Skip to content

fix names of local variables in b/*/*.eb easyconfigs #8709

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
vanzod merged 1 commit into from
Aug 9, 2019
Merged

fix names of local variables in b/*/*.eb easyconfigs #8709

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions easybuild/easyconfigs/b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,8 +16,8 @@ dependencies = [('Java', '1.8.0_112', '', True)]

prebuildopts = 'cd jni && '

suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE]
buildopts = "-f makefile.%s" % suff
local_suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE]
buildopts = "-f makefile.%s" % local_suff

files_to_copy = ['*']

Expand Down
4 changes: 2 additions & 2 deletions easybuild/easyconfigs/b/BBMap/BBMap-37.93-foss-2018a.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,8 +16,8 @@ dependencies = [('Java', '1.8.0_162', '', True)]

prebuildopts = 'cd jni && '

suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE]
buildopts = "-f makefile.%s" % suff
local_suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE]
buildopts = "-f makefile.%s" % local_suff

files_to_copy = ['*']

Expand Down
4 changes: 2 additions & 2 deletions easybuild/easyconfigs/b/BBMap/BBMap-37.93-intel-2018a.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,8 +16,8 @@ dependencies = [('Java', '1.8.0_162', '', True)]

prebuildopts = 'cd jni && '

suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE]
buildopts = "-f makefile.%s" % suff
local_suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE]
buildopts = "-f makefile.%s" % local_suff

files_to_copy = ['*']

Expand Down
4 changes: 2 additions & 2 deletions easybuild/easyconfigs/b/BBMap/BBMap-38.26-foss-2018b.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,8 +16,8 @@ dependencies = [('Java', '1.8', '', True)]

prebuildopts = 'cd jni && '

suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE]
buildopts = "-f makefile.%s" % suff
local_suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE]
buildopts = "-f makefile.%s" % local_suff

files_to_copy = ['*']

Expand Down
4 changes: 2 additions & 2 deletions easybuild/easyconfigs/b/BBMap/BBMap-38.50b-GCC-8.2.0-2.31.1.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,8 +16,8 @@ dependencies = [('Java', '11', '', True)]

prebuildopts = 'cd jni && '

suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE]
buildopts = "-f makefile.%s" % suff
local_suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE]
buildopts = "-f makefile.%s" % local_suff

files_to_copy = ['*']

Expand Down
4 changes: 2 additions & 2 deletions easybuild/easyconfigs/b/BFAST/BFAST-0.7.0a-foss-2016b.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,8 +25,8 @@ description = """BFAST facilitates the fast and accurate mapping of short reads

toolchain = {'name': 'foss', 'version': '2016b'}

verdir = ''.join(char for char in version if not char.isalpha())
source_urls = ['http://sourceforge.net/projects/bfast/files/bfast/%s/' % verdir, 'download']
local_verdir = ''.join(char for char in version if not char.isalpha())
source_urls = ['http://sourceforge.net/projects/bfast/files/bfast/%s/' % local_verdir, 'download']
sources = [SOURCELOWER_TAR_GZ]
checksums = ['ed8de49693165a87d5dbef352207c424b1bf6f670a83acf49a4f4f188444995e']

Expand Down
10 changes: 5 additions & 5 deletions easybuild/easyconfigs/b/BLASR/BLASR-20170330-intel-2017a.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
easyblock = 'MakeCp'

name = 'BLASR'
commit = 'bed926d'
local_commit = 'bed926d'
version = '20170330'

homepage = 'https://github.com/PacificBiosciences/blasr'
Expand All @@ -13,7 +13,7 @@ description = """ BLASR (Basic Local Alignment with Successive Refinement) rapid
toolchain = {'name': 'intel', 'version': '2017a'}

source_urls = ['https://github.com/PacificBiosciences/blasr/archive/']
sources = ['%s.tar.gz' % commit]
sources = ['%s.tar.gz' % local_commit]

dependencies = [
('HDF5', '1.8.18', '-serial'),
Expand All @@ -23,9 +23,9 @@ dependencies = [

prebuildopts = "./configure.py --with-szlib HDF5_INCLUDE=$EBROOTHDF5/include HDF5_LIB=$EBROOTHDF5/lib && "

binaries = ['blasr', 'utils/loadPulses', 'utils/pls2fasta', 'utils/samFilter', 'utils/samtoh5',
'utils/samtom4', 'utils/sawriter', 'utils/sdpMatcher', 'utils/toAfg']
files_to_copy = [(binaries, 'bin')]
local_binaries = ['blasr', 'utils/loadPulses', 'utils/pls2fasta', 'utils/samFilter', 'utils/samtoh5',
'utils/samtom4', 'utils/sawriter', 'utils/sdpMatcher', 'utils/toAfg']
files_to_copy = [(local_binaries, 'bin')]

sanity_check_paths = {
'files': ['bin/blasr', 'bin/loadPulses', 'bin/pls2fasta', 'bin/samFilter', 'bin/samtoh5', 'bin/samtom4',
Expand Down
4 changes: 2 additions & 2 deletions easybuild/easyconfigs/b/BWA/BWA-0.7.16a-foss-2016b.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@

name = 'BWA'
version = '0.7.16a'
subver = version[:-1]
local_subver = version[:-1]

homepage = 'http://bio-bwa.sourceforge.net/'
description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns
Expand All @@ -27,7 +27,7 @@ description = """Burrows-Wheeler Aligner (BWA) is an efficient program that alig
toolchain = {'name': 'foss', 'version': '2016b'}
toolchainopts = {'pic': True}

source_urls = ['https://github.com/lh3/bwa/releases/download/v%s/' % subver]
source_urls = ['https://github.com/lh3/bwa/releases/download/v%s/' % local_subver]
sources = ['%(namelower)s-%(version)s.tar.bz2']
checksums = ['8fecdb5f88871351bbe050c18d6078121456c36ad75c5c78f33a926560ffc170']

