mirror of
https://code.it4i.cz/sccs/easyconfigs-it4i.git
synced 2025-04-07 23:42:12 +01:00
new file: b/BCFtools/BCFtools-1.6-intel-2017a.eb
new file: b/BWA/BWA-0.7.17-intel-2017a.eb new file: c/Clang/Clang-3.8.1-GCC-6.3.0-2.27.eb new file: d/DMTCP/DMTCP-2.5.2.eb new file: d/DMTCP/DMTCP-3.0.eb new file: f/FFTW/FFTW-3.3.6-foss-2017a.eb new file: h/HTSlib/HTSlib-1.6-intel-2017a.eb new file: l/libsndfile/libsndfile-1.0.28.eb new file: m/MPC/MPC-1.0.2.eb new file: m/MPFR/MPFR-3.1.5.eb new file: m/MPICH/MPICH-3.2.1-GCC-6.3.0-2.27.eb new file: m/Mesa/Mesa-17.2.6-foss-2017a.eb new file: n/NLopt/NLopt-2.4.2.eb new file: n/nettle/nettle-3.3-foss-2017a.eb new file: o/Octave/Octave-4.2.1-intel-2017a-mic.eb new file: p/PAPI/PAPI-5.5.1.eb new file: p/PROJ/PROJ-4.9.3-foss-2017a.eb new file: r/R/R-3.4.2-intel-2017a.eb new file: r/R/R-3.4.3-foss-2017a.eb new file: s/SAMtools/SAMtools-1.6-intel-2017a.eb new file: s/Singularity/Singularity-2.4.1.eb modified: v/VASP/VASP-5.4.1-24Jun15-intel-2015b.eb modified: v/VASP/VASP-5.4.1-24Jun15-intel-2017.00.eb modified: v/VASP/VASP-5.4.1-24Jun15-intel-2017a.eb modified: v/VASP/VASP-5.4.4-intel-2015b-mkl=sequential.eb modified: v/VASP/VASP-5.4.4-intel-2016a-CUDA-8.0.44-mkl=sequential.eb modified: v/VASP/VASP-5.4.4-intel-2017a-03.eb modified: v/VASP/VASP-5.4.4-intel-2017a-mkl=cluster.eb new file: v/VASP/VASP-5.4.4-intel-2017a-mkl=paralel-test.eb modified: v/VASP/VASP-5.4.4-intel-2017a-mkl=paralel.eb modified: v/VASP/VASP-5.4.4-intel-2017a-mkl=sequential.eb modified: v/VASP/VASP-5.4.4-intel-2017a.eb modified: v/VASP/VASP-5.4.4-intel-2017b-mkl=cluster.eb
This commit is contained in:
Lukáš Krupčík
parent
8a3e562088
commit
9738176bda
42
b/BCFtools/BCFtools-1.6-intel-2017a.eb
Normal file
42
b/BCFtools/BCFtools-1.6-intel-2017a.eb
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@ -0,0 +1,42 @@
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easyblock = 'ConfigureMake'
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name = 'BCFtools'
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version = '1.6'
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homepage = 'http://www.htslib.org/'
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description = """Samtools is a suite of programs for interacting with high-throughput sequencing data.
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BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants"""
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toolchain = {'name': 'intel', 'version': '2017a'}
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toolchainopts = {'optarch': True, 'pic': True}
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sources = [SOURCELOWER_TAR_BZ2]
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source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
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#patches = ['BCFtools-%(version)s_extHTSlib_Makefile.patch']
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dependencies = [
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('zlib', '1.2.11', '', True),
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('HTSlib', '1.6'),
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('GSL', '2.3'),
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('XZ', '5.2.3', '', True),
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]
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parallel = 1
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skipsteps = ['configure']
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buildopts = 'CC="$CC" CFLAGS="$CFLAGS" USE_GSL=1'
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installopts = ' prefix=%(installdir)s'
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postinstallcmds = [
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'mkdir -p %(installdir)s/lib/plugins',
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'cp -a plugins/*.so %(installdir)s/lib/plugins/.',
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]
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sanity_check_paths = {
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'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']],
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'dirs': ['lib/plugins'],
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}
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moduleclass = 'bio'
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18
b/BWA/BWA-0.7.17-intel-2017a.eb
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18
b/BWA/BWA-0.7.17-intel-2017a.eb
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name = 'BWA'
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version = '0.7.17'
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homepage = 'http://bio-bwa.sourceforge.net/'
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description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns
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relatively short nucleotide sequences against a long reference sequence such as the human genome."""
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toolchain = {'name': 'intel', 'version': '2017a'}
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toolchainopts = {'optarch': True, 'pic': True}
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source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')]
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sources = [SOURCELOWER_TAR_BZ2]
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dependencies = [
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('zlib', '1.2.11', '', True),
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]
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moduleclass = 'bio'
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49
c/Clang/Clang-3.8.1-GCC-6.3.0-2.27.eb
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49
c/Clang/Clang-3.8.1-GCC-6.3.0-2.27.eb
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##
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# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
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#
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# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans
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# Authors:: Dmitri Gribenko <gribozavr@gmail.com>
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# Authors:: Ward Poelmans <wpoely86@gmail.com>
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# License:: GPLv2 or later, MIT, three-clause BSD.
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# $Id$
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##
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name = "Clang"
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version = "3.8.1"
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homepage = "http://clang.llvm.org/"
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description = """C, C++, Objective-C compiler, based on LLVM. Does not
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include C++ standard library -- use libstdc++ from GCC."""
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# Clang also depends on libstdc++ during runtime, but this dependency is
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# already specified as the toolchain.
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toolchain = {'name': 'GCC', 'version': '7.2.0-2.29'}
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# Do not set optarch to True: it will cause the build to fail
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toolchainopts = {'optarch': False}
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source_urls = ["http://llvm.org/release/%(version)s"]
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sources = [
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"llvm-%(version)s.src.tar.xz",
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"cfe-%(version)s.src.tar.xz",
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"compiler-rt-%(version)s.src.tar.xz",
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"polly-%(version)s.src.tar.xz",
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"openmp-%(version)s.src.tar.xz",
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]
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dependencies = [
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('GMP', '6.1.2', '', True),
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]
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builddependencies = [
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('CMake', '3.9.1', '', True),
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('Python', '2.7.13', '', True),
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('libxml2', '2.9.4', '', True),
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]
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assertions = True
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usepolly = True
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build_targets = ['X86']
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moduleclass = 'compiler'
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29
d/DMTCP/DMTCP-2.5.2.eb
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29
d/DMTCP/DMTCP-2.5.2.eb
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easyblock = 'ConfigureMake'
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name = 'DMTCP'
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version = '2.5.2'
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homepage = "http://dmtcp.sourceforge.net/index.html"
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description = """DMTCP (Distributed MultiThreaded Checkpointing)
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transparently checkpoints a single-host or distributed computation
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in user-space -- with no modifications to user code or to the O/S."""
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toolchain = {'name': 'dummy', 'version': ''}
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source_urls = ['https://github.com/dmtcp/dmtcp/archive/']
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sources = ['%(version)s.tar.gz']
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configopts = '--enable-infiniband-support'
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postinstallcmds = [
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'cp test/ %(installdir)s/test -R',
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'(cd %(installdir)s/test; make -j 8)',
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]
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sanity_check_paths = {
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'files': ['bin/dmtcp_command', 'bin/dmtcp_discover_rm', 'bin/dmtcp_nocheckpoint', 'bin/dmtcp_srun_helper',
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'bin/dmtcp_sshd', 'bin/dmtcp_coordinator', 'bin/dmtcp_launch', 'bin/dmtcp_restart', 'bin/dmtcp_ssh'],
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'dirs': [],
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}
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moduleclass = 'tools'
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29
d/DMTCP/DMTCP-3.0.eb
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29
d/DMTCP/DMTCP-3.0.eb
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easyblock = 'ConfigureMake'
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name = 'DMTCP'
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version = '3.0'
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homepage = "http://dmtcp.sourceforge.net/index.html"
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description = """DMTCP (Distributed MultiThreaded Checkpointing)
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transparently checkpoints a single-host or distributed computation
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in user-space -- with no modifications to user code or to the O/S."""
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toolchain = {'name': 'dummy', 'version': ''}
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source_urls = ['https://github.com/dmtcp/dmtcp/archive/']
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sources = ['master.tar.gz']
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configopts = '--enable-infiniband-support'
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postinstallcmds = [
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'cp test/ %(installdir)s/test -R',
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'(cd %(installdir)s/test; make -j 8)',
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]
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sanity_check_paths = {
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'files': ['bin/dmtcp_command', 'bin/dmtcp_discover_rm', 'bin/dmtcp_nocheckpoint', 'bin/dmtcp_srun_helper',
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'bin/dmtcp_sshd', 'bin/dmtcp_coordinator', 'bin/dmtcp_launch', 'bin/dmtcp_restart', 'bin/dmtcp_ssh'],
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'dirs': [],
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}
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moduleclass = 'tools'
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35
f/FFTW/FFTW-3.3.6-foss-2017a.eb
Normal file
35
f/FFTW/FFTW-3.3.6-foss-2017a.eb
Normal file
@ -0,0 +1,35 @@
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easyblock = 'ConfigureMake'
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name = 'FFTW'
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version = '3.3.6'
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homepage = 'http://www.fftw.org'
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description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)
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in one or more dimensions, of arbitrary input size, and of both real and complex data."""
