,'C',ICOMM) + #else diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_gfortran49.patch b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_gfortran49.patch new file mode 100644 index 0000000000000000000000000000000000000000..3ffd0417381235daae10cf5dd78cc3a30e9b265b --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_gfortran49.patch @@ -0,0 +1,22 @@ +--- spider/src/copy1.f.orig 2015-06-16 18:11:37.000000000 +0300 ++++ spider/src/copy1.f 2015-06-16 18:12:12.000000000 +0300 +@@ -72,6 +72,8 @@ + INTEGER, PARAMETER :: LUNXM1 = 83 + INTEGER, PARAMETER :: LUNXM2 = 84 + ++ LOGICAL :: VERBOSET ++ + C FROM/'AS','MR','PD','RA','NI','TE','VA','EM','NT','XP'/ + + C TO/'AS','BR','MR','PO','RA','TI','XP','OP','JPG'/ +--- spider/src/pr3d.f.orig 2015-06-16 18:49:45.000000000 +0300 ++++ spider/src/pr3d.f 2015-06-16 18:50:05.000000000 +0300 +@@ -75,7 +75,7 @@ + + CALL SET_MPI(ICOMM,MYPID,MPIERR) + +- WANTSQRTS = (FSCOP == .TRUE.) ++ WANTSQRTS = (FSCOP .eqv. .TRUE.) + + C INPUT FIRST IMAGE + MAXIM = 0 diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..87526d7754bf4761dcf583fd873a6d3d79292399 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-GNU-4.9.3-2.25.eb @@ -0,0 +1,38 @@ +## +# 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 = 'SQLite' +version = '3.8.10.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..fbe46bacc9c1bd8179973683d6bd7b48e215c4a8 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb @@ -0,0 +1,40 @@ +## +# 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 = 'SQLite' +version = '3.8.10.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'foss', 'version': '2015a'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..f71908ec0b0b8f3a6185a4d4b332cdf2ee7b0241 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015b.eb @@ -0,0 +1,40 @@ +## +# 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 = 'SQLite' +version = '3.8.10.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'foss', 'version': '2015b'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..068704800490922c7b972112529c5358c9e4a43c --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.4.10.eb @@ -0,0 +1,40 @@ +## +# 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 = 'SQLite' +version = '3.8.10.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..3ad3a9145ad9ac47ec57addf0d9ce18a086021a5 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-goolf-1.7.20.eb @@ -0,0 +1,40 @@ +## +# 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 = 'SQLite' +version = '3.8.10.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..03c9b50fbabb2dd183ad3118fd064f74afdd885f --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb @@ -0,0 +1,40 @@ +## +# 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 = 'SQLite' +version = '3.8.10.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'intel', 'version': '2015a'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..2008f892f3bb68d29bcc0c52c7b8decd90fe4381 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015b.eb @@ -0,0 +1,40 @@ +## +# 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 = 'SQLite' +version = '3.8.10.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'intel', 'version': '2015b'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..5e77859d0758dc3e6880c242b90029237e0552a9 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb @@ -0,0 +1,38 @@ +## +# 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 = 'SQLite' +version = '3.8.8.1' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'foss', 'version': '2015.05'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.3'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..ee10abf94853081b471a6cfaae6b205fd191a6bc --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.7.20.eb @@ -0,0 +1,38 @@ +## +# 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 = 'SQLite' +version = '3.8.8.1' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2015/'] +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.3'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SRA-Tookit/SRA-Toolkit-2.5.4-1-centos_linux64.eb b/easybuild/easyconfigs/s/SRA-Tookit/SRA-Toolkit-2.5.4-1-centos_linux64.eb new file mode 100644 index 0000000000000000000000000000000000000000..54156d430362f194c3e0815ee79c2e3c9c37d1e4 --- /dev/null +++ b/easybuild/easyconfigs/s/SRA-Tookit/SRA-Toolkit-2.5.4-1-centos_linux64.eb @@ -0,0 +1,26 @@ +# 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 = 'SRA-Toolkit' +version = '2.5.4-1' +versionsuffix = '-centos_linux64' + +homepage = 'http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=std' +description = """ The NCBI SRA Toolkit enables reading (dumping) of sequencing files + from the SRA database and writing (loading) files into the .sra format """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/%(version)s/'] +sources = ['sratoolkit.%(version)s%(versionsuffix)s.tar.gz'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["sra-stat", "sra-sort", "srapath", "bam-load"]], + 'dirs': ["example", "schema"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb new file mode 100644 index 0000000000000000000000000000000000000000..c965b7304ffcfbffbe6901bf7a68cc9efd3e9298 --- /dev/null +++ b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-i686.eb @@ -0,0 +1,35 @@ +# 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 = 'SSAHA2' +version = '2.5.5' +versionsuffix = '-i686' + +homepage = 'http://www.sanger.ac.uk/resources/software/ssaha2/' +description = """ SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a + pairwise sequence alignment program designed for the efficient mapping of sequencing + reads onto genomic reference sequences. SSAHA2 reads of most sequencing platforms + (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) + are supported. A pile-up pipeline for analysis and genotype calling is available as + a separate package. """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['ftp://ftp.sanger.ac.uk/pub/resources/software/ssaha2/'] +sources = ['%%(namelower)s_v%%(version)s_%s.tgz' % versionsuffix[1:]] + +sanity_check_paths = { + 'files': ["ssaha2", "ssaha2Build", "ssahaSNP"], + 'dirs': [], +} + +# add the installation dir to PATH +modextrapaths = { + 'PATH': "", +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb new file mode 100644 index 0000000000000000000000000000000000000000..bb97c237d90c7d939e161fb9b7d896dc1bd1b90d --- /dev/null +++ b/easybuild/easyconfigs/s/SSAHA2/SSAHA2-2.5.5-x86_64.eb @@ -0,0 +1,35 @@ +# 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 = 'SSAHA2' +version = '2.5.5' +versionsuffix = '-x86_64' + +homepage = 'http://www.sanger.ac.uk/resources/software/ssaha2/' +description = """ SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a + pairwise sequence alignment program designed for the efficient mapping of sequencing + reads onto genomic reference sequences. SSAHA2 reads of most sequencing platforms + (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) + are supported. A pile-up pipeline for analysis and genotype calling is available as + a separate package. """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['ftp://ftp.sanger.ac.uk/pub/resources/software/ssaha2/'] +sources = ['%%(namelower)s_v%%(version)s_%s.tgz' % versionsuffix[1:]] + +sanity_check_paths = { + 'files': ["ssaha2", "ssaha2Build", "ssahaSNP"], + 'dirs': [], +} + +# add the installation dir to PATH +modextrapaths = { + 'PATH': "", +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..c428723fec1ce476f55b4e38b9936cec7f7566cc --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb @@ -0,0 +1,34 @@ +# 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 = 'MakeCp' + +name = 'STAR' +version = '2.3.0e' + +homepage = 'https://code.google.com/p/rna-star/' +description = """ STAR aligns RNA-seq reads to a reference genome using + uncompressed suffix arrays. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://rna-star.googlecode.com/files/'] +sources = ['%(name)s_%(version)s.tgz'] + +patches = ['STAR_missing_includes.patch'] + +# a binary is provided with the source files. We delete it +prebuildopts = 'rm STAR && ' + +parallel = 1 + +files_to_copy = [(["STAR"], "bin"), "README.txt"] + +sanity_check_paths = { + 'files': ["bin/STAR"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb b/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..01b05100cc626639dfe354e5aa778f1ca67bbbd3 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.3.1z12' + +homepage = 'https://code.google.com/p/rna-star/' +description = """STAR: ultrafast universal RNA-seq aligner""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/alexdobin/%(name)s/archive/'] +sources = ['%(name)s_%(version)s.tar.gz'] + +checksums = ['c1e5b36a02011a73f9461f5bdc4dacaa'] + +buildopts = 'CXX="$CXX"' + +executables = [name, 'STARstatic'] +files_to_copy = [(executables, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STAR/STAR_missing_includes.patch b/easybuild/easyconfigs/s/STAR/STAR_missing_includes.patch new file mode 100644 index 0000000000000000000000000000000000000000..82d8f2d8e0a94105119f7bf8923219b53e1cd319 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR_missing_includes.patch @@ -0,0 +1,10 @@ +--- STAR_2.3.0e.orig/Genome.cpp 2013-01-22 21:51:14.000000000 +0100 ++++ STAR_2.3.0e/Genome.cpp 2014-08-23 22:06:02.954503545 +0200 +@@ -6,6 +6,7 @@ + #include "streamFuns.h" + #include + #include ++#include + + #define SHM_sizeG 0 + #define SHM_sizeSA 8 diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.7-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.7-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..95fbf9613d624ddda1f7653d0d3e5353788a15c4 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.7-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,23 @@ +name = 'SWIG' +version = '3.0.7' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.10' +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('PCRE', '8.37'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..b503f4c6397a13d4216a949f6beaf17af697f6cf --- /dev/null +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb @@ -0,0 +1,33 @@ +name = 'Sailfish' +version = '0.6.3' +easyblock = 'CMakeMake' + +homepage = 'http://www.cs.cmu.edu/~ckingsf/software/sailfish/' +description = """Sailfish is a software tool that implements a novel, alignment-free algorithm for the estimation of + isoform abundances directly from a set of reference sequences and RNA-seq reads. """ + +toolchain = {'name': 'foss', 'version': '2014b'} + +source_urls = ['https://github.com/kingsfordgroup/sailfish/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.8' +versionsuffix = '-%s-%s' % (python, pyver) + +builddependencies = [ + ('CMake', '3.0.0'), +] + +dependencies = [ + ('Boost', '1.55.0', versionsuffix), + ('tbb', '4.0.5.339', '', True), + ('Jellyfish', '2.1.3'), + ('g2log', '1.0'), +] + +configopts = "-DBOOST_ROOT=$EBROOTBOOST -DTBB_INSTALL_DIR=$EBROOTTBB" + +parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..c80c41e1d54f904953541b1e286d12746e5e24af --- /dev/null +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'Sailfish' +version = '0.7.4' + +homepage = 'http://www.cs.cmu.edu/~ckingsf/software/sailfish/' +description = """Sailfish is a software tool that implements a novel, alignment-free algorithm for the estimation of + isoform abundances directly from a set of reference sequences and RNA-seq reads. """ + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ['https://github.com/kingsfordgroup/sailfish/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = [ + 'Sailfish-%(version)s_bypass-C++11-check.patch', + 'Sailfish-%(version)s_skip-included-Jellyfish.patch', +] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) + +builddependencies = [ + ('CMake', '3.3.2'), +] + +dependencies = [ + ('Boost', '1.59.0', versionsuffix), + ('tbb', '4.3.6.211', '', True), + ('Jellyfish', '2.2.3'), + ('g2log', '1.0'), +] + +configopts = "-DBOOST_ROOT=$EBROOTBOOST -DTBB_INSTALL_DIR=$EBROOTTBB" + +parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_bypass-C++11-check.patch b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_bypass-C++11-check.patch new file mode 100644 index 0000000000000000000000000000000000000000..223ee7d99d2aa11a5431c4d387fb44af425d355d --- /dev/null +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_bypass-C++11-check.patch @@ -0,0 +1,14 @@ +bypass C++11 compatibility check, since it's unaware of Intel compilers (onlt knows about GCC & Clang) +author: Kenneth Hoste (HPC-UGent) +--- CMakeLists.txt.orig 2015-09-06 04:17:26.000000000 +0200 ++++ CMakeLists.txt 2015-09-25 15:37:42.256218132 +0200 +@@ -119,7 +119,8 @@ + set (PTHREAD_LIB "pthread") + endif() + else () +- message(FATAL_ERROR "Your C++ compiler does not support C++11.") ++ #message(FATAL_ERROR "Your C++ compiler does not support C++11.") ++ message(WARNING "Uknown C++ compiler (${CMAKE_CXX_COMPILER_ID}, going to assume that it supports C++11") + endif () + + ## TODO: Figure out how to detect this automatically diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_skip-included-Jellyfish.patch b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_skip-included-Jellyfish.patch new file mode 100644 index 0000000000000000000000000000000000000000..a47f914bc5632e170c73cb8b51bdadc5b2936236 --- /dev/null +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.7.4_skip-included-Jellyfish.patch @@ -0,0 +1,44 @@ +remove fetching/building of Jellyfish, since it's provided via EasyBuild +author: Kenneth Hoste (HPC-UGent) +--- CMakeLists.txt.orig 2015-09-06 04:17:26.000000000 +0200 ++++ CMakeLists.txt 2015-09-25 15:37:42.256218132 +0200 +@@ -274,21 +275,6 @@ + + set(EXTERNAL_LIBRARY_PATH $CMAKE_CURRENT_SOURCE_DIR/lib) + +-message("Build system will fetch and build Jellyfish") +-message("==================================================================") +-ExternalProject_Add(libjellyfish +- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external +- URL ftp://ftp.genome.umd.edu/pub/jellyfish/jellyfish-2.1.3.tar.gz +- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.1.3 +- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install +- CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.1.3/configure --prefix= CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS} +- BUILD_COMMAND ${MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS} +- BUILD_IN_SOURCE 1 +- INSTALL_COMMAND make install && +- cp config.h /include/jellyfish-2.1.3/jellyfish/ && +- cp config.h /include/ +-) +- + find_package(TBB) + ## + # +--- src/CMakeLists.txt.orig 2015-09-06 04:17:26.000000000 +0200 ++++ src/CMakeLists.txt 2015-09-29 14:10:00.134610574 +0200 +@@ -40,7 +40,6 @@ + ${GAT_SOURCE_DIR}/external/cereal/include + ${GAT_SOURCE_DIR}/external/install/include + ${GAT_SOURCE_DIR}/external/install/include/rapmap +-${GAT_SOURCE_DIR}/external/install/include/jellyfish-2.1.3 + ${ZLIB_INCLUDE_DIR} + ${TBB_INCLUDE_DIRS} + ${Boost_INCLUDE_DIRS} +@@ -85,7 +84,6 @@ + ${Boost_LIBRARIES} + gff + ${ZLIB_LIBRARY} +- ${GAT_SOURCE_DIR}/external/install/lib/libjellyfish-2.0.a + m + ${TBB_LIBRARIES} + ${LIBSAILFISH_LINKER_FLAGS} diff --git a/easybuild/easyconfigs/s/Samcef/Samcef-17.0-03.eb b/easybuild/easyconfigs/s/Samcef/Samcef-17.0-03.eb new file mode 100644 index 0000000000000000000000000000000000000000..7464a3d289d1a945d47185be1dafd0d63fafe6ea --- /dev/null +++ b/easybuild/easyconfigs/s/Samcef/Samcef-17.0-03.eb @@ -0,0 +1,14 @@ +name = 'Samcef' +version = '17.0-03' + +homepage = 'http://www.plm.automation.siemens.com/en_us/products/lms/samtech/samcef-solver-suite/' +description = """FEM solver solution suite for basic linear structures to advanced, flexible nonlinear mechanisms and + thermal applications.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# licensed software, no source URls for automatic download +# note: unpacking requires that 7z (p7zip) is available +sources = ['SamcefV%(version)s.iso'] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..758c146b8325e485f7ccda335760156c4ac8d0ca --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015b-OpenBLAS-0.2.14-LAPACK-3.5.0.eb @@ -0,0 +1,25 @@ +name = 'ScaLAPACK' +version = '2.0.2' + +homepage = 'http://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2015b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.14' +blassuff = '-LAPACK-3.5.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, ('GNU', '4.9.3-2.25'))] + +## parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..55d127b2f7d9b73bbcce60e64867ab0c60e3fba1 --- /dev/null +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-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/ +## +easyblock = 'EB_Score_minus_P' + +name = "Scalasca" +version = "2.2" + +homepage = 'http://www.scalasca.org/' +description = """Scalasca is a software tool that supports the performance optimization of + parallel programs by measuring and analyzing their runtime behavior. The analysis identifies + potential performance bottlenecks -- in particular those concerning communication and + synchronization -- and offers guidance in exploring their causes.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {"usempi": True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/scalasca/%(version_major_minor)s/dist'] + +checksums = [ + '06e0380c612811a1ff9c183fed9331a9', # scalasca-2.2.tar.gz +] + +dependencies = [ + ('Cube', '4.3'), + ('OTF2', '1.5.1'), +] + +sanity_check_paths = { + 'files': ["bin/scalasca", ("lib64/libpearl.replay.a", "lib/libpearl.replay.a")], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..137bacee9cab4f55cbfc869ca4330c81a0c97e92 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb @@ -0,0 +1,40 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Authors:: Jordi Blasco +# License:: New BSD +# +# make sure we don't fall back to the ConfigureMake easyblock + +easyblock = 'EB_Score_minus_P' + +name = "Score-P" +version = "1.2.3" + +homepage = 'http://www.score-p.org' +description = """The Score-P measurement infrastructure is a highly scalable and + easy-to-use tool suite for profiling, event tracing, and online analysis of HPC + applications.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {"usempi": True} + +# http://www.vi-hps.org/upload/packages/scorep/scorep-1.2.1.tar.gz +sources = ["scorep-%(version)s.tar.gz"] +source_urls = ['http://www.vi-hps.org/upload/packages/scorep/'] + +# compiler toolchain depencies +dependencies = [ + ('binutils', '2.22'), + ('Cube', '4.2.3'), + ('OPARI2', '1.1.2'), + ('OTF2', '1.2.1'), + ('PAPI', '5.2.0'), + ('PDT', '3.20'), +] + +sanity_check_paths = { + 'files': ["bin/scorep", "include/scorep/SCOREP_User.h", + ("lib64/libscorep_adapter_mpi_event.a", "lib/libscorep_adapter_mpi_event.a")], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..91b0941367ae6df6439ce4d8d3a890e732f8a3f3 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb @@ -0,0 +1,46 @@ +# 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/ +## +# make sure we don't fall back to the ConfigureMake easyblock +easyblock = 'EB_Score_minus_P' + +name = 'Score-P' +version = '1.4' + +homepage = 'http://www.score-p.org' +description = """The Score-P measurement infrastructure is a highly scalable and + easy-to-use tool suite for profiling, event tracing, and online analysis of HPC + applications.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {"usempi": True} + +sources = ["scorep-%(version)s.tar.gz"] +source_urls = ['http://www.vi-hps.org/upload/packages/scorep/'] + +checksums = [ + '17bd732cf54097d35157bf0d8284ad78', # scorep-1.4.tar.gz +] + +# compiler toolchain depencies +dependencies = [ + ('binutils', '2.25', '', ('GCC', '4.9.2')), + ('Cube', '4.3'), + ('OPARI2', '1.1.2'), + ('OTF2', '1.5.1'), + ('PAPI', '5.4.0'), + ('PDT', '3.20'), +] + +sanity_check_paths = { + 'files': ["bin/scorep", "include/scorep/SCOREP_User.h", + ("lib64/libscorep_adapter_mpi_event.a", "lib/libscorep_adapter_mpi_event.a")], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.6.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.6.0-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..63cb8346ded5af12407a0316d177c20b52e8990b --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.6.0-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,30 @@ +# 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 + +easyblock = "PythonPackage" + +name = 'Seaborn' +version = '0.6.0' + +homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/mwaskom/seaborn/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.5' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..febe7d2fb6a453a218f5acec10a906e702034006 --- /dev/null +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.8-foss-2015a.eb @@ -0,0 +1,38 @@ +easyblock = 'SCons' +name = 'Serf' +version = '1.3.8' + +homepage = 'http://serf.apache.org/' +description = """The serf library is a high performance C-based HTTP client library + built upon the Apache Portable Runtime (APR) library""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = [ + ('%(name)s-%(version)s_remve_c99_comment.patch'), + ('%(name)s-%(version)s_SCons_ld_lib.patch'), +] + +builddependencies = [('SCons', '2.3.6', '-Python-2.7.9')] + +dependencies = [ + ('APR', '1.5.2'), + ('APR-util', '1.5.4'), +# ('OpenSSL', '1.0.1p'), # 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 +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +buildopts = "APR=$EBROOTAPR/bin/apr-1-config APU=$EBROOTAPRMINUTIL/bin/apu-1-config" + +sanity_check_paths = { + 'files': ['include/serf-1/serf.h'] + + ['lib/libserf-1.%s' % x for x in ['a', 'so']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.8_SCons_ld_lib.patch b/easybuild/easyconfigs/s/Serf/Serf-1.3.8_SCons_ld_lib.patch new file mode 100644 index 0000000000000000000000000000000000000000..5dbaafe5c94a08dcf0c40ca7a00985862de6c562 --- /dev/null +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.8_SCons_ld_lib.patch @@ -0,0 +1,15 @@ +#SCons deletes LD_LIBRARY_PATH, and cannot use non-system python in test phase. +#This restores original LD_LIBRARY_PATH +#B. Hajgato 16th September 2015 +--- SConstruct.org 2014-02-04 21:11:10.000000000 +0100 ++++ SConstruct 2015-09-16 14:51:43.245327962 +0200 +@@ -436,7 +436,8 @@ + TEST_EXES = [ os.path.join('test', '%s' % (prog)) for prog in TEST_PROGRAMS ] + + env.AlwaysBuild(env.Alias('check', TEST_EXES, sys.executable + ' build/check.py', +- ENV={'PATH' : os.environ['PATH']})) ++ ENV={'PATH' : os.environ['PATH'], ++ 'LD_LIBRARY_PATH' : os.environ['LD_LIBRARY_PATH']})) + + # Find the (dynamic) library in this directory + tenv.Replace(RPATH=thisdir) diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.8_remve_c99_comment.patch b/easybuild/easyconfigs/s/Serf/Serf-1.3.8_remve_c99_comment.patch new file mode 100644 index 0000000000000000000000000000000000000000..ec94f9c82481b2eb06854d9c1c087f7eed1b5acc --- /dev/null +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.8_remve_c99_comment.patch @@ -0,0 +1,15 @@ +#Remove C99 style comment (from file in test phase) +#https://code.google.com/p/serf/source/detail?r=2443 +--- test/test_buckets.c.org 2015-09-16 14:22:37.884308890 +0200 ++++ test/test_buckets.c 2015-09-16 14:23:44.311351710 +0200 +@@ -1232,9 +1232,9 @@ + + /* The largest buffer we should need is 0.1% larger than the + uncompressed data, + 12 bytes. This info comes from zlib.h. ++ buf_size = orig_len + (orig_len / 1000) + 12; + Note: This isn't sufficient when using Z_NO_FLUSH and extremely compressed + data. Use a buffer bigger than what we need. */ +-// buf_size = orig_len + (orig_len / 1000) + 12; + buf_size = 100000; + + write_buf = apr_palloc(pool, buf_size); diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.4.1.eb b/easybuild/easyconfigs/s/Spark/Spark-1.4.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..fa568cc1446eb66c51aa86a2f209f6f8a9daa968 --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-1.4.1.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'Spark' +version = '1.4.1' + +homepage = 'http://spark.apache.org' +description = """Spark is Hadoop MapReduce done in memory""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s-bin-hadoop2.6.tgz'] +source_urls = [ + 'http://apache.belnet.be/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.eu.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.us.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', +] + +dependencies = [('Java', '1.7.0_80')] + +sanity_check_paths = { + 'files': ['bin/spark-shell'], + 'dirs': ['lib', 'python'] +} + +modextrapaths = {'PYTHONPATH': 'python'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.5.0.eb b/easybuild/easyconfigs/s/Spark/Spark-1.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..081d6d615b83b2e8fc67e8cd605075c665874432 --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-1.5.0.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'Spark' +version = '1.5.0' + +homepage = 'http://spark.apache.org' +description = """Spark is Hadoop MapReduce done in memory""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s-bin-hadoop2.6.tgz'] +source_urls = [ + 'http://apache.belnet.be/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.eu.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.us.