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Merge pull request #2341 from boegel/style_fixes
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remove trailing whitespace
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boegel committed Jan 19, 2016
2 parents 044454d + 31d141b commit c39340d
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Showing 275 changed files with 339 additions and 339 deletions.
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Expand Up @@ -27,7 +27,7 @@ sources = [('abinit-%s_%s.bz2' % (version, versionsuffix[1:]), 'tar xfj %s')]
source_urls = ['http://ftp.abinit.org/']

sanity_check_paths = {
'files': ["bin/abinit"],
'files': ["bin/abinit"],
'dirs': []
}

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Expand Up @@ -29,7 +29,7 @@ sources = [('abinit-%s_%s.bz2' % (version, versionsuffix[1:]), 'tar xfj %s')]
source_urls = ['http://ftp.abinit.org/']

sanity_check_paths = {
'files': ["bin/abinit"],
'files': ["bin/abinit"],
'dirs': []
}

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Expand Up @@ -30,7 +30,7 @@ sources = [('abinit-%s_%s.bz2' % (version, versionsuffix[1:]), 'tar xfj %s')]
source_urls = ['http://ftp.abinit.org/']

sanity_check_paths = {
'files': ["bin/abinit"],
'files': ["bin/abinit"],
'dirs': []
}

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Expand Up @@ -33,7 +33,7 @@ dependencies = [
]

sanity_check_paths = {
'files': ["bin/abinit"],
'files': ["bin/abinit"],
'dirs': []
}

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Expand Up @@ -26,11 +26,11 @@ toolchainopts = {'usempi': True}
sources = [SOURCELOWER_TAR_GZ]
source_urls = ['http://www.bcgsc.ca/downloads/abyss/']

dependencies = [
dependencies = [
('sparsehash', '2.0.2'),
('Boost', '1.49.0', versionsuffix),
]

sanity_check_paths = {
'files': ["bin/ABYSS", "bin/ABYSS-P"],
'dirs': []
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2 changes: 1 addition & 1 deletion easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-ictce-5.4.0.eb
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Expand Up @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ]

patches = ['ANTLR-%(version)s_cpp-headers.patch']

dependencies = [('Java', '1.7.0_60', '', True)]
dependencies = [('Java', '1.7.0_60', '', True)]

configopts = "--disable-examples --disable-csharp"

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2 changes: 1 addition & 1 deletion easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-intel-2014b.eb
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Expand Up @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TAR_GZ]

patches = ['ANTLR-%(version)s_cpp-headers.patch']

dependencies = [('Java', '1.7.0_60', '', True)]
dependencies = [('Java', '1.7.0_60', '', True)]

configopts = "--disable-examples --disable-csharp"

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Expand Up @@ -10,7 +10,7 @@ description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS)
Java, C#, C++, or Python actions."""

toolchain = {'name': 'intel', 'version': '2015a'}

source_urls = ['http://www.antlr2.org/download/']
sources = [SOURCELOWER_TAR_GZ]

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Expand Up @@ -10,7 +10,7 @@ description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS)
Java, C#, C++, or Python actions."""

toolchain = {'name': 'intel', 'version': '2015b'}

source_urls = ['http://www.antlr2.org/download/']
sources = [SOURCELOWER_TAR_GZ]

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Expand Up @@ -16,7 +16,7 @@ description = "Automake: GNU Standards-compliant Makefile generator"

source_urls = [GNU_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
toolchain = {'name': 'ictce', 'version': '5.5.0'}
toolchain = {'name': 'ictce', 'version': '5.5.0'}

dependencies = [('Autoconf', '2.69')]

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Expand Up @@ -20,7 +20,7 @@ dependencies = [
('zlib', '1.2.8'),
]

parallel = 1
parallel = 1

skipsteps = ['configure']

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Expand Up @@ -20,7 +20,7 @@ dependencies = [
('zlib', '1.2.8'),
]

parallel = 1
parallel = 1

skipsteps = ['configure']

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4 changes: 2 additions & 2 deletions easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb
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@@ -1,4 +1,4 @@
easyblock = 'ConfigureMake'
easyblock = 'ConfigureMake'

name = 'BSMAP'
version = '2.74'
Expand All @@ -13,7 +13,7 @@ sources = [SOURCELOWER_TGZ]

skipsteps = ['configure']

installopts = "DESTDIR=%(installdir)s"
installopts = "DESTDIR=%(installdir)s"

patches = [
'BSMAP-2.74_makefile-modif.patch',
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Expand Up @@ -35,7 +35,7 @@ dependencies = [

sanity_check_paths = {
'files': [],
'dirs': ['lib/python%s/site-packages/Bio' % pyshortver,
'dirs': ['lib/python%s/site-packages/Bio' % pyshortver,
'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version,\
pyshortver),
'lib/python%s/site-packages/BioSQL' % pyshortver]
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Expand Up @@ -35,7 +35,7 @@ dependencies = [