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toolchain = {'name': 'foss', 'version': '2017a'}
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toolchainopts = {'optarch': True, 'pic': True}
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source_urls = [homepage]
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sources = ['fftw-%(version)s-pl1.tar.gz']
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checksums = ['682a0e78d6966ca37c7446d4ab4cc2a1']
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common_configopts = "--enable-threads --enable-openmp --with-pic"
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configopts = [
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common_configopts + " --enable-single --enable-sse2 --enable-mpi",
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common_configopts + " --enable-long-double --enable-mpi",
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common_configopts + " --enable-quad-precision",
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common_configopts + " --enable-sse2 --enable-mpi", # default as last
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]
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sanity_check_paths = {
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'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] +
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['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03',
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'.h', 'l-mpi.f03', 'l.f03', 'q.f03']] +
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['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] +
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['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'],
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'dirs': ['lib/pkgconfig'],
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}
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moduleclass = 'numlib'
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25
h/HTSlib/HTSlib-1.6-intel-2017a.eb
Normal file
25
h/HTSlib/HTSlib-1.6-intel-2017a.eb
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easyblock = 'ConfigureMake'
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name = 'HTSlib'
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version = '1.6'
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homepage = "http://www.htslib.org/"
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description = """ A C library for reading/writing high-throughput sequencing data.
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This package includes the utilities bgzip and tabix """
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toolchain = {'name': 'intel', 'version': '2017a'}
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source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/']
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sources = [SOURCELOWER_TAR_BZ2]
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dependencies = [
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('zlib', '1.2.11', '', True),
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('XZ', '5.2.3', '', True),
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]
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sanity_check_paths = {
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'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT],
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'dirs': [],
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}
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moduleclass = 'bio'
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23
l/libsndfile/libsndfile-1.0.28.eb
Normal file
23
l/libsndfile/libsndfile-1.0.28.eb
Normal file
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easyblock = 'ConfigureMake'
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name = 'libsndfile'
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version = '1.0.28'
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homepage = 'http://www.mega-nerd.com/libsndfile'
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description = """Libsndfile is a C library for reading and writing files containing sampled sound
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(such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface."""
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toolchain = {'name': 'dummy', 'version': ''}
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source_urls = ['http://www.mega-nerd.com/libsndfile/files/']
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sources = [SOURCE_TAR_GZ]
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||||
checksums = ['1ff33929f042fa333aed1e8923aa628c3ee9e1eb85512686c55092d1e5a9dfa9']
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||||
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builddependencies = [('binutils', '2.29')]
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sanity_check_paths = {
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||||
'files': ['include/sndfile.h', 'include/sndfile.hh', 'lib/libsndfile.a', 'lib/libsndfile.%s' % SHLIB_EXT],
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||||
'dirs': ['bin'],
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||||
}
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||||
moduleclass = 'lib'
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||||
30
m/MPC/MPC-1.0.2.eb
Normal file
30
m/MPC/MPC-1.0.2.eb
Normal file
@ -0,0 +1,30 @@
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||||
easyblock = 'ConfigureMake'
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||||
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||||
name = 'MPC'
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||||
version = '1.0.2'
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||||
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||||
homepage = 'http://www.multiprecision.org/'
|
||||
description = """Gnu Mpc is a C library for the arithmetic of
|
||||
complex numbers with arbitrarily high precision and correct
|
||||
rounding of the result. It extends the principles of the IEEE-754
|
||||
standard for fixed precision real floating point numbers to
|
||||
complex numbers, providing well-defined semantics for every
|
||||
operation. At the same time, speed of operation at high precision
|
||||
is a major design goal."""
|
||||
|
||||
toolchain = {'name': 'dummy', 'version': ''}
|
||||
|
||||
source_urls = ['http://www.multiprecision.org/mpc/download/']
|
||||
sources = [SOURCELOWER_TAR_GZ]
|
||||
|
||||
dependencies = [('GMP', '6.1.2'),
|
||||
('MPFR', '3.1.5')]
|
||||
|
||||
runtest = 'check'
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ['lib/libmpc.%s' % SHLIB_EXT, 'include/mpc.h'],
|
||||
'dirs': []
|
||||
}
|
||||
|
||||
moduleclass = 'math'
|
||||
24
m/MPFR/MPFR-3.1.5.eb
Normal file
24
m/MPFR/MPFR-3.1.5.eb
Normal file
@ -0,0 +1,24 @@
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||||
easyblock = 'ConfigureMake'
|
||||
|
||||
name = 'MPFR'
|
||||
version = '3.1.5'
|
||||
|
||||
homepage = 'http://www.mpfr.org'
|
||||
description = """The MPFR library is a C library for multiple-precision
|
||||
floating-point computations with correct rounding."""
|
||||
|
||||
toolchain = {'name': 'dummy', 'version': ''}
|
||||
|
||||
source_urls = ['http://www.mpfr.org/mpfr-%(version)s/']
|
||||
sources = [SOURCELOWER_TAR_BZ2]
|
||||
|
||||
dependencies = [('GMP', '6.1.2')]
|
||||
|
||||
# runtest = 'check'
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'],
|
||||
'dirs': []
|
||||
}
|
||||
|
||||
moduleclass = 'math'
|
||||
18
m/MPICH/MPICH-3.2.1-GCC-6.3.0-2.27.eb
Normal file
18
m/MPICH/MPICH-3.2.1-GCC-6.3.0-2.27.eb
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|
||||
name = 'MPICH'
|
||||
version = '3.2.1'
|
||||
|
||||
homepage = 'http://www.mpich.org/'
|
||||
description = """MPICH v3.x is an open source high-performance MPI 3.0 implementation.
|
||||
It does not support InfiniBand (use MVAPICH2 with InfiniBand devices)."""
|
||||
|
||||
toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
|
||||
|
||||
sources = [SOURCELOWER_TAR_GZ]
|
||||
source_urls = ['http://www.mpich.org/static/tarballs/%(version)s']
|
||||
|
||||
configopts="--enable-shared"
|
||||
|
||||
# Let's store the checksum in order to be sure it doesn't suddenly change
|
||||
# checksums = ['f414cfa77099cd1fa1a5ae4e22db508a']
|
||||
|
||||
moduleclass = 'mpi'
|
||||
66
m/Mesa/Mesa-17.2.6-foss-2017a.eb
Normal file
66
m/Mesa/Mesa-17.2.6-foss-2017a.eb
Normal file
@ -0,0 +1,66 @@
|
||||
# the purpose of the easyconfig is to build a Mesa for software rendering,
|
||||
# not hardware rendering. This means you want at least SSE4.2. We build:
|
||||
# - llvmpipe: the high-performance Gallium LLVM driver
|
||||
# - swr: Intel's OpenSWR
|
||||
# it will try to use the llvmpipe by default. It you want swr, do:
|
||||
# GALLIUM_DRIVER=swr
|
||||
|
||||
easyblock = 'ConfigureMake'
|
||||
|
||||
name = 'Mesa'
|
||||
version = '17.2.6'
|
||||
|
||||
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': 'foss', 'version': '2017a'}
|
||||
# swr detects and builds parts specific for AVX and AVX2. If we use
|
||||
# -xHost, this always gets overwritten and will fail.
|
||||
toolchainopts = {'optarch': False}
|
||||
|
||||
sources = [SOURCELOWER_TAR_XZ]
|
||||
source_urls = [
|
||||
'https://mesa.freedesktop.org/archive/',
|
||||
'https://mesa.freedesktop.org/archive/%(version)s',
|
||||
'ftp://ftp.freedesktop.org/pub/mesa/%(version)s',
|
||||
'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s',
|
||||
]
|
||||
#patches = ['Mesa-17.0.2_fix-strip-llvm-flags.patch']
|
||||
|
||||
builddependencies = [
|
||||
('flex', '2.6.4', '', True),
|
||||
('Bison', '3.0.4', '', True),
|
||||
('Autotools', '20150215', '', True),
|
||||
('pkg-config', '0.29.1', '', True),
|
||||
('Mako', '1.0.6', '-Python-2.7.13', True),
|
||||
('libxml2', '2.9.4', '-Python-2.7.13', True),
|
||||
]
|
||||
|
||||
dependencies = [
|
||||
('zlib', '1.2.11', '', True),
|
||||
('nettle', '3.3'),
|
||||
('libdrm', '2.4.76', '', True),
|
||||
('LLVM', '4.0.0', '', ('GCC', '6.3.0-2.27')),
|
||||
('X11', '20170314', '', True),
|
||||
]