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', +] + +dependencies = [('Java', '1.7.0_80')] + +sanity_check_paths = { + 'files': ['bin/spark-shell'], + 'dirs': ['lib', 'python'] +} + +modextrapaths = {'PYTHONPATH': 'python'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9bae8b637e1c02963100cc848cd72284fe371ae6 --- /dev/null +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.8.14-foss-2015a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Subversion' +version = '1.8.14' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [ + 'http://apache.belnet.be/%(namelower)s', + 'http://www.eu.apache.org/dist/%(namelower)s', + 'http://www.us.apache.org/dist/%(namelower)s', +] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('APR', '1.5.2'), + ('APR-util', '1.5.4'), + ('SQLite', '3.8.8.1'), + ('zlib', '1.2.8'), + ('Serf', '1.3.8'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-serf=$EBROOTSERF" + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.3-intel-2015a-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.3-intel-2015a-ParMETIS-4.0.3.eb index 267fa3a4ce772317c7bf02f728be2e81806e5beb..ace5e2598532ee40dfa355f455135b9d6e834b6c 100644 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.3-intel-2015a-ParMETIS-4.0.3.eb +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.4.3-intel-2015a-ParMETIS-4.0.3.eb @@ -5,7 +5,7 @@ homepage = 'http://www.cise.ufl.edu/research/sparse/SuiteSparse/' description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" toolchain = {'name': 'intel', 'version': '2015a'} -toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'static': True} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True} source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] sources = [SOURCE_TAR_GZ] diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2014b.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..9d1f75c5eb86da7db35e3da92c6efccddcfa985a --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2014b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'foss', 'version': '2014b'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-5.4.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..43e89506aa9109ba49c579d236b3c1d76791cf46 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-5.4.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'ictce', 'version': '5.4.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-6.1.5.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-6.1.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..d90d48702e0469fa4f0aa9cf1081706f00641106 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-6.1.5.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'ictce', 'version': '6.1.5'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.so"] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..42f9a9c3ff6485e0a4f13088d6615f0f899c70a7 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'scikit-image' +version = '0.11.3' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' + +versionsuffix = "-%s-%s" % (python, pyver) +dependencies = [ + (python, pyver), + ('Qhull', '2012.1'), + ('matplotlib', '1.4.3', versionsuffix), + ('networkx', '1.10', versionsuffix), + ('Pillow', '2.9.0', versionsuffix), +] + +options = {'modulename': 'skimage'} + +pyshortver = '.'.join(pyver.split('.')[:-1]) +pylibdir = 'lib/python%s/site-packages' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': ['%s/scikit_image-%%(version)s-py%s-linux-x86_64.egg' % (pylibdir, pyshortver)], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-3.5.0.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-3.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..6d4468286e6314f717a67a0543d1368320d2dfb2 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.11.3-intel-2015b-Python-3.5.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'scikit-image' +version = '0.11.3' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '3.5.0' + +versionsuffix = "-%s-%s" % (python, pyver) +dependencies = [ + (python, pyver), + ('Qhull', '2012.1'), + ('matplotlib', '1.4.3', versionsuffix), + ('networkx', '1.10', versionsuffix), + ('Pillow', '2.9.0', versionsuffix), +] + +options = {'modulename': 'skimage'} + +pyshortver = '.'.join(pyver.split('.')[:-1]) +pylibdir = 'lib/python%s/site-packages' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': ['%s/scikit_image-%%(version)s-py%s-linux-x86_64.egg' % (pylibdir, pyshortver)], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 96310147cf3f7cc403d0533305ec957cebba3f0a..fcb7b2818b50714cd33871991bac9a9813b6331f 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -1,7 +1,7 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' -name = "scikit-learn" -version = "0.13" +name = 'scikit-learn' +version = '0.13' homepage = 'http://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, @@ -14,15 +14,20 @@ toolchain = {'version': '1.1.0-no-OFED', 'name': 'goalf'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:2]) +python = 'Python' +pyver = '2.7.3' -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ - (python, pythonversion), + (python, pyver), ('matplotlib', '1.1.1', versionsuffix), ] -options = {'modulename': "sklearn"} +options = {'modulename': 'sklearn'} + +pyshortver = '.'.join(pyver.split('.')[:2]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sklearn' % pyshortver], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-4.1.13-Python-2.7.3.eb index 568e256fdc759e20381e90035f5fe8f6b1178f4d..1323b9230cb618c3824da8c0f924f2eacaa213a3 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-4.1.13-Python-2.7.3.eb @@ -1,6 +1,7 @@ -easyblock = "PythonPackage" -name = "scikit-learn" -version = "0.13" +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.13' homepage = 'http://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, @@ -13,15 +14,20 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +python = 'Python' +pyver = '2.7.3' -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ - (python, pythonversion), + (python, pyver), ('matplotlib', '1.2.0', versionsuffix), ] -options = {'modulename': "sklearn"} +options = {'modulename': 'sklearn'} + +pyshortver = '.'.join(pyver.split('.')[:-1]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sklearn' % pyshortver], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-5.3.0-Python-2.7.3.eb index e7e1f0c3228f6a9ea973535408d86adf29c83acd..5cce29e1eaa1819d7d41a261af4daa548ccccbed 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.13-ictce-5.3.0-Python-2.7.3.eb @@ -1,6 +1,7 @@ -easyblock = "PythonPackage" -name = "scikit-learn" -version = "0.13" +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.13' homepage = 'http://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, @@ -13,15 +14,20 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.3' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +python = 'Python' +pyver = '2.7.3' -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ - (python, pythonversion), + (python, pyver), ('matplotlib', '1.2.0', versionsuffix), ] -options = {'modulename': "sklearn"} +options = {'modulename': 'sklearn'} + +pyshortver = '.'.join(pyver.split('.')[:-1]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sklearn' % pyshortver], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-4.1.13-Python-2.7.5.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-4.1.13-Python-2.7.5.eb index 202d34e1119d40f331f29b207b005e6fd551de31..0ca848e977dfdeae12eb40c34fad48a1116d9fc9 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-4.1.13-Python-2.7.5.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-4.1.13-Python-2.7.5.eb @@ -1,7 +1,7 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' -name = "scikit-learn" -version = "0.14" +name = 'scikit-learn' +version = '0.14' homepage = 'http://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, @@ -14,16 +14,21 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.5' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +python = 'Python' +pyver = '2.7.5' -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ - (python, pythonversion), + (python, pyver), ('matplotlib', '1.3.0', versionsuffix), ] -options = {'modulename': "sklearn"} +options = {'modulename': 'sklearn'} + +pyshortver = '.'.join(pyver.split('.')[:-1]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sklearn' % pyshortver], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb index 380fb7075a50401c7944cd605babc0ce1bf51564..3f7d9ba4f767fb86810bc1751ec937580758c3e4 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.3.0-Python-2.7.5.eb @@ -1,7 +1,7 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' -name = "scikit-learn" -version = "0.14" +name = 'scikit-learn' +version = '0.14' homepage = 'http://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, @@ -14,16 +14,21 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.5' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +python = 'Python' +pyver = '2.7.5' -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ - (python, pythonversion), + (python, pyver), ('matplotlib', '1.3.0', versionsuffix), ] -options = {'modulename': "sklearn"} +options = {'modulename': 'sklearn'} + +pyshortver = '.'.join(pyver.split('.')[:-1]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sklearn' % pyshortver], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb index 22f760cf88210dd3eb079847ab2231961a58da5c..8ef7bdd7ea0d2f3a61c1b7cf3a717ba7a5e865fe 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.14-ictce-5.5.0-Python-2.7.6.eb @@ -1,7 +1,7 @@ -easyblock = "PythonPackage" +easyblock = 'PythonPackage' -name = "scikit-learn" -version = "0.14" +name = 'scikit-learn' +version = '0.14' homepage = 'http://scikit-learn.org/stable/index.html' description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, @@ -14,16 +14,21 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -python = "Python" -pythonversion = '2.7.6' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +python = 'Python' +pyver = '2.7.6' -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ - (python, pythonversion), + (python, pyver), ('matplotlib', '1.3.1', versionsuffix), ] -options = {'modulename': "sklearn"} +options = {'modulename': 'sklearn'} + +pyshortver = '.'.join(pyver.split('.')[:-1]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sklearn' % pyshortver], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb index 8b997036dd3d105b2ad03a19cf8e61af6ffedf51..ea3aa7a366d747e7a9d2e56f7308c959da6ff8e2 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb @@ -15,15 +15,20 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' -pythonversion = '2.7.9' -pythonshortversion = ".".join(pythonversion.split(".")[:-1]) +pyver = '2.7.9' -versionsuffix = "-%s-%s" % (python, pythonversion) +versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ - (python, pythonversion), + (python, pyver), ('matplotlib', '1.4.3', versionsuffix), ] -options = {'modulename': "sklearn"} +options = {'modulename': 'sklearn'} + +pyshortver = '.'.join(pyver.split('.')[:-1]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sklearn' % pyshortver], +} moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015b-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..d7c757bc8257c9366f38792b7c6424f72ce247f2 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015b-Python-2.7.10.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.16.1' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' + +versionsuffix = "-%s-%s" % (python, pyver) +dependencies = [ + (python, pyver), + ('matplotlib', '1.4.3', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +pyshortver = '.'.join(pyver.split('.')[:-1]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sklearn' % pyshortver], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015b-Python-3.5.0.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015b-Python-3.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..27c24dc20dbac8ca67881f1ff845f60d028dcbf3 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015b-Python-3.5.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.16.1' + +homepage = 'http://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '3.5.0' + +versionsuffix = "-%s-%s" % (python, pyver) +dependencies = [ + (python, pyver), + ('matplotlib', '1.4.3', versionsuffix), +] + +options = {'modulename': 'sklearn'} + +pyshortver = '.'.join(pyver.split('.')[:-1]) +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sklearn' % pyshortver], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-GCC-4.9.2.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-GCC-4.9.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..551924427db6983d92bab23312dfba6e75b0a384 --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-GCC-4.9.2.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'snappy' +version = '1.1.2' + +# snappy was migrated from code.google.com to github.com and this commit +# corresponds to release 1.1.2 (which they haven't tagged). +# see https://github.com/google/snappy/commit/1ff9be9 +commit = '1ff9be9' + +homepage = 'http://code.google.com/p/snappy/' +description = """Snappy is a compression/decompression library. It does not aim +for maximum compression, or compatibility with any other compression library; +instead, it aims for very high speeds and reasonable compression.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +source_urls = ['https://github.com/google/snappy/archive'] +sources = ['%s.tar.gz' % commit] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['lib/libsnappy.so'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..1043087833fca0e54aba1eb3a677560c0d4a926a --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.3-GCC-4.9.3.