sanity_check_paths = {
'files': [],
'dirs': ['lib/python%s/site-packages/Bio' % pyshortver,
'dirs': ['lib/python%s/site-packages/Bio' % pyshortver,
'lib/python%s/site-packages/biopython-%s-py%s.egg-info' % (pyshortver, version,\
pyshortver),
'lib/python%s/site-packages/BioSQL' % pyshortver]
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Expand Up @@ -23,9 +23,9 @@ sources = ['%s_v%s.tar.gz' % (name.lower(), version) ]
dependencies = [('Bowtie2', '2.0.2')]

sanity_check_paths = {
'files': ["bismark", "bismark2bedGraph", "bismark2report", "bismark_genome_preparation",
'files': ["bismark", "bismark2bedGraph", "bismark2report", "bismark_genome_preparation",
"bismark_methylation_extractor", "coverage2cytosine", "deduplicate_bismark"],
'dirs': [],
}
}

moduleclass = 'bio'
2 changes: 1 addition & 1 deletion easybuild/easyconfigs/b/Bison/Bison-2.7-goolf-1.5.14.eb
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Expand Up @@ -7,7 +7,7 @@ homepage = 'http://www.gnu.org/software/bison'
description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar
into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables."""

toolchain = {'name': 'goolf', 'version': '1.5.14'}
toolchain = {'name': 'goolf', 'version': '1.5.14'}

sources = [SOURCELOWER_TAR_GZ]
source_urls = [GNU_SOURCE]
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Expand Up @@ -24,7 +24,7 @@ sources = [SOURCE_TAR_GZ]
# put here the list of generated executables when compiling
list_of_executables = ["convertSamples", "estimateDE", "estimateExpression", "estimateHyperPar",
"estimateVBExpression", "extractSamples", "getFoldChange", "getGeneExpression",
"getPPLR", "getVariance", "getWithinGeneExpression", "parseAlignment",
"getPPLR", "getVariance", "getWithinGeneExpression", "parseAlignment",
"transposeLargeFile", "getCounts.py", "extractTranscriptInfo.py"]

# this is the real EasyBuild line to copy all the executables to "bin"
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Expand Up @@ -4,7 +4,7 @@ version = '1.55.0'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""

toolchain = {'name': 'foss', 'version': '2015a'}
toolchain = {'name': 'foss', 'version': '2015a'}
toolchainopts = {'pic': True, 'usempi': True}

source_urls = [SOURCEFORGE_SOURCE]
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Expand Up @@ -4,7 +4,7 @@ version = '1.55.0'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""

toolchain = {'name': 'intel', 'version': '2015a'}
toolchain = {'name': 'intel', 'version': '2015a'}
toolchainopts = {'pic': True, 'usempi': True}

source_urls = [SOURCEFORGE_SOURCE]
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Expand Up @@ -4,7 +4,7 @@ version = '1.57.0'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""

toolchain = {'name': 'foss', 'version': '2015a'}
toolchain = {'name': 'foss', 'version': '2015a'}
toolchainopts = {'pic': True, 'usempi': True}

source_urls = [SOURCEFORGE_SOURCE]
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Expand Up @@ -4,7 +4,7 @@ version = '1.57.0'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""

toolchain = {'name': 'intel', 'version': '2015a'}
toolchain = {'name': 'intel', 'version': '2015a'}
toolchainopts = {'pic': True, 'usempi': True}

source_urls = [SOURCEFORGE_SOURCE]
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Expand Up @@ -4,7 +4,7 @@ version = '1.58.0'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""

toolchain = {'name': 'foss', 'version': '2015a'}
toolchain = {'name': 'foss', 'version': '2015a'}
toolchainopts = {'pic': True, 'usempi': True}

source_urls = [SOURCEFORGE_SOURCE]
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Expand Up @@ -4,7 +4,7 @@ version = '1.58.0'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""

toolchain = {'name': 'intel', 'version': '2015a'}
toolchain = {'name': 'intel', 'version': '2015a'}
toolchainopts = {'pic': True, 'usempi': True}

source_urls = [SOURCEFORGE_SOURCE]
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Expand Up @@ -24,7 +24,7 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'}
sources = [SOURCE_TAR_BZ2]
source_urls = ['http://bbftppro.myftp.org/']

unpack_options = '--strip-components=1' # we need to dive one level deep inside the tarball
unpack_options = '--strip-components=1' # we need to dive one level deep inside the tarball

start_dir = 'bbftpc'

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Expand Up @@ -24,7 +24,7 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'}
sources = [SOURCE_TAR_BZ2]
source_urls = ['http://bbftppro.myftp.org/']

unpack_options = '--strip-components=1' # we need to dive one level deep inside the tarball
unpack_options = '--strip-components=1' # we need to dive one level deep inside the tarball

start_dir = 'bbftpc'

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Expand Up @@ -24,7 +24,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'}
sources = [SOURCE_TAR_BZ2]
source_urls = ['http://bbftppro.myftp.org/']

unpack_options = '--strip-components=1' # we need to dive one level deep inside the tarball
unpack_options = '--strip-components=1' # we need to dive one level deep inside the tarball

start_dir = 'bbftpc'