|
||||
|
||||
# GLU is not part anymore of Mesa package!
|
||||
configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri"
|
||||
configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl"
|
||||
configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs "
|
||||
|
||||
buildopts = 'V=1'
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT,
|
||||
'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT,
|
||||
'include/GL/glext.h', 'include/GL/gl_mangle.h',
|
||||
'include/GL/glx.h', 'include/GL/osmesa.h',
|
||||
'include/GL/gl.h', 'include/GL/glxext.h',
|
||||
'include/GL/glx_mangle.h', 'include/GLES/gl.h',
|
||||
'include/GLES2/gl2.h', 'include/GLES3/gl3.h'],
|
||||
'dirs': []
|
||||
}
|
||||
|
||||
moduleclass = 'vis'
|
||||
30
n/NLopt/NLopt-2.4.2.eb
Normal file
30
n/NLopt/NLopt-2.4.2.eb
Normal file
@ -0,0 +1,30 @@
|
||||
# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
|
||||
# Author: Pablo Escobar Lopez
|
||||
# Swiss Institute of Bioinformatics
|
||||
# Biozentrum - University of Basel
|
||||
|
||||
easyblock = 'ConfigureMake'
|
||||
|
||||
name = 'NLopt'
|
||||
version = '2.4.2'
|
||||
|
||||
homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt'
|
||||
description = """ NLopt is a free/open-source library for nonlinear optimization,
|
||||
providing a common interface for a number of different free optimization routines
|
||||
available online as well as original implementations of various other algorithms. """
|
||||
|
||||
toolchain = {'name': 'dummy', 'version': ''}
|
||||
toolchainopts = {'pic': True}
|
||||
|
||||
source_urls = ['http://ab-initio.mit.edu/nlopt/']
|
||||
sources = [SOURCELOWER_TAR_GZ]
|
||||
checksums = ['8099633de9d71cbc06cd435da993eb424bbcdbded8f803cdaa9fb8c6e09c8e89']
|
||||
|
||||
configopts = '--enable-shared'
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ['lib/libnlopt.a', 'lib/libnlopt.%s' % SHLIB_EXT, 'include/nlopt.h'],
|
||||
'dirs': ['lib/pkgconfig'],
|
||||
}
|
||||
|
||||
moduleclass = 'numlib'
|
||||
28
n/nettle/nettle-3.3-foss-2017a.eb
Normal file
28
n/nettle/nettle-3.3-foss-2017a.eb
Normal file
@ -0,0 +1,28 @@
|
||||
easyblock = 'ConfigureMake'
|
||||
|
||||
name = 'nettle'
|
||||
version = '3.3'
|
||||
|
||||
homepage = 'http://www.lysator.liu.se/~nisse/nettle/'
|
||||
description = """Nettle is a cryptographic library that is designed to fit easily
|
||||
in more or less any context: In crypto toolkits for object-oriented
|
||||
languages (C++, Python, Pike, ...), in applications like LSH or GNUPG,
|
||||
or even in kernel space."""
|
||||
|
||||
toolchain = {'name': 'foss', 'version': '2017a'}
|
||||
|
||||
source_urls = [GNU_SOURCE]
|
||||
sources = [SOURCE_TAR_GZ]
|
||||
|
||||
dependencies = [
|
||||
('GMP', '6.1.2', '', True),
|
||||
]
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] +
|
||||
['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT,
|
||||
'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT],
|
||||
'dirs': ['include/nettle'],
|
||||
}
|
||||
|
||||
moduleclass = 'lib'
|
||||
57
o/Octave/Octave-4.2.1-intel-2017a-mic.eb
Normal file
57
o/Octave/Octave-4.2.1-intel-2017a-mic.eb
Normal file
@ -0,0 +1,57 @@
|
||||
easyblock = 'ConfigureMake'
|
||||
|
||||
name = 'Octave'
|
||||
version = '4.2.1'
|
||||
versionsuffix = '-mic'
|
||||
|
||||
homepage = 'http://www.gnu.org/software/octave/'
|
||||
description = """GNU Octave is a high-level interpreted language, primarily intended for numerical computations."""
|
||||
|
||||
toolchain = {'name': 'intel', 'version': '2017a'}
|
||||
|
||||
source_urls = [GNU_SOURCE]
|
||||
sources = [SOURCELOWER_TAR_GZ]
|
||||
|
||||
patches = ['%(name)s-%(version)s_intel.patch']
|
||||
|
||||
builddependencies = [
|
||||
('Bison', '3.0.4', '', True),
|
||||
('flex', '2.6.4', '', True),
|
||||
('Autotools', '20150215', '', True),
|
||||
('libtool', '2.4.6', '', True),
|
||||
('gperf', '3.0.4'),
|
||||
]
|
||||
|
||||
dependencies = [
|
||||
('PCRE', '8.40', '', True),
|
||||
('ncurses', '6.0', '', True),
|
||||
('libreadline', '7.0', '', True),
|
||||
('arpack-ng', '3.5.0'),
|
||||
('cURL', '7.56.1', '', True),
|
||||
('FLTK', '1.3.4', '', True),
|
||||
('GLPK', '4.61'),
|
||||
('GL2PS', '1.4.0'),
|
||||
('Java', '1.8.0_121', '', True),
|
||||
('zlib', '1.2.11', '', True),
|
||||
('Qhull', '2015.2', '', True),
|
||||
('Qt5', '5.8.0', '', ('GCC', '6.3.0-2.27')),
|
||||
('HDF5', '1.8.18', '-serial'),
|
||||
('qrupdate', '1.1.2'),
|
||||
('SuiteSparse', '4.5.5', '-METIS-5.1.0'),
|
||||
]
|
||||
|
||||
configopts = ' CC="icc -mmic" MOC=$EBROOTQT5/bin/moc '
|
||||
configopts += 'UIC=$EBROOTQT5/bin/uic '
|
||||
configopts += 'RCC=$EBROOTQT5/bin/rcc '
|
||||
configopts += 'LRELEASE=$EBROOTQT5/bin/lrelease '
|
||||
# correct for both GCC and Intel compilers
|
||||
configopts += '--enable-fortran-calling-convention=gfortran'
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ['bin/octave'],
|
||||
'dirs': []
|
||||
}
|
||||
|
||||
sanity_check_commands = [('octave', '--eval "1+2"')]
|
||||
|
||||
moduleclass = 'math'
|
||||
56
p/PAPI/PAPI-5.5.1.eb
Normal file
56
p/PAPI/PAPI-5.5.1.eb
Normal file
@ -0,0 +1,56 @@
|
||||
##
|
||||
# This file is an EasyBuild reciPY as per https://github.com/easybuilders
|
||||
#
|
||||
# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
|
||||
# Authors:: Fotis Georgatos <fotis@cern.ch>
|
||||
# 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 = '5.5.1'
|
||||
|
||||
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': 'dummy', 'version': ''}
|
||||
toolchainopts = {'pic': True}
|
||||
|
||||
source_urls = ['http://icl.cs.utk.edu/projects/papi/downloads/']
|
||||
sources = [SOURCELOWER_TAR_GZ]
|
||||
checksums = ['49dc2c2323f6164c4a7e81b799ed690ee73158671205e71501f849391dd2c2d4']
|
||||
|
||||
builddependencies = [
|
||||
('binutils', '2.29'),
|
||||
]
|
||||
|
||||
start_dir = 'src'
|
||||
|
||||
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'
|
||||
30
p/PROJ/PROJ-4.9.3-foss-2017a.eb
Normal file
30
p/PROJ/PROJ-4.9.3-foss-2017a.eb
Normal file
@ -0,0 +1,30 @@
|
||||
##
|
||||
# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
|
||||
#
|
||||
# Copyright:: Copyright 2014-2015 The Cyprus Institute
|
||||
# Authors:: Thekla Loizou <t.loizou@cyi.ac.cy>
|
||||
# License:: MIT/GPL
|
||||
#
|
||||
##
|
||||
easyblock = 'ConfigureMake'
|
||||
|
||||
name = 'PROJ'
|
||||
version = '4.9.3'
|
||||
|
||||
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': 'foss', 'version': '2017a'}
|
||||
toolchainopts = {'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'
|
||||
522
r/R/R-3.4.2-intel-2017a.eb
Normal file
522
r/R/R-3.4.2-intel-2017a.eb
Normal file
@ -0,0 +1,522 @@
|
||||
name = 'R'
|
||||
version = '3.4.2'
|
||||
|
||||
homepage = 'http://www.r-project.org/'
|
||||
description = """R is a free software environment for statistical computing and graphics."""
|
||||
|
||||
toolchain = {'name': 'intel', 'version': '2017a'}
|
||||
|
||||
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=yes --enable-R-shlib"
|
||||
# Actually use Tcl/Tk
|
||||
configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh '