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'snappy' +version = '1.1.3' + +# snappy was migrated from code.google.com to github.com and this commit +# corresponds to release 1.1.2 (which they haven't tagged). +# see https://github.com/google/snappy/commit/1ff9be9 +commit = '1ff9be9' + +homepage = 'http://code.google.com/p/snappy/' +description = """Snappy is a compression/decompression library. It does not aim +for maximum compression, or compatibility with any other compression library; +instead, it aims for very high speeds and reasonable compression.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3'} + +source_urls = ['https://github.com/google/snappy/archive'] +sources = ['%s.tar.gz' % commit] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['lib/libsnappy.so'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb new file mode 100644 index 0000000000000000000000000000000000000000..eb194cd37cc756f5b9ea0038082aa08ff50e90f0 --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb @@ -0,0 +1,28 @@ +easyblock = 'PackedBinary' + +name = 'snpEff' +version = '3.6' + +homepage = 'http://sourceforge.net/projects/snpeff/' +description = """SnpEff is a variant annotation and effect prediction tool. + It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) + +source_urls = [SOURCEFORGE_SOURCE] +sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] + +dependencies = [(java, javaver)] + +checksums = ['f4571413833df913261ff76b6f40bb76'] + +sanity_check_paths = { + 'files': ['snpEff.jar', 'SnpSift.jar'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb new file mode 100644 index 0000000000000000000000000000000000000000..8b1570a18150845687b89346f1c32f6eeb2a6e47 --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb @@ -0,0 +1,28 @@ +easyblock = 'PackedBinary' + +name = 'snpEff' +version = '4.1d' + +homepage = 'http://sourceforge.net/projects/snpeff/' +description = """SnpEff is a variant annotation and effect prediction tool. + It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) + +source_urls = [SOURCEFORGE_SOURCE] +sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] + +dependencies = [(java, javaver)] + +checksums = ['23b48ebe02288c1e3c5c0391949eea5a'] + +sanity_check_paths = { + 'files': ['snpEff.jar', 'SnpSift.jar'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..2e71f2ce6be53d7dec7f0e8613cd700076c66cb9 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-CrayGNU-5.2.40.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'spglib' +version = '1.7.3' + +homepage = 'http://spglib.sourceforge.net/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'dynamic': True, } + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +start_dir = '%(name)s-%(version)s' + +sanity_check_paths = { + 'files': ['lib/libsymspg.a', 'lib/libsymspg.so'], + 'dirs': ['include/spglib'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..ffcc2cbe6ccfedd0bd29d0b7e1033bd99d41eb8e --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '0.7.6' + +homepage = 'http://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://github.com/sympy/sympy/releases/download/sympy-%(version)s/'] +sources = [SOURCE_TAR_GZ] + +patches = ['sympy-%(version)s_fix-numpy-include.patch'] + +python = 'Python' +pyver = '2.7.10' +pyshortver = '.'.join(pyver.split('.')[:-1]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [(python, pyver)] + +runtest = 'python setup.py test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sympy' % pyshortver], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.9.eb index 4722866acfba5f7a604033484922154903cdf825..7d47c242de032667deabfba024fc89fcb0217122 100644 --- a/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.9.eb @@ -14,6 +14,8 @@ toolchain = {'name': 'intel', 'version': '2015a'} source_urls = ['https://github.com/sympy/sympy/releases/download/sympy-%(version)s/'] sources = [SOURCE_TAR_GZ] +patches = ['sympy-%(version)s_fix-numpy-include.patch'] + python = "Python" pythonversion = '2.7.9' pythonshortversion = '.'.join(pythonversion.split('.')[:-1]) diff --git a/easybuild/easyconfigs/s/sympy/sympy-0.7.6_fix-numpy-include.patch b/easybuild/easyconfigs/s/sympy/sympy-0.7.6_fix-numpy-include.patch new file mode 100644 index 0000000000000000000000000000000000000000..6e2d922faddb8cedfc3ffa689fc33c35d6bb95a7 --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-0.7.6_fix-numpy-include.patch @@ -0,0 +1,98 @@ +see https://github.com/sympy/sympy/pull/8848 + +From 1615390dff374f67fe12a13a424435e2725f3e79 Mon Sep 17 00:00:00 2001 +From: "Jason K. Moore" +Date: Mon, 19 Jan 2015 09:48:48 -0800 +Subject: [PATCH] Added np.get_include() to Cython autowrapper, fixes #8847. + +- Made CodeWrapper a new style class. +- Moved _need_numpy into __init__ so it doesn't pollute other instances. +- Optionally include numpy include directories in Cython setup.py. +--- + sympy/utilities/autowrap.py | 51 ++++++++++++++++++++++++++++----------------- + 1 file changed, 32 insertions(+), 19 deletions(-) + +diff --git a/sympy/utilities/autowrap.py b/sympy/utilities/autowrap.py +index bed39ef..8af7fbf 100644 +--- a/sympy/utilities/autowrap.py ++++ b/sympy/utilities/autowrap.py +@@ -93,7 +93,7 @@ class CodeWrapError(Exception): + pass + + +-class CodeWrapper: ++class CodeWrapper(object): + """Base Class for code wrappers""" + _filename = "wrapped_code" + _module_basename = "wrapper_module" +@@ -211,30 +211,35 @@ class CythonCodeWrapper(CodeWrapper): + """Wrapper that uses Cython""" + + setup_template = ( +- "from distutils.core import setup\n" +- "from distutils.extension import Extension\n" +- "from Cython.Distutils import build_ext\n" +- "\n" +- "setup(\n" +- " cmdclass = {{'build_ext': build_ext}},\n" +- " ext_modules = [Extension({ext_args}, extra_compile_args=['-std=c99'])]\n" +- " )") ++ "from distutils.core import setup\n" ++ "from distutils.extension import Extension\n" ++ "from Cython.Distutils import build_ext\n" ++ "{np_import}" ++ "\n" ++ "setup(\n" ++ " cmdclass = {{'build_ext': build_ext}},\n" ++ " ext_modules = [Extension({ext_args},\n" ++ " extra_compile_args=['-std=c99'])],\n" ++ "{np_includes}" ++ " )") + + pyx_imports = ( +- "import numpy as np\n" +- "cimport numpy as np\n\n") ++ "import numpy as np\n" ++ "cimport numpy as np\n\n") + + pyx_header = ( +- "cdef extern from '{header_file}.h':\n" +- " {prototype}\n\n") ++ "cdef extern from '{header_file}.h':\n" ++ " {prototype}\n\n") + + pyx_func = ( +- "def {name}_c({arg_string}):\n" +- "\n" +- "{declarations}" +- "{body}") ++ "def {name}_c({arg_string}):\n" ++ "\n" ++ "{declarations}" ++ "{body}") + +- _need_numpy = False ++ def __init__(self, *args, **kwargs): ++ super(CythonCodeWrapper, self).__init__(*args, **kwargs) ++ self._need_numpy = False + + @property + def command(self): +@@ -251,8 +256,16 @@ def _prepare_files(self, routine): + + # setup.py + ext_args = [repr(self.module_name), repr([pyxfilename, codefilename])] ++ if self._need_numpy: ++ np_import = 'import numpy as np\n' ++ np_includes = ' include_dirs = [np.get_include()],\n' ++ else: ++ np_import = '' ++ np_includes = '' + with open('setup.py', 'w') as f: +- f.write(self.setup_template.format(ext_args=", ".join(ext_args))) ++ f.write(self.setup_template.format(ext_args=", ".join(ext_args), ++ np_import=np_import, ++ np_includes=np_includes)) + + @classmethod + def _get_wrapped_function(cls, mod, name): diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..bd202e0e1bf8a43b6fd3ea50ee862a587774a3e8 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.3' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.7.20.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..41060701af9d916894364e98bb050cbfe6e2e6ed --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.7.20.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.3' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..9f6e6c6b27adb24d3a4940810d39a5f64505d878 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-GNU-4.9.3-2.25.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8', '', ('GCC', '4.9.3-binutils-2.25')), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015b.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ba9826c847cd16c54dd51efc766448bb74559faa --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..fe02a2bc48eb5b655c5b8cf32493aa2a126492d7 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.4.10.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.7.20.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..e2124cc24dd1bd2fd38f2e70acc86afe3d7ba90f --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.7.20.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-ictce-7.3.5.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-ictce-7.3.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..ab1bbc53d31b00003a7e6f78f26dedd3ebaa3230 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-ictce-7.3.5.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015b.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ae2268790f4ac75746b456e016e11d0644a77515 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.4' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..335241b80726b196c98de41bb1409b9db0df06ee --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'Theano' +version = '0.6.0' + +homepage = 'http://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://pypi.python.org/packages/source/T/%s' % name] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.3' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [(python, pythonver)] + +sanity_check_paths = { + 'files': ['bin/theano-cache', 'lib/python%s/site-packages/%s-%s-py%s.egg' + % (pythonshortver, name, version, pythonshortver)], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..a9aa394aab847d79036b6f808f6ed0476689fee3 --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'Theano' +version = '0.6.0' + +homepage = 'http://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/T/%s' % name] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.3' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [(python, pythonver)] + +sanity_check_paths = { + 'files': ['bin/theano-cache', 'lib/python%s/site-packages/%s-%s-py%s.egg' + % (pythonshortver, name, version, pythonshortver)], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..a79397a5f8d8bc0d83be477080f2029970327ffa --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.1-ictce-5.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.1' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain +that provides a library of basic elements for building a graphical user +interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [('Tcl', version)] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..602101704ac40739961538d102c4e94d3d2da717 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.3' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..8ff29d34a28dd637d9b8ea3b684e3144f2ae75c4 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.3' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..c34f24fd99b7d222605dc64889c19d9310eb082e --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.3' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..a292e06eb8d354f8f350dd93a00f2cdba642f757 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.3' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'gompi', 'version': '1.5.16'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..cd4da6afb65ea2c76938a0a1ab28ece42f2ed959 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.3' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..025f5e64769cc609b4615df61b60138d4101d5cf --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.3' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..d841e7bd84c473523c5a9279634389b6e9572d7b --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.3' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..e5657f531c0f318c6466d460e29c386888351fa0 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-GNU-4.9.3-2.25-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..a7e3e3028a1a1ed8bf616106bd12302ef1c21e35 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015b-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..2b006409f00220f88b5b480250a90e785eff2dcf --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.4.10-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..5d72cc8d790953b40950a662062b17a3c547e1e9 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..2363e89fc918cbdd0f68d3b8cf4811bb6e42be1e --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..2a26e9ef0a1fe12d484f52561f3e2a160214b4be --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015b-no-X11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +versionsuffix = '-no-X11' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building + a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intel', 'version': '2015b'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..d99d70b100c2417eddd9b9f880f16acc2a59ca79 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'TopHat' +version = '2.0.13' + +homepage = 'http://ccb.jhu.edu/software/tophat/' +description = """TopHat is a fast splice junction mapper for RNA-Seq reads.