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Expand Up @@ -30,7 +30,7 @@ configopts = '--with-sysroot=/'
binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm',
'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ]
sanity_check_paths = {
'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] +
'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] +
['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']],
'dirs': [],
}
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Expand Up @@ -30,7 +30,7 @@ configopts = '--with-sysroot=/'
binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm',
'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ]
sanity_check_paths = {
'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] +
'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] +
['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']],
'dirs': [],
}
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Expand Up @@ -29,7 +29,7 @@ configopts = '--with-sysroot=/'
binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm',
'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ]
sanity_check_paths = {
'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] +
'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] +
['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']],
'dirs': [],
}
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Expand Up @@ -27,7 +27,7 @@ source_urls = [GNU_SOURCE]
binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm',
'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ]
sanity_check_paths = {
'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] +
'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] +
['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']],
'dirs': [],
}
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Expand Up @@ -29,7 +29,7 @@ list_of_executables = ["cd-hit", "cd-hit-est", "cd-hit-2d", "cd-hit-est-2d", "cd
# this is the real EasyBuild line to copy all the executables and perl scripts to "bin"
files_to_copy = [
(list_of_executables, "bin"),
(["*.pl"], 'bin'),
(["*.pl"], 'bin'),
(["psi-cd-hit/*.pl"], 'bin'),
"README",
"doc",
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2 changes: 1 addition & 1 deletion easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-intel-2015a.eb
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Expand Up @@ -19,6 +19,6 @@ builddependencies = [('CMake', '3.1.3')]

separate_build_dir = True

configopts = '-DCMAKE_BUILD_TYPE=Release'
configopts = '-DCMAKE_BUILD_TYPE=Release'

moduleclass = 'numlib'
2 changes: 1 addition & 1 deletion easybuild/easyconfigs/c/CMake/CMake-2.8.12-ictce-7.1.2.eb
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Expand Up @@ -7,7 +7,7 @@ homepage = 'http://www.cmake.org'
description = """CMake, the cross-platform, open-source build system.
CMake is a family of tools designed to build, test and package software."""

toolchain = {'name': 'ictce', 'version': '7.1.2'}
toolchain = {'name': 'ictce', 'version': '7.1.2'}

source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s']
sources = [SOURCELOWER_TAR_GZ]
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2 changes: 1 addition & 1 deletion easybuild/easyconfigs/c/CMake/CMake-2.8.12-intel-2014b.eb
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Expand Up @@ -7,7 +7,7 @@ homepage = 'http://www.cmake.org'
description = """CMake, the cross-platform, open-source build system.
CMake is a family of tools designed to build, test and package software."""

toolchain = {'name': 'intel', 'version': '2014b'}
toolchain = {'name': 'intel', 'version': '2014b'}

source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s']
sources = [SOURCELOWER_TAR_GZ]
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Expand Up @@ -31,13 +31,13 @@ installopts += 'cp -a tools/ %(installdir)s && '
installopts += 'cp -a README doc/ %(installdir)s'

sanity_check_paths = {
'files': ["bin/%s" % x for x in ["chipcenter", "chipcor", "chipextract", "chippart", "chippeak",
'files': ["bin/%s" % x for x in ["chipcenter", "chipcor", "chipextract", "chippart", "chippeak",
"chipscore", "compactsga", "counts_filter", "countsga", "featreplace"]],
'dirs': []
}

# add tools dir to PATH
modextrapaths = {
modextrapaths = {
'PATH': "tools",
}

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Expand Up @@ -31,13 +31,13 @@ installopts += 'cp -a tools/ %(installdir)s && '
installopts += 'cp -a README doc/ %(installdir)s'

sanity_check_paths = {
'files': ["bin/%s" % x for x in ["chipcenter", "chipcor", "chipextract", "chippart", "chippeak",
'files': ["bin/%s" % x for x in ["chipcenter", "chipcor", "chipextract", "chippart", "chippeak",
"chipscore", "compactsga", "counts_filter", "countsga", "featreplace"]],
'dirs': []
}

# add tools dir to PATH
modextrapaths = {
modextrapaths = {
'PATH': "tools",
}

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2 changes: 1 addition & 1 deletion easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ sources = [
dependencies = [
('GMP', '6.0.0a'),
('ISL', '0.14'),
]
]

builddependencies = [
('CMake', '3.1.3'),
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2 changes: 1 addition & 1 deletion easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb
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Expand Up @@ -32,7 +32,7 @@ sources = [
dependencies = [
('GMP', '6.0.0a'),
('ISL', '0.14'),
]
]

builddependencies = [
('CMake', '3.2.1'),
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Expand Up @@ -32,7 +32,7 @@ sources = [
dependencies = [
('GMP', '6.0.0a'),
('ISL', '0.15'),
]
]

builddependencies = [
('CMake', '3.3.2'),
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Expand Up @@ -32,7 +32,7 @@ sources = [
dependencies = [
('GMP', '6.1.0'),
('ISL', '0.15'),
]
]

builddependencies = [
('CMake', '3.4.1', '', ('GCCcore', '4.9.3')),
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