|
||||
# Enable graphics capabilities for plotting.
|
||||
configopts += " --with-cairo --with-libpng --with-jpeglib --with-libtiff"
|
||||
# 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 = [
|
||||
('cairo', '1.14.8', '', True),
|
||||
('libreadline', '7.0', '', True),
|
||||
('ncurses', '6.0', '', True),
|
||||
('bzip2', '1.0.6', '', True),
|
||||
('XZ', '5.2.3', '', True),
|
||||
('zlib', '1.2.11', '', True),
|
||||
('SQLite', '3.17.0', '', True),
|
||||
('PCRE', '8.40', '', True),
|
||||
('libpng', '1.6.29', '', True), # for plotting in R
|
||||
('libjpeg-turbo', '1.5.1', '', True), # for plottting in R
|
||||
('LibTIFF', '4.0.7', '', True),
|
||||
('Java', '1.8.0_144', '', True), # Java bindings are built if Java is found, might as well provide it
|
||||
('Tcl', '8.6.6', '', True), # for tcltk
|
||||
('Tk', '8.6.6', '', True), # for tcltk
|
||||
('cURL', '7.53.1', '', True), # for RCurl
|
||||
('libxml2', '2.9.4', '', True), # for XML
|
||||
('GDAL', '2.1.3', '-Python-2.7.13', True), # for rgdal
|
||||
('PROJ', '4.9.3'), # for rgdal
|
||||
('GMP', '6.1.2', '', True), # for igraph
|
||||
('NLopt', '2.4.2'), # for nloptr
|
||||
('FFTW', '3.3.6'), # for fftw
|
||||
('libsndfile', '1.0.28'), # for seewave
|
||||
# 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', '1.0.2h'),
|
||||
]
|
||||
|
||||
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
|
||||
|
||||
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 May 11th 2017
|
||||
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', '0.6-6', ext_options),
|
||||
('abind', '1.4-5', ext_options),
|
||||
('magic', '1.5-6', ext_options),
|
||||
('geometry', '0.3-6', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])),
|
||||
('bit', '1.1-12', ext_options),
|
||||
('filehash', '2.4-1', ext_options),
|
||||
('ff', '2.2-13', ext_options),
|
||||
('bnlearn', '4.1.1', ext_options),
|
||||
('bootstrap', '2017.2', ext_options),
|
||||
('combinat', '0.0-8', ext_options),
|
||||
('deal', '1.2-37', ext_options),
|
||||
('fdrtool', '1.2.15', ext_options),
|
||||
('formatR', '1.5', ext_options),
|
||||
('gtools', '3.5.0', ext_options),
|
||||
('gdata', '2.17.0', ext_options),
|
||||
('GSA', '1.03', ext_options),
|
||||
('highr', '0.6', ext_options),
|
||||
('infotheo', '1.2.0', ext_options),
|
||||
('lars', '1.2', ext_options),
|
||||
('lazy', '1.2-15', ext_options),
|
||||
('kernlab', '0.9-25', ext_options),
|
||||
('mime', '0.5', ext_options),
|
||||
('markdown', '0.8', ext_options),
|
||||
('mlbench', '2.1-1', ext_options),
|
||||
('NLP', '0.1-10', ext_options),
|
||||
('mclust', '5.3', ext_options),
|
||||
('RANN', '2.5', ext_options),
|
||||
('rmeta', '2.16', ext_options),
|
||||
('segmented', '0.5-1.4', ext_options),
|
||||
('som', '0.3-5.1', ext_options),
|
||||
('SuppDists', '1.1-9.4', ext_options),
|
||||
('stabledist', '0.7-1', 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', '1.7-6', ext_options),
|
||||
('AlgDesign', '1.1-7.3', ext_options),
|
||||
('base64enc', '0.1-3', ext_options),
|
||||
('BH', '1.62.0-1', ext_options),
|
||||
('brew', '1.0-6', ext_options),
|
||||
('Brobdingnag', '1.2-4', ext_options),
|
||||
('corpcor', '1.6.9', ext_options),
|
||||
('longitudinal', '1.1.12', ext_options),
|
||||
('backports', '1.0.5', ext_options),
|
||||
('checkmate', '1.8.2', ext_options),
|
||||
('Rcpp', '0.12.10', ext_options),
|
||||
('cubature', '1.3-8', ext_options),
|
||||
('DEoptimR', '1.0-8', ext_options),
|
||||
('digest', '0.6.12', ext_options),
|
||||
('fastmatch', '1.1-0', ext_options),
|
||||
('ffbase', '0.12.3', ext_options),
|
||||
('iterators', '1.0.8', ext_options),
|
||||
('maps', '3.1.1', ext_options),
|
||||
('nnls', '1.4', ext_options),
|
||||
('sendmailR', '1.2-1', ext_options),
|
||||
('spam', '1.4-0', ext_options),
|
||||
('subplex', '1.2-2', ext_options),
|
||||
('stringi', '1.1.5', ext_options),
|
||||
('magrittr', '1.5', ext_options),
|
||||
('stringr', '1.2.0', ext_options),
|
||||
('evaluate', '0.10', ext_options),
|
||||
('logspline', '2.1.9', ext_options),
|
||||
('ncbit', '2013.03.29', ext_options),
|
||||
('permute', '0.9-4', ext_options),
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
('htmlwidgets', '0.8', ext_options),
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
('interpretR', '0.2.4', ext_options),
|
||||
('cvAUC', '1.1.0', ext_options),
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
('abc', '2.1', ext_options),
|
||||
('lhs', '0.14', ext_options),
|
||||
('tensorA', '0.36', ext_options),
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
('psych', '1.7.5', ext_options),
|
||||
('pbivnorm', '0.6.0', ext_options),
|
||||
('lavaan', '0.5-23.1097', ext_options),
|
||||
('matrixcalc', '1.0-3', ext_options),
|
||||
('arm', '1.9-3', ext_options),
|
||||
('mi', '1.0', ext_options),
|
||||
('visNetwork', '1.0.3', ext_options),
|
||||
('rgexf', '0.15.3', ext_options),
|
||||
('influenceR', '0.1.0', ext_options),
|
||||
('DiagrammeR', '0.9.0', ext_options),
|
||||
('sem', '3.1-9', ext_options),
|
||||
('jpeg', '0.1-8', ext_options),
|
||||
('network', '1.13.0', ext_options),
|
||||
('statnet.common', '3.3.0', ext_options),
|
||||
('sna', '2.4', ext_options),
|
||||
('glasso', '1.8', dict(ext_options.items() + [('patches', [('glasso-1.8-ifort-no-fixed.patch', 1)])])),
|
||||
('huge', '1.2.7', ext_options),
|
||||
('d3Network', '0.5.2.1', ext_options),
|
||||
('ggm', '2.3', ext_options),
|
||||
('qgraph', '1.4.3', ext_options),
|
||||
('diveRsity', '1.9.90', ext_options),
|
||||
('doSNOW', '1.0.14', ext_options),
|
||||
('phangorn', '2.2.0', ext_options),
|
||||
('geepack', '1.2-1', ext_options),
|
||||
('lubridate', '1.6.0', ext_options),
|
||||
('biom', '0.3.12', ext_options),
|
||||
('pim', '2.0.1', ext_options),
|
||||
('minpack.lm', '1.2-1', ext_options),
|
||||
('rootSolve', '1.7', ext_options),
|
||||
('diagram', '1.6.3', ext_options),
|
||||
('FME', '1.3.5', ext_options),
|
||||
('bmp', '0.2', ext_options),
|
||||
('readbitmap', '0.1-4', ext_options),
|
||||
('purrr', '0.2.2', ext_options),
|
||||
('downloader', '0.4', ext_options),
|
||||
('imager', '0.40.2', dict(ext_options.items() + [('patches', ['imager-0.40.2_icpc-wd308.patch'])])),
|
||||
('pracma', '2.0.4', ext_options),
|
||||
('signal', '0.7-6', ext_options),
|
||||
('tuneR', '1.3.2', ext_options),
|
||||
('pastecs', '1.3-18', ext_options),
|
||||
('audio', '0.1-5', ext_options),
|
||||
('fftw', '1.0-4', ext_options),
|
||||
('seewave', '2.0.5', ext_options),
|
||||
('gsw', '1.0-3', ext_options),
|
||||
('oce', '0.9-21', ext_options),
|
||||
('ineq', '0.2-13', ext_options),
|
||||
('soundecology', '1.3.2', ext_options),
|
||||
# ('KFAS', '1.2.9', ext_options),
|
||||
]
|
||||
|
||||
moduleclass = 'lang'
|
||||
556
r/R/R-3.4.3-foss-2017a.eb
Normal file
556
r/R/R-3.4.3-foss-2017a.eb
Normal file
@ -0,0 +1,556 @@
|
||||
# IT4Innovations 2017
|
||||
|
||||
name = 'R'
|
||||
version = '3.4.2'
|
||||
|
||||
homepage = 'http://www.r-project.org/'
|
||||
description = """R is a free software environment for statistical computing and graphics."""
|
||||
|
||||
toolchain = {'name': 'foss', 'version': '2017a'}
|
||||
|
||||
sources = [SOURCE_TAR_GZ]
|
||||
source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s']
|
||||
|
||||
#checksums = ['02b1135d15ea969a3582caeb95594a05e830a6debcdb5b85ed2d5836a6a3fc78']
|
||||
|
||||
preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"'
|
||||
configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=yes --enable-R-shlib"
|
||||
# actually use Tcl/Tk
|
||||
configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh '