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] + +patches = ['tophat-%(version)s-zlib.patch'] + +dependencies = [ + ('Boost', '1.55.0'), + ('zlib', '1.2.8'), +] + +configopts = '--with-boost=$EBROOTBOOST' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/tophat'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..6743572399208ab0950369ed77f5e3a8357cfc1a --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.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 = 'ConfigureMake' + +name = 'TopHat' +version = '2.0.14' + +homepage = 'http://ccb.jhu.edu/software/tophat/' +description = """TopHat is a fast splice junction mapper for RNA-Seq reads.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] + +patches = ['tophat-2.0.13-zlib.patch'] + +dependencies = [ + ('Boost', '1.58.0'), + ('zlib', '1.2.8'), +] + +configopts = '--with-boost=$EBROOTBOOST' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/tophat'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch b/easybuild/easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch new file mode 100644 index 0000000000000000000000000000000000000000..6021cbe107fb5f9f9b25ebfe6dbff72ec0eb3038 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch @@ -0,0 +1,12 @@ +diff -ru tophat-2.0.13.orig/src/samtools-0.1.18/Makefile tophat-2.0.13/src/samtools-0.1.18/Makefile +--- tophat-2.0.13.orig/src/samtools-0.1.18/Makefile 2014-09-25 04:38:49.000000000 +0200 ++++ tophat-2.0.13/src/samtools-0.1.18/Makefile 2015-06-03 18:10:39.588554000 +0200 +@@ -12,7 +12,7 @@ + PROG= samtools_0.1.18 + INCLUDES= -I. + SUBDIRS= . bcftools +-LIBPATH= ++LIBPATH= -L$(EBROOTZLIB)/lib + LIBCURSES= -lcurses + + .SUFFIXES:.c .o diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..53e79949f3235b70465eed1f46917e833f84c6d1 --- /dev/null +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.3.7-goolf-1.4.10.eb @@ -0,0 +1,28 @@ +easyblock = "PackedBinary" + +name = 'Trim_Galore' +version = '0.3.7' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' +description = """A wrapper tool around Cutadapt and FastQC to consistently apply + quality and adapter trimming to FastQ files, with some extra functionality for + MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = ['%(namelower)s_v%(version)s.zip'] +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s'] + +install_cmd = "cp -a %(namelower)s_zip/* %(installdir)s && chmod +x %(installdir)s/%(namelower)s" + +dependencies = [ + ('FastQC', '0.10.1'), + ('cutadapt', '1.5', '-Python-2.7.10'), +] + +sanity_check_paths = { + 'files': ["trim_galore"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.eb new file mode 100644 index 0000000000000000000000000000000000000000..a89bd3216ae95b6189d1f43939cda6d2bb4be060 --- /dev/null +++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.32-Java-1.7.0_80.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 + +easyblock = 'Tarball' + +name = 'Trimmomatic' +version = '0.32' + +homepage = 'http://www.usadellab.org/cms/?page=trimmomatic' +description = """Trimmomatic performs a variety of useful trimming tasks for illumina + paired-end and single ended data.The selection of trimming steps and their associated + parameters are supplied on the command line. """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/'] +sources = [SOURCE_ZIP] + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +modloadmsg = """To execute Trimmomatic run: java -jar \\$EBROOTTRIMMOMATIC/trimmomatic-%(version)s.jar""" + +sanity_check_paths = { + 'files': ["trimmomatic-%(version)s.jar"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..4ab3c4b882088688322a148927a4bae7ce718c7b --- /dev/null +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.eb @@ -0,0 +1,38 @@ +# 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 +# Author: Jens Timmerman, Ghent University + +easyblock = 'MakeCp' + +name = 'tabix' +version = '0.2.6' + +homepage = 'http://samtools.sourceforge.net' +description = """ Generic indexer for TAB-delimited genome position files """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [('http://sourceforge.net/projects/samtools/files/', 'download')] +sources = [SOURCE_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +buildopts = 'CFLAGS="-L$EBROOTZLIB/lib"' + +files_to_copy = [ + (["tabix", "bgzip", "tabix.py"], "bin"), + (["tabix.1"], "man/man1"), + "example.gtf.gz", + "example.gtf.gz.tbi", + "NEWS", + "ChangeLog" +] + +sanity_check_paths = { + 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..355e0eb0ad04f64903e2d076425ac06aa09873d3 --- /dev/null +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Author: Jens Timmerman, Ghent University + +easyblock = 'MakeCp' + +name = 'tabix' +version = '0.2.6' + +homepage = 'http://samtools.sourceforge.net' +description = """ Generic indexer for TAB-delimited genome position files """ + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [('http://sourceforge.net/projects/samtools/files/', 'download')] +sources = [SOURCE_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +buildopts = 'CFLAGS="-L$EBROOTZLIB/lib"' + +files_to_copy = [ + (["tabix", "bgzip", "tabix.py"], "bin"), + (["tabix.1"], "man/man1"), + "example.gtf.gz", + "example.gtf.gz.tbi", + "NEWS", + "ChangeLog" +] + +sanity_check_paths = { + 'files': ["bin/tabix", "bin/bgzip", "bin/tabix.py"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb b/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb index b371961dbf0ca78b742ea1218a610e780d97fe22..a157686a4a744d0ac6a524d584ffc418f6862532 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb @@ -13,14 +13,14 @@ description = """Intel Threading Building Blocks 4.0 (Intel TBB) toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['l_%s_%s.tgz' % (name, version)] +sources = ['l_%(name)s_%(version)s.tgz'] -patches = ['tbb_productsdb.patch'] - -moduleclass = 'lib' +patches = ['tbb-4.0_productsdb.patch'] dontcreateinstalldir = 'True' # license file import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb b/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb index f5ecd2fd390e3002b142c22297818bdee8e2e88b..150aaf30f9922c5e4f0dcfb2e2fc92d3f6ad6f92 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb @@ -13,14 +13,14 @@ description = """Intel Threading Building Blocks 4.0 (Intel TBB) toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['l_%s_%s.tgz' % (name, version)] +sources = ['l_%(name)s_%(version)s.tgz'] -patches = ['tbb_productsdb.patch'] - -moduleclass = 'lib' +patches = ['tbb-4.0_productsdb.patch'] dontcreateinstalldir = 'True' # license file import os license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tbb/tbb_productsdb.patch b/easybuild/easyconfigs/t/tbb/tbb-4.0_productsdb.patch similarity index 100% rename from easybuild/easyconfigs/t/tbb/tbb_productsdb.patch rename to easybuild/easyconfigs/t/tbb/tbb-4.0_productsdb.patch diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb b/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb new file mode 100644 index 0000000000000000000000000000000000000000..27609d139ffd72804cb514bf9f6cc71325d57223 --- /dev/null +++ b/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb @@ -0,0 +1,24 @@ +name = 'tbb' +version = '4.3.6.211' + +homepage = 'http://software.intel.com/en-us/articles/intel-tbb/' +description = """Intel Threading Building Blocks 4.0 (Intel TBB) + is a widely used, award-winning C++ template library for creating reliable, + portable, and scalable parallel applications. + Use Intel TBB for a simple and rapid way of developing robust task-based + parallel applications that scale to available processor cores, are compatible + with multiple environments, and are easier to maintain. + Intel TBB is the most proficient way to implement future-proof parallel applications + that tap into the power and performance of multicore and manycore hardware platforms.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_%(name)s_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4b5f7237ff41083d2d456bc2eae3cb1bbc8daef7 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2015a.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..ef7cef982f17551132450c2e3478cc7b8107c568 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.19.00-intel-2015a.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.19.00' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb new file mode 100644 index 0000000000000000000000000000000000000000..40607b696078338253ed8b22aea8d9883ced9f7a --- /dev/null +++ b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb @@ -0,0 +1,24 @@ +easyblock = 'Binary' + +name = 'tecplot360ex' +version = 'linux64' + +homepage = 'http://www.tecplot.com/products/tecplot-360/' +description = """ + Quickly plot and animate your CFD results exactly the way you want. Analyze complex solutions, arrange multiple layouts, + and communicate your results with professional images and animations. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# fi. http://www.tecplot.com/my/product-releases/ +installername = '%(name)s_%(version)s.sh' +sources = [installername] + +sanity_check_paths = { + 'files': ['bin/tec360'], + 'dirs': [] +} +install_cmd = 'chmod +x %s && ./%s --skip-license --prefix=%%(installdir)s' % (installername, installername) + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb index 233c5a0e62e907bbf8af2e875b8e3d0ea8dd2dfb..7e2b9ee6aa1f505f71fa4453fb7d28f1788796c5 100644 --- a/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/t/texinfo/texinfo-5.2-GCC-4.8.2.eb @@ -1,8 +1,3 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild -# -## - easyblock = 'ConfigureMake' name = 'texinfo' @@ -16,8 +11,20 @@ sources = [SOURCELOWER_TAR_XZ] toolchain = {'name': 'GCC', 'version': '4.8.2'} +osdependencies = ['texlive'] + +preinstallopts = "make TEXMF=%(installdir)s/texmf install-tex && " + +# This will overwrite a users $TEXMFHOME so this module is best used as a build dependency +modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} +modloadmsg = "\n\nWARNING: This texinfo module has (re)defined the value for the environment variable \\$TEXMFHOME.\n" +modloadmsg += "If you use a custom texmf directory (such as ~/texmf) you should copy files found in the\n" +modloadmsg += "new \\$TEXMFHOME to your custom directory and reset the value of \\$TEXMFHOME to point to that space:\n" +modloadmsg += "\tcp -r $TEXMFHOME/* /path/to/your/texmf\n" +modloadmsg += "\texport TEXMFHOME=/path/to/your/texmf\n\n" + sanity_check_paths = { - 'files': ['bin/info', 'bin/makeinfo', 'bin/pod2texi', 'bin/texi2pdf'], + 'files': ['bin/info', 'bin/makeinfo', 'bin/pod2texi', 'bin/texi2pdf', 'texmf/tex/texinfo/texinfo.tex'], 'dirs': [], } diff --git a/easybuild/easyconfigs/t/time/time-1.7.eb b/easybuild/easyconfigs/t/time/time-1.7.eb new file mode 100644 index 0000000000000000000000000000000000000000..1c4c9402350aad657321dd34d234f5a09a857fa8 --- /dev/null +++ b/easybuild/easyconfigs/t/time/time-1.7.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'time' +version = '1.7' + +homepage = 'http://www.gnu.org/software/time/' +description = """The `time' command runs another program, then displays information about the resources used by that + program, collected by the system while the program was running.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +postinstallcmds = ["ln -s %(installdir)s/bin/%(name)s %(installdir)s/bin/gtime"] + +sanity_check_paths = { + 'files': ['bin/gtime', 'bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..e3a2a31a1906e323dbe172c6ce5c285246425995 --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-ictce-5.4.0.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, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.1.24' + +homepage = 'http://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'ictce', 'version': '5.4.0'} +toolchainopts = {'opt': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits'] + +parallel = 1 + +sanity_check_paths = { + 'files': [ + 'bin/udunits2', + 'include/converter.h', + 'include/udunits2.h', + 'include/udunits.h', + 'lib/libudunits2.a', + 'lib/libudunits2.so', + ], + 'dirs': ['share'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-intel-2014b.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..e9bf8e9075f196b4dea7024270eb604fdd3fd7bd --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.1.24-intel-2014b.