|
||||
# Enable graphics capabilities for plotting.
|
||||
configopts += " --with-cairo --with-libpng --with-jpeglib --with-libtiff"
|
||||
# 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 = [
|
||||
('X11', '20170314', '', True),
|
||||
('Mesa', '17.2.6'),
|
||||
('libGLU', '9.0.0', '', True),
|
||||
('cairo', '1.14.8', '', True),
|
||||
('libreadline', '7.0', '', True),
|
||||
('ncurses', '6.0', '', True),
|
||||
('bzip2', '1.0.6', '', True),
|
||||
('XZ', '5.2.3', '', True),
|
||||
('zlib', '1.2.11', '', True),
|
||||
('SQLite', '3.17.0', '', True),
|
||||
('PCRE', '8.40', '', True),
|
||||
('libpng', '1.6.29', '', True), # for plotting in R
|
||||
('libjpeg-turbo', '1.5.1', '', True), # for plottting in R
|
||||
('LibTIFF', '4.0.7', '', True),
|
||||
('Java', '1.8.0_144', '', True), # Java bindings are built if Java is found, might as well provide it
|
||||
('Tcl', '8.6.6', '', True), # for tcltk
|
||||
('Tk', '8.6.6', '', True), # for tcltk
|
||||
('cURL', '7.53.1', '', True), # for RCurl
|
||||
('libxml2', '2.9.4', '', True), # for XML
|
||||
('GDAL', '2.1.3', '-Python-2.7.13', True), # for rgdal
|
||||
('PROJ', '4.9.3'), # for rgdal
|
||||
('GMP', '6.1.2', '', True), # for igraph
|
||||
('NLopt', '2.4.2', '', True), # for nloptr
|
||||
('FFTW', '3.3.6'), # for fftw
|
||||
('libsndfile', '1.0.28', '', True), # for seewave
|
||||
# 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', '1.0.2h'),
|
||||
]
|
||||
|
||||
osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
|
||||
|
||||
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 and selected on August 24 2017
|
||||
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', '0.6-6', ext_options),
|
||||
('abind', '1.4-5', ext_options),
|
||||
('magic', '1.5-6', ext_options),
|
||||
('geometry', '0.3-6', ext_options),
|
||||
('bit', '1.1-12', ext_options),
|
||||
('bit64', '0.9-7', ext_options),
|
||||
('filehash', '2.4-1', ext_options),
|
||||
('ff', '2.2-13', ext_options),
|
||||
('bnlearn', '4.2', ext_options),
|
||||
('bootstrap', '2017.2', ext_options),
|
||||
('combinat', '0.0-8', ext_options),
|
||||
('deal', '1.2-37', ext_options),
|
||||
('fdrtool', '1.2.15', ext_options),
|
||||
('formatR', '1.5', ext_options),
|
||||
('gtools', '3.5.0', ext_options),
|
||||
('gdata', '2.18.0', ext_options),
|
||||
('GSA', '1.03', ext_options),
|
||||
('highr', '0.6', ext_options),
|
||||
('infotheo', '1.2.0', ext_options),
|
||||
('lars', '1.2', ext_options),
|
||||
('lazy', '1.2-15', ext_options),
|
||||
('kernlab', '0.9-25', ext_options),
|
||||
('mime', '0.5', ext_options),
|
||||
('markdown', '0.8', ext_options),
|
||||
('mlbench', '2.1-1', ext_options),
|
||||
('NLP', '0.1-11', ext_options),
|
||||
('mclust', '5.3', ext_options),
|
||||
('RANN', '2.5.1', ext_options),
|
||||
('rmeta', '2.16', ext_options),
|
||||
('segmented', '0.5-2.1', ext_options),
|
||||
('som', '0.3-5.1', ext_options),
|
||||
('SuppDists', '1.1-9.4', ext_options),
|
||||
('stabledist', '0.7-1', ext_options),
|
||||
('survivalROC', '1.0.3', ext_options),
|
||||
('pspline', '1.0-18', ext_options),
|
||||
('timeDate', '3012.100', ext_options),
|
||||
('longmemo', '1.0-0', ext_options),
|
||||
('ADGofTest', '0.3', ext_options),
|
||||
('ade4', '1.7-8', ext_options),
|
||||
('AlgDesign', '1.1-7.3', ext_options),
|
||||
('base64enc', '0.1-3', ext_options),
|
||||
('BH', '1.62.0-1', ext_options),
|
||||
('brew', '1.0-6', ext_options),
|
||||
('Brobdingnag', '1.2-4', ext_options),
|
||||
('corpcor', '1.6.9', ext_options),
|
||||
('longitudinal', '1.1.12', ext_options),
|
||||
('backports', '1.1.0', ext_options),
|
||||
('checkmate', '1.8.3', ext_options),
|
||||
('Rcpp', '0.12.12', ext_options),
|
||||
('cubature', '1.3-11', ext_options),
|
||||
('DEoptimR', '1.0-8', ext_options),
|
||||
('digest', '0.6.12', ext_options),
|
||||
('fastmatch', '1.1-0', ext_options),
|
||||
('ffbase', '0.12.3', ext_options),
|
||||
('iterators', '1.0.8', ext_options),
|
||||
('maps', '3.2.0', ext_options),
|
||||
('nnls', '1.4', ext_options),
|
||||
('sendmailR', '1.2-1', ext_options),
|
||||
('dotCall64', '0.9-04', ext_options),
|
||||
('spam', '2.1-1', ext_options),
|
||||
('subplex', '1.4-1', ext_options),
|
||||
('stringi', '1.1.5', ext_options),
|
||||
('magrittr', '1.5', ext_options),
|
||||
('stringr', '1.2.0', ext_options),
|
||||
('evaluate', '0.10.1', ext_options),
|
||||
('logspline', '2.1.9', ext_options),
|
||||
('ncbit', '2013.03.29', ext_options),
|
||||
('permute', '0.9-4', ext_options),
|
||||
('plotrix', '3.6-6', ext_options),
|
||||
('randomForest', '4.6-12', ext_options),
|
||||
('scatterplot3d', '0.3-40', ext_options),
|
||||
('SparseM', '1.77', ext_options),
|
||||
('tripack', '1.3-8', ext_options),
|
||||
('irace', '2.4', ext_options),
|
||||
('rJava', '0.9-8', ext_options),
|
||||
('lattice', '0.20-35', ext_options),
|
||||
('RColorBrewer', '1.1-2', ext_options),
|
||||
('latticeExtra', '0.6-28', ext_options),
|
||||
('Matrix', '1.2-11', ext_options),
|
||||
('png', '0.1-7', ext_options),
|
||||
('RcppArmadillo', '0.7.960.1.1', ext_options),
|
||||
('plyr', '1.8.4', ext_options),
|
||||
('pROC', '1.9.1', ext_options),
|
||||
('quadprog', '1.5-5', ext_options),
|
||||
('BB', '2014.10-1', ext_options),
|
||||
('BBmisc', '1.11', ext_options),
|
||||
('fail', '1.3', ext_options),
|
||||
('rlecuyer', '0.3-4', ext_options),
|
||||
('snow', '0.4-2', ext_options),
|
||||
('MASS', '7.3-47', ext_options),
|
||||
('tree', '1.0-37', ext_options),
|
||||
('pls', '2.6-0', ext_options),
|
||||
('class', '7.3-14', ext_options),
|
||||
('e1071', '1.6-8', ext_options),
|
||||
('nnet', '7.3-12', ext_options),
|
||||
('nlme', '3.1-131', ext_options),
|
||||
('minqa', '1.2.4', ext_options),
|
||||
('RcppEigen', '0.3.3.3.0', ext_options),
|
||||
('MatrixModels', '0.4-1', ext_options),
|
||||
('quantreg', '5.33', ext_options),
|
||||
('mgcv', '1.8-18', ext_options),
|
||||
('colorspace', '1.3-2', ext_options),
|
||||
('robustbase', '0.92-7', ext_options),
|
||||
('sp', '1.2-5', ext_options),
|
||||
('zoo', '1.8-0', ext_options),
|
||||
('lmtest', '0.9-35', ext_options),
|
||||
('vcd', '1.4-3', ext_options),
|
||||
('snowfall', '1.84-6.1', ext_options),
|
||||
('rpart', '4.1-11', ext_options),
|
||||
('survival', '2.41-3', ext_options),
|
||||
('mice', '2.30', ext_options),
|
||||
('urca', '1.3-0', ext_options),
|
||||
('fracdiff', '1.4-2', ext_options),
|
||||
('logistf', '1.22', ext_options),
|
||||
('akima', '0.6-2', ext_options),
|
||||
('bitops', '1.0-6', ext_options),
|
||||
('boot', '1.3-20', ext_options),
|
||||
('mixtools', '1.1.0', ext_options),
|
||||
('cluster', '2.0.6', ext_options),
|
||||
('gclus', '1.3.1', ext_options),
|
||||
('coda', '0.19-1', ext_options),
|
||||
('codetools', '0.2-15', ext_options),
|
||||
('foreach', '1.4.3', ext_options),
|
||||
('doMC', '1.3.4', ext_options),
|
||||
('DBI', '0.7', ext_options),
|
||||
('foreign', '0.8-69', ext_options),
|
||||
('gam', '1.14-4', ext_options),
|
||||
('gamlss.data', '5.0-0', ext_options),
|
||||
('gamlss.dist', '5.0-2', ext_options),
|
||||
('hwriter', '1.3.2', ext_options),
|
||||
('KernSmooth', '2.23-15', ext_options),
|
||||
('xts', '0.10-0', ext_options),
|
||||
('curl', '2.8.1', ext_options),
|
||||
('TTR', '0.23-2', ext_options),
|
||||
('quantmod', '0.4-10', ext_options),
|
||||
('mnormt', '1.5-5', ext_options),
|
||||
('mvtnorm', '1.0-6', ext_options),
|
||||
('pcaPP', '1.9-72', ext_options),
|
||||
('numDeriv', '2016.8-1', ext_options),
|
||||
('lava', '1.5', ext_options),
|
||||
('prodlim', '1.6.1', ext_options),
|
||||
('pscl', '1.4.9', ext_options),
|
||||
('memoise', '1.1.0', ext_options),
|
||||
('plogr', '0.1-1', ext_options),
|
||||
('sandwich', '2.4-0', ext_options),
|
||||
('sfsmisc', '1.1-1', ext_options),
|
||||
('spatial', '7.3-11', ext_options),
|
||||
('VGAM', '1.0-4', ext_options),
|
||||
('waveslim', '1.7.5', ext_options),
|
||||
('xtable', '1.8-2', ext_options),
|
||||
('profileModel', '0.5-9', ext_options),
|
||||
('brglm', '0.6.1', ext_options),
|
||||
('deSolve', '1.20', ext_options),
|
||||
('tseriesChaos', '0.1-13', ext_options),
|
||||
('tseries', '0.10-42', ext_options),
|
||||
('fastICA', '1.2-1', ext_options),
|
||||
('R.methodsS3', '1.7.1', ext_options),
|
||||
('R.oo', '1.21.0', ext_options),
|
||||
('cgdsr', '1.2.6', ext_options),
|
||||
('R.utils', '2.5.0', ext_options),
|
||||
('R.matlab', '3.6.1', ext_options),
|
||||
('gbm', '2.1.3', ext_options),
|
||||
('dichromat', '2.0-0', ext_options),
|
||||
('Formula', '1.2-2', ext_options),
|
||||
('acepack', '1.4.1', ext_options),
|
||||
('reshape2', '1.4.2', ext_options),
|
||||
('gtable', '0.2.0', ext_options),
|
||||
('munsell', '0.4.3', ext_options),
|
||||
('labeling', '0.3', ext_options),
|
||||
('viridisLite', '0.2.0', ext_options),
|
||||
('R6', '2.2.2', ext_options),
|
||||
('scales', '0.4.1', ext_options),
|
||||
('proto', '1.0.0', ext_options),
|
||||
('lazyeval', '0.2.0', ext_options),
|
||||
('assertthat', '0.2.0', ext_options),
|
||||
('rlang', '0.1.2', ext_options),
|
||||
('tibble', '1.3.4', ext_options),
|
||||
('blob', '1.1.0', ext_options),
|
||||
('pkgconfig', '2.0.1', ext_options),
|
||||
('RSQLite', '1.1-2', ext_options),
|
||||
('BatchJobs', '1.6', ext_options),
|
||||
('ggplot2', '2.2.1', ext_options),
|
||||
('pROC', '1.10.0', ext_options),
|
||||
('gridExtra', '2.2.1', ext_options),
|
||||
('chron', '2.3-50', ext_options),
|
||||
('data.table', '1.10.4', ext_options),
|
||||
('viridis', '0.4.0', ext_options),
|
||||
('yaml', '2.1.14', ext_options),
|
||||
('jsonlite', '1.5', ext_options),
|
||||
('htmltools', '0.3.6', ext_options),
|
||||
('htmlwidgets', '0.9', ext_options),
|
||||
('knitr', '1.17', ext_options),
|
||||
('htmlTable', '1.9', ext_options),
|
||||
('Hmisc', '4.0-3', ext_options),
|
||||
('fastcluster', '1.1.24', ext_options),
|
||||
('registry', '0.3', ext_options),
|
||||
('pkgmaker', '0.22', ext_options),
|
||||
('rngtools', '1.2.4', ext_options),
|
||||
('doParallel', '1.0.10', ext_options),
|
||||
('gridBase', '0.4-7', ext_options),
|
||||
('NMF', '0.20.6', ext_options),
|
||||
('irlba', '2.2.1', ext_options),
|
||||
('igraph', '1.1.2', ext_options),
|
||||
('GeneNet', '1.2.13', ext_options),
|
||||
('ape', '4.1', ext_options),
|
||||
('RJSONIO', '1.3-0', ext_options),
|
||||
('caTools', '1.17.1', ext_options),
|
||||
('gplots', '3.0.1', ext_options),
|
||||
('ROCR', '1.0-7', ext_options),
|
||||
('httpuv', '1.3.5', ext_options),
|
||||
('rjson', '0.2.15', ext_options),
|
||||
('sourcetools', '0.1.6', ext_options),
|
||||
('shiny', '1.0.4', ext_options),
|
||||
('seqinr', '3.4-5', ext_options),
|
||||
('LearnBayes', '2.15', ext_options),
|
||||
('deldir', '0.1-14', ext_options),
|
||||
('gmodels', '2.16.2', ext_options),
|
||||
('expm', '0.999-2', ext_options),
|
||||
('spdep', '0.6-13', ext_options),
|
||||
('bindr', '0.1', ext_options),
|
||||
('bindrcpp', '0.2', ext_options),
|
||||
('glue', '1.1.1', ext_options),
|
||||
('dplyr', '0.7.2', ext_options),
|
||||
('vegan', '2.4-3', ext_options),
|
||||
('adegenet', '2.0.1', ext_options),
|
||||
('prettyunits', '1.0.2', ext_options),
|
||||
('progress', '1.1.2', ext_options),
|
||||
('rncl', '0.8.2', ext_options),
|
||||
('XML', '3.98-1.9', ext_options),
|
||||
('crayon', '1.3.2', ext_options),
|
||||
('praise', '1.0.0', ext_options),
|
||||
('testthat', '1.0.2', ext_options),
|
||||
('rprojroot', '1.2', ext_options),
|
||||
('rmarkdown', '1.6', ext_options),
|
||||
('openssl', '0.9.6', ext_options),
|
||||
('httr', '1.3.1', ext_options),
|
||||
('reshape', '0.8.7', ext_options),
|
||||
('xml2', '1.1.1', ext_options),
|
||||
('triebeard', '0.3.0', ext_options),
|
||||
('urltools', '1.6.0', ext_options),
|
||||
('httpcode', '0.2.0', ext_options),
|
||||
('crul', '0.3.8', ext_options),
|
||||
('bold', '0.5.0', ext_options),
|
||||
('rredlist', '0.3.0', ext_options),
|
||||
('rentrez', '1.1.0', ext_options),
|
||||
('rotl', '3.0.3', ext_options),
|
||||
('solrium', '0.4.0', ext_options),
|
||||
('ritis', '0.5.4', ext_options),
|
||||
('worrms', '0.1.0', ext_options),
|
||||
('natserv', '0.1.4', ext_options),
|
||||
('WikipediR', '1.5.0', ext_options),
|
||||
('WikidataR', '1.3.0', ext_options),
|
||||
('wikitaxa', '0.1.4', ext_options),
|
||||
('taxize', '0.8.9', ext_options),
|
||||
('tidyselect', '0.1.1', ext_options),
|
||||
('purrr', '0.2.3', ext_options),
|
||||
('tidyr', '0.7.0', ext_options),
|
||||
('uuid', '0.1-2', ext_options),
|
||||
('RNeXML', '2.0.7', ext_options),
|
||||
('phylobase', '0.8.4', ext_options),
|
||||
('adephylo', '1.1-10', ext_options),
|
||||
('animation', '2.5', ext_options),
|
||||
('bigmemory.sri', '0.1.3', ext_options),
|
||||
('bigmemory', '4.5.19', ext_options),
|
||||
('calibrate', '1.7.2', ext_options),
|
||||
('clusterGeneration', '1.3.4', ext_options),
|
||||
('raster', '2.5-8', ext_options),
|
||||
('dismo', '1.1-4', ext_options),
|
||||
('extrafontdb', '1.0', ext_options),
|
||||
('Rttf2pt1', '1.3.4', ext_options),
|
||||
('extrafont', '0.17', ext_options),
|
||||
('fields', '9.0', ext_options),
|
||||
('shapefiles', '0.7', ext_options),
|
||||
('fossil', '0.3.7', ext_options),
|
||||
('geiger', '2.0.6', ext_options),
|
||||
('glmnet', '2.0-10', ext_options),
|
||||
('rgl', '0.98.1', ext_options),
|
||||
('labdsv', '1.8-0', ext_options),
|
||||
('stabs', '0.6-3', ext_options),
|
||||
('modeltools', '0.2-21', ext_options),
|
||||
('strucchange', '1.5-1', ext_options),
|
||||
('TH.data', '1.0-8', ext_options),
|
||||
('multcomp', '1.4-6', ext_options),
|
||||
('coin', '1.2-1', ext_options),
|
||||
('party', '1.2-3', ext_options),
|
||||
('mboost', '2.8-1', ext_options),
|
||||
('msm', '1.6.4', ext_options),
|
||||
('nor1mix', '1.2-2', ext_options),
|
||||
('np', '0.60-3', ext_options),
|
||||
('polynom', '1.3-9', ext_options),
|
||||
('polspline', '1.1.12', ext_options),
|
||||
('rms', '5.1-1', ext_options),
|
||||
('RWekajars', '3.9.1-3', ext_options),
|
||||
('RWeka', '0.4-34', ext_options),
|
||||
('slam', '0.1-40', ext_options),
|
||||
('tm', '0.7-1', ext_options),
|
||||
('TraMineR', '2.0-7', ext_options),
|
||||
('chemometrics', '1.4.2', ext_options),
|
||||
('FNN', '1.1', ext_options),
|
||||
('ipred', '0.9-6', ext_options),
|
||||
('statmod', '1.4.30', ext_options),
|
||||
('miscTools', '0.6-22', ext_options),
|
||||
('maxLik', '1.3-4', ext_options),
|
||||
('mlogit', '0.2-4', ext_options),
|
||||
('getopt', '1.20.0', ext_options),
|
||||
('gsalib', '2.1', ext_options),
|
||||
('optparse', '1.4.4', ext_options),
|
||||
('klaR', '0.6-12', ext_options),
|
||||
('neuRosim', '0.2-12', ext_options),
|
||||
('locfit', '1.5-9.1', ext_options),
|
||||
('GGally', '1.3.2', ext_options),
|
||||
('beanplot', '1.2', ext_options),
|
||||
('clValid', '0.6-6', ext_options),
|
||||
('matrixStats', '0.52.2', ext_options),
|
||||
('DiscriMiner', '0.1-29', ext_options),
|
||||
('ellipse', '0.3-8', ext_options),
|
||||
('leaps', '3.0', ext_options),
|
||||
('nloptr', '1.0.4', ext_options),
|
||||
('lme4', '1.1-13', ext_options),
|
||||
('pbkrtest', '0.4-7', ext_options),
|
||||
('car', '2.1-5', ext_options),
|
||||
('flashClust', '1.01-2', ext_options),
|
||||
('FactoMineR', '1.36', ext_options),
|
||||
('flexclust', '1.3-4', ext_options),
|
||||
('flexmix', '2.3-14', ext_options),
|
||||
('prabclus', '2.2-6', ext_options),
|
||||
('diptest', '0.75-7', ext_options),
|
||||
('trimcluster', '0.1-2', ext_options),
|
||||
('fpc', '2.1-10', ext_options),
|
||||
('BiasedUrn', '1.07', ext_options),
|
||||
('TeachingDemos', '2.10', ext_options),
|
||||