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, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.1.24' + +homepage = 'http://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'opt': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits'] + +sanity_check_paths = { + 'files': [ + 'bin/udunits2', + 'include/converter.h', + 'include/udunits2.h', + 'include/udunits.h', + 'lib/libudunits2.a', + 'lib/libudunits2.so', + ], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..dc874b1a62fe2986c85058a879b4b7232dfc0a43 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.26.1' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = '--disable-chfn-chsh --disable-login --disable-su ' +configopts += '--disable-wall --disable-use-tty-group ' +configopts += '--disable-makeinstall-chown --disable-makeinstall-setuid ' +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.2-intel-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0d1eb341d5bdce6e4d7cdd8acbc3aa9d1191c604 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.2-intel-2015a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.26.2' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = '--disable-chfn-chsh --disable-login --disable-su ' +configopts += '--disable-wall --disable-use-tty-group ' +configopts += '--disable-makeinstall-chown --disable-makeinstall-setuid ' +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb new file mode 100644 index 0000000000000000000000000000000000000000..44f692903f0e41917736d8694c88fc073ec3a934 --- /dev/null +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb @@ -0,0 +1,44 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 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 = 'Binary' + +name = "Vampir" +version = "8.4.1" +versionsuffix = "-demo" +variant = "linux-x86_64" + +homepage = 'http://www.vampir.eu' +description = """The Vampir software tool provides an easy-to-use framework that enables + developers to quickly display and analyze arbitrary program behavior at any level of detail. + The tool suite implements optimized event analysis algorithms and customizable displays that + enable fast and interactive rendering of very complex performance monitoring data.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['vampir-%s%s-%s-setup.bin' % (version, versionsuffix, variant)] + +# Adjust this variable to point to the location of your Vampir license file +license_file = '/example/licenses/path/vampir.license' + +install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" + +sanity_check_paths = { + 'files': ["bin/vampir", "doc/vampir-manual.pdf"], + 'dirs': [] +} + +modextravars = { + 'VAMPIR_LICENSE': license_file, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..5596a89f02442f10f19bf1942e7d6af6aab59965 --- /dev/null +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb @@ -0,0 +1,47 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 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 = 'Binary' + +name = "Vampir" +version = "8.4.1" +variant = "linux-x86_64" + +homepage = 'http://www.vampir.eu' +description = """The Vampir software tool provides an easy-to-use framework that enables + developers to quickly display and analyze arbitrary program behavior at any level of detail. + The tool suite implements optimized event analysis algorithms and customizable displays that + enable fast and interactive rendering of very complex performance monitoring data.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['vampir-%s-%s-setup.bin' % (version, variant)] + +checksums = [ + '471840910cd552a5a788df3b69251d29', # vampir-8.4.1-linux-x86_64-setup.bin +] + +# Adjust this variable to point to the location of your Vampir license file +license_file = '/example/licenses/path/vampir.license' + +install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" + +sanity_check_paths = { + 'files': ["bin/vampir", "doc/vampir-manual.pdf"], + 'dirs': [] +} + +modextravars = { + 'VAMPIR_LICENSE': license_file, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5b068e3cf704aa9f792ebf374f73eb95d57caa6c --- /dev/null +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb @@ -0,0 +1,48 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 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 = 'Binary' + +name = "VampirServer" +version = "8.4.1" +variant = "linux-x86_64" + +homepage = 'http://www.vampir.eu' +description = """The Vampir software tool provides an easy-to-use framework that enables + developers to quickly display and analyze arbitrary program behavior at any level of detail. + The tool suite implements optimized event analysis algorithms and customizable displays that + enable fast and interactive rendering of very complex performance monitoring data.""" + +toolchain = {'name': 'gompi', 'version': '2015a'} +toolchainopts = {"usempi": True} + +sources = ['vampirserver-%s-%s-setup.bin' % (version, variant)] + +checksums = [ + '2a2236bb071168b7d488c83363c30ac8', # vampirserver-8.4.1-linux-x86_64-setup.bin +] + +# Adjust this variable to point to the location of your Vampir license file +license_file = '/example/licenses/path/vampir.license' + +install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s && %(installdir)s/bin/vampirserver config --silent" + +sanity_check_paths = { + 'files': ["bin/vampirserver", "doc/vampirserver-manual.pdf", "lib/vampirserver-driver.so"], + 'dirs': [] +} + +modextravars = { + 'VAMPIR_LICENSE': license_file, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..1d1bbb0d8acf0a4cc7e9f088a437da70d9127115 --- /dev/null +++ b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'verifyBamID' +version = '1.1.2' + +homepage = "http://csg.sph.umich.edu/kang/verifyBamID/index.html" +description = """verifyBamID is a software that verifies whether the reads in particular file match previously known + genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of + two samples. verifyBamID can detect sample contamination and swaps when external genotypes are available. When + external genotypes are not available, verifyBamID still robustly detects sample swaps. +""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/statgen/%(name)s/releases/download/v%(version)s'] +sources = ['%(name)sLibStatGen.%(version)s.tgz'] + +checksums = ['fafc6fa58ba2bd51d0324ae616f5b29e'] + +buildopts = 'CXX="$CXX"' + +executables = ['%(name)s/bin/%(name)s'] +files_to_copy = [(executables, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb index c1d224e11ee60c51c43bb0c164adb46314020e31..dfd259613d83ab3a74c139b326fb6544cc0c0371 100644 --- a/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.3.0-ictce-5.5.0-Python-2.7.6.eb @@ -24,4 +24,9 @@ dependencies = [ options = {'modulename': 'vsc.mympirun.scoop'} +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/vsc/mympirun/scoop'], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0.eb b/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0.eb index 2b715acacf7c8c6f5dd8266eddbb2494baaf00bb..e6b6aa4d7475fd92deefc6815690206fd5499b97 100644 --- a/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0.eb +++ b/easybuild/easyconfigs/v/vsc-processcontrol/vsc-processcontrol-1.0.eb @@ -17,4 +17,9 @@ dependencies = [('vsc-base', '1.7.3')] options = {'modulename': 'sys; print sys.path; import vsc; print vsc.__path__; import vsc.processcontrol'} +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/vsc/processcontrol'], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.eb new file mode 100644 index 0000000000000000000000000000000000000000..a65ca2295bb5b413363782b9ab37c797e52b69c2 --- /dev/null +++ b/easybuild/easyconfigs/w/WEKA/WEKA-3.6.12-Java-1.7.0_80.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 + +easyblock = "Tarball" + +name = 'WEKA' +version = '3.6.12' + +homepage = 'http://www.cs.waikato.ac.nz/ml/weka/index.html' +description = """ Weka is a collection of machine learning algorithms for data mining tasks. + The algorithms can either be applied directly to a dataset or called from your own Java code. + Weka contains tools for data pre-processing, classification, regression, clustering, + association rules, and visualization. It is also well-suited for developing new machine + learning schemes.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://prdownloads.sourceforge.net/weka/'] +sources = ['%s-%s.zip' % (name.lower(), version.replace('.', '-'))] + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': ["weka.jar"], + 'dirs': [] +} + +modextravars = { + 'WEKAINSTALL': '$root', +} + +modloadmsg = " execute WEKA: java -jar \\$EBROOTWEKA/weka.jar " + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-foss-2015a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-foss-2015a-dmpar.eb new file mode 100644 index 0000000000000000000000000000000000000000..5e773ca4e846ed36d1220b28794f644615a4aee9 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-foss-2015a-dmpar.eb @@ -0,0 +1,40 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('netCDF', '4.3.2'), + ('netCDF-Fortran', '4.4.0'), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_netCDF-Fortran_separate_path.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/x/XML-Dumper/XML-Dumper-0.81-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/x/XML-Dumper/XML-Dumper-0.81-intel-2014b-Perl-5.20.0.eb index 744de7be27d965a88fd2d55a24af44ceb01335d9..876f399a735f69a608927b150d6d990aece0ab92 100644 --- a/easybuild/easyconfigs/x/XML-Dumper/XML-Dumper-0.81-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/x/XML-Dumper/XML-Dumper-0.81-intel-2014b-Perl-5.20.0.eb @@ -23,4 +23,10 @@ dependencies = [ options = {'modulename': 'XML::Dumper'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['lib/perl%s/site_perl/%s/XML/Dumper.pm' % (perlmajver, perlver)], + 'dirs': [], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..fe8c2f1f48bce39ad2b8fe709492ead19cbcfa87 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,30 @@ +easyblock = 'PerlModule' + +name = 'XML-Parser' +version = '2.41' + +homepage = 'http://search.cpan.org/~toddr/XML-Parser-2.41/' +description = """This is a Perl extension interface to James Clark's XML parser, expat.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +source_urls = ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ('expat', '2.1.0') +] + +options = {'modulename': 'XML::Parser'} + +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/XML' % (perlmajver, perlver)], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-intel-2014b-Perl-5.20.0.eb index 95ee785c732d9f0d1225cc60a7b4c83a65ab0888..7e5833d70b9c9258e9f9c202f22296e9573826df 100644 --- a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-intel-2014b-Perl-5.20.0.eb @@ -21,4 +21,10 @@ dependencies = [ options = {'modulename': 'XML::Parser'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/XML' % (perlmajver, perlver)], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..b28c4775b7e931f68d8b0e35e9245d4190f9603b --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,30 @@ +easyblock = 'PerlModule' + +name = 'XML-Twig' +version = '3.48' + +homepage = 'http://search.cpan.org/~mirod/XML-Twig-3.48/' +description = """XML::Twig is (yet another!) XML transformation module.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +source_urls = ['http://cpan.metacpan.org/authors/id/M/MI/MIROD/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ('XML-Parser', '2.41', versionsuffix) +] + +options = {'modulename': 'XML::Twig'} + +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['bin/xml_grep', 'bin/xml_merge', 'bin/xml_pp', 'bin/xml_spellcheck', 'bin/xml_split'], + 'dirs': ['lib/perl%s/site_perl/%s/XML/Twig' % (perlmajver, perlver)], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-intel-2014b-Perl-5.20.0.eb index 41318259ee64b9665b765d61ed32ff6c802f1a43..72f33a067d432451916272314146dce870625d53 100644 --- a/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-intel-2014b-Perl-5.20.0.eb +++ b/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-intel-2014b-Perl-5.20.0.eb @@ -21,4 +21,10 @@ dependencies = [ options = {'modulename': 'XML::Twig'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': ['bin/xml_grep', 'bin/xml_merge', 'bin/xml_pp', 'bin/xml_spellcheck', 'bin/xml_split'], + 'dirs': ['lib/perl%s/site_perl/%s/XML/Twig' % (perlmajver, perlver)], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goalf-1.1.0-no-OFED-R-2.15.2.eb b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goalf-1.1.0-no-OFED-R-2.15.2.eb index dfbf3d08493045c443964df81976de5e9633b9b7..f9b761e2bb3a983680941b5c01fcfbdf25e5f423 100644 --- a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goalf-1.1.0-no-OFED-R-2.15.2.eb +++ b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goalf-1.1.0-no-OFED-R-2.15.2.eb @@ -18,11 +18,16 @@ rver = '2.15.2' versionsuffix = '-%s-%s' % (r, rver) dependencies = [ - (r, rver), - ('libxml2', '2.9.0'), - ('zlib', '1.2.7'), - ] + (r, rver), + ('libxml2', '2.9.0'), + ('zlib', '1.2.7'), +] options = {'modulename': name} +sanity_check_paths = { + 'files': [], + 'dirs': ['XML'], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goolf-1.4.10-R-2.15.2.eb b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goolf-1.4.10-R-2.15.2.eb index 366fa8a2aa6992e931d45e5889b0153bb7593fa2..e2975b99583216d1ec3090a78f7515cb8f71a6a6 100644 --- a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goolf-1.4.10-R-2.15.2.eb +++ b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-goolf-1.4.10-R-2.15.2.eb @@ -22,4 +22,9 @@ dependencies = [ options = {'modulename': name} +sanity_check_paths = { + 'files': [], + 'dirs': ['XML'], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-4.0.6-R-2.15.2.eb b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-4.0.6-R-2.15.2.eb index 695f7960bc5aca892b13fc48dec394b8334603c1..41f30ad32da2800ee6e7cbc1eccc7fe0e82f1575 100644 --- a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-4.0.6-R-2.15.2.eb +++ b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-4.0.6-R-2.15.2.eb @@ -18,11 +18,16 @@ rver = '2.15.2' versionsuffix = '-%s-%s' % (r, rver) dependencies = [ - (r, rver), - ('libxml2', '2.9.0'), - ('zlib', '1.2.7'), - ] + (r, rver), + ('libxml2', '2.9.0'), + ('zlib', '1.2.7'), +] options = {'modulename': name} +sanity_check_paths = { + 'files': [], + 'dirs': ['XML'], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-5.3.0-R-2.15.2.eb b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-5.3.0-R-2.15.2.eb index e5358dc0d24825ff20cf44e5d8cfcfa3dc21f631..628ddd6ba41ced4415d54337c9fb8f5f0478308a 100644 --- a/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-5.3.0-R-2.15.2.eb +++ b/easybuild/easyconfigs/x/XML/XML-3.95-0.1-ictce-5.3.0-R-2.15.2.eb @@ -16,11 +16,16 @@ rver = '2.15.2' versionsuffix = '-%s-%s' % (r, rver) dependencies = [ - (r, rver), - ('libxml2', '2.9.0'), - ('zlib', '1.2.7'), - ] + (r, rver), + ('libxml2', '2.9.0'), + ('zlib', '1.2.7'), +] options = {'modulename': name} +sanity_check_paths = { + 'files': [], + 'dirs': ['XML'], +} + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-foss-2015a.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d7fbf9539451b6d046b38936e7edda3aa57110af --- /dev/null +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-foss-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'XQilla' +version = '2.3.2' + +homepage = 'http://xqilla.sourceforge.net/HomePage' + +description = """XQilla is an XQuery and XPath 2 library and command line +utility written in C++, implemented on top of the Xerces-C++ library.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [ + 'http://downloads.sourceforge.net/project/xqilla/', +] + +configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' + +xerces_version = '3.1.2' + +dependencies = [ + ('Xerces-C++', xerces_version), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..c6db3af286f8f7d64ac0f915f9950397eaf998d9 --- /dev/null +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'XQilla' +version = '2.3.2' + +homepage = 'http://xqilla.sourceforge.net/HomePage' + +description = """XQilla is an XQuery and XPath 2 library and command line +utility written in C++, implemented on top of the Xerces-C++ library.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = [SOURCE_TAR_GZ] +source_urls = [ + 'http://downloads.sourceforge.net/project/xqilla/', +] + +configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' + +xerces_version = '3.1.2' + +dependencies = [ + ('Xerces-C++', xerces_version), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-intel-2015a.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..1fe033551cbd732240c8abe22d636b90773a8682 --- /dev/null +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'XQilla' +version = '2.3.2' + +homepage = 'http://xqilla.sourceforge.net/HomePage' + +description = """XQilla is an XQuery and XPath 2 library and command line +utility written in C++, implemented on top of the Xerces-C++ library.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [ + 'http://downloads.sourceforge.net/project/xqilla/', +] + +configopts = '--with-xerces=$EBROOTXERCESMINCPLUSPLUS' + +xerces_version = '3.1.2' + +dependencies = [ + ('Xerces-C++', xerces_version), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-GCC-4.8.2.eb b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-GCC-4.8.2.eb index fad6a95d952964d69defda099f851efd254579cb..3d54b29efd3f8e5025a8ca701c921aab5ee0d7c7 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-GCC-4.8.2.eb @@ -6,12 +6,13 @@ version = '5.0.5' homepage = 'http://tukaani.org/xz/' description = "xz: XZ utilities" +toolchain = {'name': 'GCC', 'version': '4.8.2'} + sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] -toolchain = {'name': 'GCC', 'version': '4.8.2'} - -# configopts = ' --disable-assembler ' # may become useful in non-x86 archs +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-goolf-1.4.10.eb index 171e02c46b23a78b4e822c229801b1fe0f4db022..e60568da6efb51ea8badca0ae8d6b0148b95214d 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-goolf-1.4.10.eb @@ -6,12 +6,13 @@ version = '5.0.5' homepage = 'http://tukaani.org/xz/' description = "xz: XZ utilities" +toolchain = {'name': 'goolf', 'version': '1.4.10'} + sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -# configopts = ' --disable-assembler ' # may become useful in non-x86 archs +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-ictce-5.3.0.eb index c7b17522590816f7c467197afeabf43f1925467e..6f7148a406a89fecde26a47a660497697bbbbf78 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-ictce-5.3.0.eb @@ -6,12 +6,13 @@ version = '5.0.5' homepage = 'http://tukaani.org/xz/' description = "xz: XZ utilities" +toolchain = {'name': 'ictce', 'version': '5.3.0'} + sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] -toolchain = {'name': 'ictce', 'version': '5.3.0'} - -# configopts = ' --disable-assembler ' # may become useful in non-x86 archs +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb index 5a6ed9b1225b2a7c9e67733bcd0329272729b46c..99b4d29f28dcda07be4ea7b3f1a039383fdb5c4c 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb @@ -6,10 +6,13 @@ version = '5.2.0' homepage = 'http://tukaani.org/xz/' description = "xz: XZ utilities" +toolchain = {'name': 'GCC', 'version': '4.9.2'} + sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] -toolchain = {'name': 'GCC', 'version': '4.9.2'} +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e2bfd14b2a0921b583518b5fe25ac1197ebfd869 --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Xerces-C++' +version = '3.1.2' + +homepage = 'http://xerces.apache.org/xerces-c/' + +description = """Xerces-C++ is a validating XML parser written in a portable +subset of C++. Xerces-C++ makes it easy to give your application the ability to +read and write XML data. A shared library is provided for parsing, generating, +manipulating, and validating XML documents using the DOM, SAX, and SAX2 +APIs.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['xerces-c-%(version)s.tar.gz'] +source_urls = [ + 'http://apache.belnet.be/xerces/c/%(version_major)s/sources/' +] + +dependencies = [ + ('cURL', '7.44.0'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..258f78b64aeeeeb05191053d9985d71e28f117dc --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-goolf-1.7.20.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Xerces-C++' +version = '3.1.2' + +homepage = 'http://xerces.apache.org/xerces-c/' + +description = """Xerces-C++ is a validating XML parser written in a portable +subset of C++. Xerces-C++ makes it easy to give your application the ability to +read and write XML data. A shared library is provided for parsing, generating, +manipulating, and validating XML documents using the DOM, SAX, and SAX2 +APIs.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = ['xerces-c-%(version)s.tar.gz'] +source_urls = [ + 'http://apache.belnet.be/xerces/c/%(version_major)s/sources/' +] + +dependencies = [ + ('cURL', '7.44.0'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..78f997327e45f6ef7c9b544169cc501705b6e546 --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'Xerces-C++' +version = '3.1.2' + +homepage = 'http://xerces.apache.org/xerces-c/' + +description = """Xerces-C++ is a validating XML parser written in a portable +subset of C++. Xerces-C++ makes it easy to give your application the ability to +read and write XML data. A shared library is provided for parsing, generating, +manipulating, and validating XML documents using the DOM, SAX, and SAX2 +APIs.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['xerces-c-%(version)s.tar.gz'] +source_urls = [ + 'http://apache.belnet.be/xerces/c/%(version_major)s/sources/' +] + +dependencies = [ + ('cURL', '7.44.0'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..fc928c6c5783657b8fd914d7e699b5a76da73e86 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,32 @@ +name = 'Xmipp' +version = '3.1' + +homepage = 'http://xmipp.cnb.csic.es/' +description = "Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy." + +source_urls = ['http://xmipp.cnb.csic.es/Downloads/'] +sources = ['Xmipp-%(version)s-src.tar.gz'] + +toolchain = {'name': 'foss', 'version': '2015a'} + +patches = [ + 'Xmipp-%(version)s_fix-sqlite-includes.patch', + 'Xmipp-%(version)s_fix-library-includes.patch', + 'Xmipp_install-script.patch', +] + +pyver = '2.7.9' +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Java', '1.8.0_40', '', True), + ('Python', pyver), # should have a working sqlite, and provide numpy/mpi4py + ('LibTIFF', '4.0.4beta'), + ('HDF5', '1.8.14'), + ('libjpeg-turbo', '1.4.0'), + ('FFTW', '3.3.4', '', ('gompi', '2015a')), + ('SQLite', '3.8.8.1'), # must match SQLite used by Python + ('matplotlib', '1.4.3', versionsuffix), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb new file mode 100644 index 0000000000000000000000000000000000000000..c1f4fa485c8a52d3abe146c463fab96e0ccb498b --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb @@ -0,0 +1,16 @@ +name = 'Xmipp' +version = '3.1' +versionsuffix = '-with-incl-deps' + +homepage = 'http://xmipp.cnb.csic.es/' +description = "Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy." + +source_urls = ['http://xmipp.cnb.csic.es/Downloads/'] +sources = ['Xmipp-%(version)s-src.tar.gz'] + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +# note: all other dependencies are taken care of by Xmipp itself +dependencies = [('Java', '1.7.0_80', '', True)] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb similarity index 61% rename from easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb rename to easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb index bd7faf390987c3efa8b5d675d087ecd6a437f64b..82d76eef0e88122546444a7d5e09fae201a18931 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb @@ -9,17 +9,24 @@ sources = ['Xmipp-%(version)s-src.tar.gz'] toolchain = {'name': 'intel', 'version': '2015a'} -patches = ['sqlite_imports.patch', 'library_imports.patch'] +patches = [ + 'Xmipp-%(version)s_fix-sqlite-includes.patch', + 'Xmipp-%(version)s_fix-library-includes.patch', + 'Xmipp_install-script.patch', +] + +pyver = '2.7.9' +versionsuffix = '-Python-%s' % pyver dependencies = [ ('Java', '1.8.0_40', '', True), - ('Python', '2.7.9'), # should have a working sqlite, and provide numpy - ('freetype', '2.5.5'), + ('Python', pyver), # should have a working sqlite, and provide numpy/mpi4py ('LibTIFF', '4.0.4beta'), - ('HDF5', '1.8.14', '-gpfs'), + ('HDF5', '1.8.14'), ('libjpeg-turbo', '1.4.0'), ('FFTW', '3.3.4'), ('SQLite', '3.8.8.1'), # must match SQLite used by Python + ('matplotlib', '1.4.3', versionsuffix), ] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/Xmipp/library_imports.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1_fix-library-includes.patch similarity index 100% rename from easybuild/easyconfigs/x/Xmipp/library_imports.patch rename to easybuild/easyconfigs/x/Xmipp/Xmipp-3.1_fix-library-includes.patch diff --git a/easybuild/easyconfigs/x/Xmipp/sqlite_imports.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1_fix-sqlite-includes.patch similarity index 100% rename from easybuild/easyconfigs/x/Xmipp/sqlite_imports.patch rename to easybuild/easyconfigs/x/Xmipp/Xmipp-3.1_fix-sqlite-includes.patch diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp_install-script.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp_install-script.patch new file mode 100644 index 0000000000000000000000000000000000000000..c79477e52b65c151f432a870d4043a29f0c479c2 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp_install-script.patch @@ -0,0 +1,13 @@ +--- install.sh.orig 2014-04-03 10:46:46.000000000 +0300 ++++ install.sh 2015-06-17 10:09:32.000000000 +0300 +@@ -820,8 +820,8 @@ + DO_PYTHON=1 + DO_PYMOD=1 + elif [ "${WITH_PYTHON}" = "false" ]; then +- DO_PYTHON=1 +- DO_PYMOD=1 ++ DO_PYTHON=0 ++ DO_PYMOD=0 + else + echoRed "Parameter --python only accept true or false values. Ignored and assuming default value." + fi diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..32ea56a932f28900507c4dd9c2a1cc7e6e9677e9 --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.11-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-proto' +version = '1.11' + +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': 'intel', 'version': '2015a'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.10' +versionsuffix = '-%s-%s' % (python, pyver) +dependencies = [(python, pyver)] + +pyshortver = '.'.join(pyver.split('.')[0:2]) + +sanity_check_paths = { + 'files': ['lib/pkgconfig/xcb-proto.pc'], + 'dirs': ['lib/python%s/site-packages/xcbgen' % pyshortver] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2015a.