('kohonen', '3.0.2', ext_options),
|
||||
('base64', '2.0', ext_options),
|
||||
('doRNG', '1.6.6', ext_options),
|
||||
('nleqslv', '3.3.1', ext_options),
|
||||
('Deriv', '3.8.1', ext_options),
|
||||
('RGCCA', '2.1.2', ext_options),
|
||||
('pheatmap', '1.0.8', ext_options),
|
||||
('openxlsx', '4.0.17', ext_options),
|
||||
('pvclust', '2.0-0', ext_options),
|
||||
('RCircos', '1.2.0', ext_options),
|
||||
('lambda.r', '1.1.9', ext_options),
|
||||
('futile.options', '1.0.0', ext_options),
|
||||
('futile.logger', '1.4.3', ext_options),
|
||||
('VennDiagram', '1.6.17', ext_options),
|
||||
('xlsxjars', '0.6.1', ext_options),
|
||||
('xlsx', '0.5.7', ext_options),
|
||||
('forecast', '8.1', ext_options),
|
||||
('fma', '2.3', ext_options),
|
||||
('expsmooth', '2.3', ext_options),
|
||||
('fpp', '0.5', ext_options),
|
||||
('maptools', '0.9-2', ext_options),
|
||||
('tensor', '1.5', ext_options),
|
||||
('polyclip', '1.6-1', ext_options),
|
||||
('goftest', '1.1-1', ext_options),
|
||||
('spatstat.utils', '1.7-0', ext_options),
|
||||
('spatstat', '1.52-1', ext_options),
|
||||
('rgdal', '1.2-8', ext_options),
|
||||
('gdalUtils', '2.0.1.7', ext_options),
|
||||
('pracma', '2.0.7', ext_options),
|
||||
('RCurl', '1.95-4.8', ext_options),
|
||||
('bio3d', '2.3-3', ext_options),
|
||||
('AUC', '0.3.0', ext_options),
|
||||
('interpretR', '0.2.4', ext_options),
|
||||
('cvAUC', '1.1.0', ext_options),
|
||||
('SuperLearner', '2.0-22', ext_options),
|
||||
('lpSolve', '5.6.13', ext_options),
|
||||
('mediation', '4.4.6', ext_options),
|
||||
('ModelMetrics', '1.1.0', ext_options),
|
||||
('caret', '6.0-76', ext_options),
|
||||
('adabag', '4.1', ext_options),
|
||||
('parallelMap', '1.3', ext_options),
|
||||
('ParamHelpers', '1.10', ext_options),
|
||||
('ggvis', '0.4.3', ext_options),
|
||||
('mlr', '2.11', ext_options),
|
||||
('unbalanced', '2.0', ext_options),
|
||||
('RSNNS', '0.4-9', ext_options),
|
||||
('abc.data', '1.0', ext_options),
|
||||
('abc', '2.1', ext_options),
|
||||
('lhs', '0.14', ext_options),
|
||||
('tensorA', '0.36', ext_options),
|
||||
('EasyABC', '1.5', ext_options),
|
||||
('shape', '1.4.3', ext_options),
|
||||
('whisker', '0.3-2', ext_options),
|
||||
('rstudioapi', '0.6', ext_options),
|
||||
('commonmark', '1.2', ext_options),
|
||||
('desc', '1.1.1', ext_options),
|
||||
('roxygen2', '6.0.1', ext_options),
|
||||
('git2r', '0.19.0', ext_options),
|
||||
('rversions', '1.0.3', ext_options),
|
||||
('withr', '2.0.0', ext_options),
|
||||
('devtools', '1.13.3', ext_options),
|
||||
('Rook', '1.1-1', ext_options),
|
||||
('Cairo', '1.5-9', dict(ext_options.items() + [('patches', ['Cairo-1.5-9.patch'])])),
|
||||
('RMTstat', '0.3', ext_options),
|
||||
('Lmoments', '1.2-3', ext_options),
|
||||
('distillery', '1.0-4', ext_options),
|
||||
('extRemes', '2.0-8', ext_options),
|
||||
('pixmap', '0.4-11', ext_options),
|
||||
('tkrplot', '0.0-23', ext_options),
|
||||
('misc3d', '0.8-4', ext_options),
|
||||
('multicool', '0.1-10', ext_options),
|
||||
('ks', '1.10.7', ext_options),
|
||||
('logcondens', '2.1.5', ext_options),
|
||||
('Iso', '0.0-17', ext_options),
|
||||
('penalized', '0.9-50', ext_options),
|
||||
('clusterRepro', '0.5-1.1', ext_options),
|
||||
('randomForestSRC', '2.5.0', ext_options),
|
||||
('sm', '2.2-5.4', ext_options),
|
||||
('psych', '1.7.5', ext_options),
|
||||
('pbivnorm', '0.6.0', ext_options),
|
||||
('lavaan', '0.5-23.1097', ext_options),
|
||||
('matrixcalc', '1.0-3', ext_options),
|
||||
('arm', '1.9-3', ext_options),
|
||||
('mi', '1.0', ext_options),
|
||||
('visNetwork', '2.0.1', ext_options),
|
||||
('rgexf', '0.15.3', ext_options),
|
||||
('influenceR', '0.1.0', ext_options),
|
||||
('sem', '3.1-9', ext_options),
|
||||
('jpeg', '0.1-8', ext_options),
|
||||
('network', '1.13.0', ext_options),
|
||||
('statnet.common', '4.0.0', ext_options),
|
||||
('sna', '2.4', ext_options),
|
||||
('glasso', '1.8', ext_options),
|
||||
('huge', '1.2.7', ext_options),
|
||||
('d3Network', '0.5.2.1', ext_options),
|
||||
('ggm', '2.3', ext_options),
|
||||
('qgraph', '1.4.3', ext_options),
|
||||
('diveRsity', '1.9.90', ext_options),
|
||||
('doSNOW', '1.0.14', ext_options),
|
||||
('phangorn', '2.2.0', ext_options),
|
||||
('geepack', '1.2-1', ext_options),
|
||||
('lubridate', '1.6.0', ext_options),
|
||||
('pim', '2.0.1', ext_options),
|
||||
('minpack.lm', '1.2-1', ext_options),
|
||||
('rootSolve', '1.7', ext_options),
|
||||
('diagram', '1.6.4', ext_options),
|
||||
('FME', '1.3.5', ext_options),
|
||||
('bmp', '0.2', ext_options),
|
||||
('readbitmap', '0.1-4', ext_options),
|
||||
('downloader', '0.4', ext_options),
|
||||
('imager', '0.40.2', ext_options),
|
||||
('bbmle', '1.0.19', ext_options),
|
||||
('unmarked', '0.12-2', ext_options),
|
||||
('AICcmodavg', '2.1-1', ext_options),
|
||||
('boot', '1.3-20', ext_options),
|
||||
('GlobalOptions', '0.0.12', ext_options),
|
||||
('circlize', '0.4.1', ext_options),
|
||||
('emdbook', '1.3.9', ext_options),
|
||||
('hash', '2.2.6', ext_options),
|
||||
('hms', '0.3', ext_options),
|
||||
('forcats', '0.2.0', ext_options),
|
||||
('feather', '0.3.1', ext_options),
|
||||
('readr', '1.1.1', ext_options),
|
||||
('DiagrammeR', '0.9.1', ext_options),
|
||||
('haven', '1.1.0', ext_options),
|
||||
('rematch', '1.0.1', ext_options),
|
||||
('cellranger', '1.1.0', ext_options),
|
||||
('readxl', '1.0.0', ext_options),
|
||||
('selectr', '0.3-1', ext_options),
|
||||
('rvest', '0.3.2', ext_options),
|
||||
('broom', '0.4.2', ext_options),
|
||||
('modelr', '0.1.1', ext_options),
|
||||
('limSolve', '1.5.5.3', ext_options),
|
||||
('MuMIn', '1.15.6', ext_options),
|
||||
('R2WinBUGS', '2.1-21', ext_options),
|
||||
('rslurm', '0.3.3', ext_options),
|
||||
('RUnit', '0.4.31', ext_options),
|
||||
('tidyverse', '1.1.1', ext_options),
|
||||
('KFAS', '1.2.9', ext_options),
|
||||
]
|
||||
|
||||
moduleclass = 'lang'
|
||||
23
s/SAMtools/SAMtools-1.6-intel-2017a.eb
Normal file
23
s/SAMtools/SAMtools-1.6-intel-2017a.eb
Normal file
@ -0,0 +1,23 @@
|
||||
name = 'SAMtools'
|
||||
version = '1.6'
|
||||
|
||||
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': '2017a'}
|
||||
toolchainopts = {'optarch': True, 'pic': True}
|
||||
|
||||
source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
|
||||
sources = [SOURCELOWER_TAR_BZ2]
|
||||
|
||||
# Patch Makefile to link against zlib provided by EB
|
||||
#patches = ['SAMtools-1.3_Makefile.patch']
|
||||
|
||||
dependencies = [
|
||||
('ncurses', '6.0', '', True),
|
||||
('zlib', '1.2.11', '', True),
|
||||
('XZ', '5.2.3', '', True),
|
||||
]
|
||||
|
||||
moduleclass = 'bio'
|
||||
22
s/Singularity/Singularity-2.4.1.eb
Normal file
22
s/Singularity/Singularity-2.4.1.eb
Normal file
@ -0,0 +1,22 @@
|
||||
easyblock = 'ConfigureMake'
|
||||
|
||||
name = 'Singularity'
|
||||
version = '2.4.1'
|
||||
|
||||
homepage = 'http://gmkurtzer.github.io/singularity'
|
||||
description = """Singularity is a container platform focused on supporting \"Mobility of Compute\""""
|
||||
|
||||
toolchain = {'name': 'dummy', 'version': ''}
|
||||
|
||||
source_urls = ['https://github.com/gmkurtzer/singularity/archive/']
|
||||
sources = ['%(version)s.tar.gz']
|
||||
|
||||
builddependencies = [('Autotools', '20150215')]
|
||||
|
||||
preconfigopts = './autogen.sh && '
|
||||
|
||||
modextravars = {'SINGULARITY_OVERLAYFS_ENABLED': '1'}
|
||||
|
||||
modluafooter = 'add_property("state","experimental")'
|
||||
|
||||
moduleclass = 'tools'
|
||||
@ -7,7 +7,11 @@ versionsuffix = '-24Jun15'
|
||||
homepage = 'http://www.vasp.at'
|
||||
description = """The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale
|
||||
materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics,
|
||||
from first principles."""