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..195ab46393e93d4cb678619aa2ef261194d6bbbc --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.17-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.17' + +homepage = 'http://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://cgit.freedesktop.org/xorg/util/macros/snapshot'] # no slash ('/') at the end! +sources = ['util-macros-%(version)s.tar.gz'] + +dependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb index 587b16d7480c74bff269bc194e492420ff9f26ab..b409a46b6b073e54b56eef15e81180aeea9c4b24 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-goolf-1.4.10-Perl-5.16.3.eb @@ -32,4 +32,10 @@ dependencies = [ options = {'modulename': 'YAML::Syck'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/YAML' % (perlmajver, perlver)], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb index a394ff11d014da77b7f3e03011443108a8d18036..fa45b910fb7db23e18330645f3d502d658ac6cbd 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-4.1.13-Perl-5.16.3.eb @@ -32,4 +32,10 @@ dependencies = [ options = {'modulename': 'YAML::Syck'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/YAML' % (perlmajver, perlver)], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb index 94ef6fae9e71e4d6c5e3f2db0d45f383f1c0611a..f2c952182bddd6e54a4a125e7fdd00956524c8c2 100644 --- a/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/y/YAML-Syck/YAML-Syck-1.27-ictce-5.3.0-Perl-5.16.3.eb @@ -32,4 +32,10 @@ dependencies = [ options = {'modulename': 'YAML::Syck'} +perlmajver = perlver.split('.')[0] +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl%s/site_perl/%s/x86_64-linux-thread-multi/YAML' % (perlmajver, perlver)], +} + moduleclass = 'data' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-foss-2015a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..537ac748fee1b628be5ac893fc9ffb85a660ad10 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-foss-2015a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '3.2.5' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://download.zeromq.org/'] +sources = [SOURCELOWER_TAR_GZ] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.26.1'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.3-intel-2015a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.3-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e23ec179be069f5fa56dbd8e1f3c1965cafc12ef --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.3-intel-2015a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.1.3' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://download.zeromq.org/'] +sources = [SOURCELOWER_TAR_GZ] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.26.2'), + ('libsodium', '1.0.3'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..b5a38518237b8a096ef0c48281cda74b922b1987 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-5.4.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.7' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'ictce', 'version': '5.4.0'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-6.1.5.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-6.1.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..62b9777b1c06b1fbded08b09b802f5041d09927e --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-6.1.5.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.7' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'ictce', 'version': '6.1.5'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb index 3f419579d90b7884e4e9582f9c2d9f95e1a20a1b..71c0cc0f498681bf6df37c060e3e3ab549974584 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2-binutils-2.25'} sources = [SOURCELOWER_TAR_GZ] source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] +# use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.25', '', True)] sanity_check_paths = { diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..dc4517d9501a95a89a596f178356758f714e9e49 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.3-binutils-2.25.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-binutils-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.25', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..797739b09af41b607bd1bf405893e3e62f0700b4 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCC', 'version': '5.1.0-binutils-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.25', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GNU-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..5390ac9f19369a89f7561fd4c2d4b72af7133f4a --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GNU-4.9.3-2.25.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..76686828729cfb404785d90a97c2cee8133a5f89 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015b.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..e39bc788041f73cf50a98f00cd001d11df96bc0a --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'foss', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.16.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.16.eb new file mode 100644 index 0000000000000000000000000000000000000000..9b56c2bffb789bcf6da6637e14a3b70771dc9bed --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.16.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..25bf52883baa504070d3dc3c41342fdeb943df91 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-5.4.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'version': '5.4.0', 'name': 'ictce'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-7.3.5.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-7.3.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..8254f78ac9a7ff9d394f3ab2f42d0495f54523bc --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-7.3.5.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%s' % version, 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2015b.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..a09231ac5841d9569b5d51f5a52be80ca9e3c367 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2015b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.8' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%(version)s', 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/setup.py b/setup.py index 9e5dd5137ccda46cd9e2aba6ed4e3ab1a40284c6..460e2b5145209ae8f73785fde9b98ef4a5ba4452 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,13 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = '2.2.0dev' +# +# important note: dev versions should follow the 'X.Y.Z.dev0' format +# see https://www.python.org/dev/peps/pep-0440/#developmental-releases +# recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like +# UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' +# This causes problems further up the dependency chain... +VERSION = '2.4.0.dev0' API_VERSION = VERSION.split('.')[0] EB_VERSION = '.'.join(VERSION.split('.')[0:2]) @@ -51,9 +57,11 @@ rc_regexp = re.compile("^.*(rc[0-9]*)$") res = rc_regexp.search(str(VERSION)) if res: suff = res.group(1) -dev_regexp = re.compile("^.*[0-9]dev$") -if dev_regexp.match(VERSION): - suff = 'dev' + +dev_regexp = re.compile("^.*[0-9](.?dev[0-9])$") +res = dev_regexp.search(VERSION) +if res: + suff = res.group(1) API_VERSION += suff EB_VERSION += suff diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 6efa3b178f94379d869d43e2d785df3df72bf509..c4be1123723eb4821702977e453bb76ed497b08a 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -32,10 +32,11 @@ import copy import glob import os import re +import shutil import sys import tempfile from distutils.version import LooseVersion -from vsc import fancylogger +from vsc.utils import fancylogger from vsc.utils.missing import nub from unittest import TestCase, TestLoader, main @@ -43,12 +44,14 @@ import easybuild.main as main import easybuild.tools.options as eboptions from easybuild.easyblocks.generic.configuremake import ConfigureMake from easybuild.framework.easyblock import EasyBlock -from easybuild.framework.easyconfig.easyconfig import ActiveMNS, EasyConfig +from easybuild.framework.easyconfig.easyconfig import EasyConfig from easybuild.framework.easyconfig.easyconfig import get_easyblock_class from easybuild.framework.easyconfig.parser import fetch_parameters_from_easyconfig from easybuild.framework.easyconfig.tools import dep_graph, get_paths_for, process_easyconfig from easybuild.tools import config +from easybuild.tools.filetools import write_file from easybuild.tools.module_naming_scheme import GENERAL_CLASS +from easybuild.tools.module_naming_scheme.easybuild_mns import EasyBuildMNS from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version from easybuild.tools.modules import modules_tool from easybuild.tools.robot import resolve_dependencies @@ -71,6 +74,7 @@ class EasyConfigTest(TestCase): 'force': True, 'optarch': 'test', 'robot_path': get_paths_for("easyconfigs")[0], + 'silent': True, 'suffix_modules_path': GENERAL_CLASS, 'valid_module_classes': config.module_classes(), 'valid_stops': [x[0] for x in EasyBlock.get_steps()], @@ -79,10 +83,10 @@ class EasyConfigTest(TestCase): config.set_tmpdir() del eb_go - # mock 'exist' and 'load' methods of modules tool, which are used for 'craype' external module - modtool = modules_tool() - modtool.exist = lambda m: [True]*len(m) - modtool.load = lambda m: True + # put dummy 'craype-test' module in place, which is required for parsing easyconfigs using Cray* toolchains + TMPDIR = tempfile.mkdtemp() + os.environ['MODULEPATH'] = TMPDIR + write_file(os.path.join(TMPDIR, 'craype-test'), '#%Module\n') log = fancylogger.getLogger("EasyConfigTest", fname=False) @@ -107,9 +111,6 @@ class EasyConfigTest(TestCase): for dep in ec['dependencies'][:]: if dep.get('external_module', False): ec['dependencies'].remove(dep) - for dep in ec['unresolved_deps'][:]: - if dep.get('external_module', False): - ec['unresolved_deps'].remove(dep) self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs, retain_all_deps=True) @@ -124,7 +125,7 @@ class EasyConfigTest(TestCase): if self.ordered_specs is None: self.process_all_easyconfigs() - dep_graph(fn, self.ordered_specs, silent=True) + dep_graph(fn, self.ordered_specs) try: os.remove(fn) @@ -144,13 +145,15 @@ class EasyConfigTest(TestCase): self.process_all_easyconfigs() def mk_dep_mod_name(spec): - return tuple(ActiveMNS().det_full_module_name(spec).split(os.path.sep)) + return tuple(EasyBuildMNS().det_full_module_name(spec).split(os.path.sep)) # construct a dictionary: (name, installver) tuple to (build) dependencies depmap = {} for spec in self.ordered_specs: - build_deps = map(mk_dep_mod_name, spec['builddependencies']) - deps = map(mk_dep_mod_name, spec['unresolved_deps']) + # exclude external modules, since we can't check conflicts on them (we don't even know the software name) + build_deps = [mk_dep_mod_name(d) for d in spec['builddependencies'] if not d.get('external_module', False)] + deps = [mk_dep_mod_name(d) for d in spec['ec'].all_dependencies if not d.get('external_module', False)] + # separate runtime deps from build deps runtime_deps = [d for d in deps if d not in build_deps] key = tuple(spec['full_mod_name'].split(os.path.sep)) @@ -227,6 +230,10 @@ class EasyConfigTest(TestCase): if not (dirpath.endswith('/easybuild/easyconfigs') and filenames == ['TEMPLATE.eb']): self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames)) + def test_zzz_cleanup(self): + """Dummy test to clean up global temporary directory.""" + shutil.rmtree(self.TMPDIR) + def template_easyconfig_test(self, spec): """Tests for an individual easyconfig: parsing, instantiating easyblock, check patches, ...""" @@ -235,7 +242,7 @@ def template_easyconfig_test(self, spec): prev_single_tests_ok = single_tests_ok single_tests_ok = False - # parse easyconfig + # parse easyconfig ecs = process_easyconfig(spec) if len(ecs) == 1: ec = ecs[0]['ec'] @@ -250,7 +257,7 @@ def template_easyconfig_test(self, spec): name, easyblock = fetch_parameters_from_easyconfig(ec.rawtxt, ['name', 'easyblock']) # sanity check for software name - self.assertTrue(ec['name'], name) + self.assertTrue(ec['name'], name) # instantiate easyblock with easyconfig file app_class = get_easyblock_class(easyblock, name=name) @@ -297,6 +304,25 @@ def template_easyconfig_test(self, spec): app.close_log() os.remove(app.logfile) + # dump the easyconfig file + handle, test_ecfile = tempfile.mkstemp() + os.close(handle) + + ec.dump(test_ecfile) + dumped_ec = EasyConfig(test_ecfile) + os.remove(test_ecfile) + + # inject dummy values for templates that are only known at a later stage + dummy_template_values = { + 'builddir': '/dummy/builddir', + 'installdir': '/dummy/installdir', + } + ec.template_values.update(dummy_template_values) + dumped_ec.template_values.update(dummy_template_values) + + for key in sorted(ec._config): + self.assertEqual(ec[key], dumped_ec[key]) + # cache the parsed easyconfig, to avoid that it is parsed again self.parsed_easyconfigs.append(ecs[0]) diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index 65497da038f366e6c3aa544afc3b63bdb06b98e2..6afbd6ffb15accfe319e11c510c9e60e6131d8ba 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -36,7 +36,8 @@ import shutil import sys import tempfile import unittest -from vsc import fancylogger + +from vsc.utils import fancylogger import easybuild.tools.build_log # initialize EasyBuild logging, so we disable it import test.easyconfigs.easyconfigs as e