|
||||
from first principles.
|
||||
|
||||
To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs.
|
||||
|
||||
Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment."""
|
||||
|
||||
toolchain = {'name': 'intel', 'version': '2015b'}
|
||||
toolchainopts = {'pic': True, 'usempi': True}
|
||||
|
||||
@ -7,7 +7,11 @@ versionsuffix = '-24Jun15'
|
||||
homepage = 'http://www.vasp.at'
|
||||
description = """The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale
|
||||
materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics,
|
||||
from first principles."""
|
||||
from first principles.
|
||||
|
||||
To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs.
|
||||
|
||||
Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment."""
|
||||
|
||||
toolchain = {'name': 'intel', 'version': '2017.00'}
|
||||
toolchainopts = {'pic': True, 'usempi': True}
|
||||
|
||||
@ -7,7 +7,11 @@ versionsuffix = '-24Jun15'
|
||||
homepage = 'http://www.vasp.at'
|
||||
description = """The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale
|
||||
materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics,
|
||||
from first principles."""
|
||||
from first principles.
|
||||
|
||||
To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs.
|
||||
|
||||
Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment."""
|
||||
|
||||
toolchain = {'name': 'intel', 'version': '2017a}
|
||||
toolchainopts = {'pic': True, 'usempi': True}
|
||||
|
||||
@ -7,7 +7,11 @@ versionsuffix = '-mkl=sequential'
|
||||
homepage = 'http://www.vasp.at'
|
||||
description = """The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale
|
||||
materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics,
|
||||
from first principles."""
|
||||
from first principles.
|
||||
|
||||
To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs.
|
||||
|
||||
Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment."""
|
||||
|
||||
toolchain = {'name': 'intel', 'version': '2015b'}
|
||||
toolchainopts = {'pic': True, 'usempi': True}
|
||||
|
||||
@ -7,7 +7,11 @@ versionsuffix = '-CUDA-8.0.44-mkl=sequential'
|
||||
homepage = 'http://www.vasp.at'
|
||||
description = """The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale
|
||||
materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics,
|
||||
from first principles."""
|
||||
from first principles.
|
||||
|
||||
To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs.
|
||||
|
||||
Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment."""
|
||||
|
||||
toolchain = {'name': 'intel', 'version': '2016a'}
|
||||
toolchainopts = {'pic': True, 'usempi': True}
|
||||
|
||||
@ -7,7 +7,11 @@ versionsuffix = '-O3'
|
||||
homepage = 'http://www.vasp.at'
|
||||
description = """The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale
|
||||
materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics,
|
||||
from first principles."""
|
||||
from first principles.
|
||||
|
||||
To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs.
|
||||
|
||||
Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment."""
|
||||
|
||||
toolchain = {'name': 'intel', 'version': '2017a'}
|
||||
toolchainopts = {'pic': True, 'usempi': True}
|
||||
|
||||
@ -7,7 +7,11 @@ versionsuffix = '-mkl=cluster'
|
||||
homepage = 'http://www.vasp.at'
|
||||
description = """The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale
|
||||
materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics,
|
||||
from first principles."""
|
||||
from first principles.
|
||||
|
||||
To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs.
|
||||
|
||||
Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment."""
|
||||
|
||||
toolchain = {'name': 'intel', 'version': '2017a'}
|
||||
toolchainopts = {'pic': True, 'usempi': True}
|
||||
|
||||
58
v/VASP/VASP-5.4.4-intel-2017a-mkl=paralel-test.eb
Normal file
58
v/VASP/VASP-5.4.4-intel-2017a-mkl=paralel-test.eb
Normal file
@ -0,0 +1,58 @@
|
||||
easyblock = 'MakeCp'
|
||||
|
||||
name = 'VASP'
|
||||
version = '5.4.4'
|
||||
versionsuffix = '-mkl=paralel-test'
|
||||
|
||||
homepage = 'http://www.vasp.at'
|
||||
description = """The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale
|
||||
materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics,
|
||||
from first principles.
|
||||
|
||||
To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs.
|
||||
|
||||
Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment."""
|
||||
|
||||
toolchain = {'name': 'intel', 'version': '2017b'}
|
||||
toolchainopts = {'pic': True, 'usempi': True}
|
||||
|
||||
# Vasp is proprietary software, see http://www.vasp.at/index.php/faqs on how to get access to the code
|
||||
sources = ['%(namelower)s.%(version)s.tar.gz']
|
||||
|
||||
#checksums = ['8ac646b108f974371eef398973373bf6']
|
||||
|
||||
#dependencies = [
|
||||
# ('zlib', '1.2.11', '', True),
|
||||
#]
|
||||
|
||||
prebuildopts = 'cp arch/makefile.include.linux_intel ./makefile.include && '
|
||||
|
||||
# path to libfftw3xf_intel.a is hardcoded in makefile.include
|
||||
prebuildopts += 'sed -i "s|\$(MKLROOT)/interfaces/fftw3xf|\$(FFTW_LIB_DIR)|" makefile.include && '
|
||||
|
||||
# remove mkl flag to prevent mixing dynamic libs with the static libs in LIBBLACS/SCALAPACK
|
||||
prebuildopts += 'sed -i "s|-mkl=sequential|-mkl=paralel|" makefile.include && '
|
||||
|
||||
# OFLAG = -O2 -xAVX
|
||||
prebuildopts += 'sed -i "s|OFLAG = -O2|OFLAG = -O3 -xAVX|" makefile.include && '
|
||||
|
||||
# objects add MKLROOT
|
||||
prebuildopts += 'sed -i "s|OBJECTS = fftmpiw.o fftmpi_map.o fft3dlib.o fftw3d.o|OBJECTS = fftmpiw.o fftmpi_map.o fft3dlib.o fftw3d.o \$\(MKLROOT\)/lib/intel64_lin/libfftw3xf_intel.a|" makefile.include && '
|
||||
|
||||
# VASP uses LIBS as a list of folders
|
||||
prebuildopts += 'unset LIBS && '
|
||||
|
||||
#prebuildopts += 'exit 1'
|
||||
|
||||
buildopts = 'all BLACS="$LIBBLACS" SCALAPACK="$LIBSCALAPACK"'
|
||||
|
||||
parallel = 1
|
||||
|
||||
files_to_copy = [(['bin/vasp_std', 'bin/vasp_gam', 'bin/vasp_ncl'], 'bin')]
|
||||
|
||||
sanity_check_paths = {
|
||||
'files': ['bin/vasp_std', 'bin/vasp_gam', 'bin/vasp_ncl'],
|
||||
'dirs': []
|
||||
}
|
||||
|
||||
moduleclass = 'phys'
|
||||
@ -7,7 +7,11 @@ versionsuffix = '-mkl=paralel'
|
||||
homepage = 'http://www.vasp.at'
|
||||
description = """The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale
|
||||
materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics,
|
||||
from first principles."""
|
||||
from first principles.
|
||||
|
||||
To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs.
|
||||
|
||||
Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment."""
|
||||
|
||||
toolchain = {'name': 'intel', 'version': '2017a'}
|
||||
toolchainopts = {'pic': True, 'usempi': True}
|
||||
|
||||
@ -7,7 +7,11 @@ versionsuffix = '-mkl=sequential'
|
||||
homepage = 'http://www.vasp.at'
|
||||
description = """The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale
|
||||
materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics,
|
||||
from first principles."""
|
||||
from first principles.
|
||||
|
||||
To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs.
|
||||
|
||||
Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment."""
|
||||
|
||||
toolchain = {'name': 'intel', 'version': '2017a'}
|
||||
toolchainopts = {'pic': True, 'usempi': True}
|
||||
|
||||
@ -7,7 +7,11 @@ versionsuffix = '-test-fftw'
|
||||
homepage = 'http://www.vasp.at'
|
||||
description = """The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale
|
||||
materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics,
|
||||
from first principles."""
|
||||
from first principles.
|
||||
|
||||
To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs.
|
||||
|
||||
Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment."""
|
||||
|
||||
toolchain = {'name': 'intel', 'version': '2017a'}
|
||||
toolchainopts = {'pic': True, 'usempi': True}
|
||||
|
||||
@ -7,7 +7,11 @@ versionsuffix = '-mkl=cluster'
|
||||
homepage = 'http://www.vasp.at'
|
||||
description = """The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale
|
||||
materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics,
|
||||
from first principles."""
|
||||
from first principles.
|
||||
|
||||
To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs.
|
||||
|
||||
Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment."""
|
||||
|
||||
toolchain = {'name': 'intel', 'version': '2017b'}
|
||||
toolchainopts = {'pic': True, 'usempi': True}
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user