Expand Down
4 changes: 2 additions & 2 deletions easybuild/easyconfigs/b/BWA/BWA-0.7.16a-intel-2017a.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@

name = 'BWA'
version = '0.7.16a'
subver = version[:-1]
local_subver = version[:-1]

homepage = 'http://bio-bwa.sourceforge.net/'
description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns
Expand All @@ -27,7 +27,7 @@ description = """Burrows-Wheeler Aligner (BWA) is an efficient program that alig
toolchain = {'name': 'intel', 'version': '2017a'}
toolchainopts = {'pic': True}

source_urls = ['https://github.com/lh3/bwa/releases/download/v%s/' % subver]
source_urls = ['https://github.com/lh3/bwa/releases/download/v%s/' % local_subver]
sources = ['%(namelower)s-%(version)s.tar.bz2']
checksums = ['8fecdb5f88871351bbe050c18d6078121456c36ad75c5c78f33a926560ffc170']

Expand Down
6 changes: 3 additions & 3 deletions easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,9 +28,9 @@ buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2
installopts = 'INSTDIR=%(installdir)s'

sanity_check_paths = {
'files': ['bin/' + prog + '.' + flavor + '.x'
for prog in ['epsilon', 'sigma', 'kernel', 'absorption']
for flavor in ['real', 'cplx']],
'files': ['bin/' + p + '.' + f + '.x'
for p in ['epsilon', 'sigma', 'kernel', 'absorption']
for f in ['real', 'cplx']],
'dirs': []
}

Expand Down
6 changes: 3 additions & 3 deletions easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,9 +28,9 @@ buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2
installopts = 'INSTDIR=%(installdir)s'

sanity_check_paths = {
'files': ['bin/' + prog + '.' + flavor + '.x'
for prog in ['epsilon', 'sigma', 'kernel', 'absorption']
for flavor in ['real', 'cplx']],
'files': ['bin/' + p + '.' + f + '.x'
for p in ['epsilon', 'sigma', 'kernel', 'absorption']
for f in ['real', 'cplx']],
'dirs': []
}

Expand Down
6 changes: 3 additions & 3 deletions easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2017a.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,9 +31,9 @@ preinstallopts = 'sed -i "s/install: all-flavors/install: all/" Makefile && '
installopts = 'INSTDIR=%(installdir)s'

sanity_check_paths = {
'files': ['bin/' + prog + '.' + flavor + '.x'
for prog in ['epsilon', 'sigma', 'kernel', 'absorption', 'nonlinearoptics']
for flavor in ['real', 'cplx']],
'files': ['bin/' + p + '.' + f + '.x'
for p in ['epsilon', 'sigma', 'kernel', 'absorption', 'nonlinearoptics']
for f in ['real', 'cplx']],
'dirs': []
}

Expand Down
6 changes: 3 additions & 3 deletions easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-1.2.0-intel-2018a.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -35,9 +35,9 @@ preinstallopts = 'sed -i "s/install: all-flavors/install: all/" Makefile && '
installopts = 'INSTDIR=%(installdir)s'

sanity_check_paths = {
'files': ['bin/' + prog + '.' + flavor + '.x'
for prog in ['epsilon', 'sigma', 'kernel', 'absorption', 'nonlinearoptics']
for flavor in ['real', 'cplx']],
'files': ['bin/' + p + '.' + f + '.x'
for p in ['epsilon', 'sigma', 'kernel', 'absorption', 'nonlinearoptics']
for f in ['real', 'cplx']],
'dirs': []
}

Expand Down
6 changes: 3 additions & 3 deletions easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-2.0.0-foss-2017b.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,9 +45,9 @@ preinstallopts = 'sed -i "s/install: all-flavors/install: all/" Makefile && '
installopts = 'INSTDIR=%(installdir)s'

sanity_check_paths = {
'files': ['bin/' + prog + '.' + flavor + '.x'
for prog in ['epsilon', 'sigma', 'kernel', 'absorption', 'nonlinearoptics', 'parabands']
for flavor in ['real', 'cplx']],
'files': ['bin/' + p + '.' + f + '.x'
for p in ['epsilon', 'sigma', 'kernel', 'absorption', 'nonlinearoptics', 'parabands']
for f in ['real', 'cplx']],
'dirs': []
}

Expand Down
6 changes: 3 additions & 3 deletions easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-2.0.0-foss-2018b.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,9 +45,9 @@ preinstallopts = 'sed -i "s/install: all-flavors/install: all/" Makefile && '
installopts = 'INSTDIR=%(installdir)s'

sanity_check_paths = {
'files': ['bin/' + prog + '.' + flavor + '.x'
for prog in ['epsilon', 'sigma', 'kernel', 'absorption', 'nonlinearoptics', 'parabands']
for flavor in ['real', 'cplx']],
'files': ['bin/' + p + '.' + f + '.x'
for p in ['epsilon', 'sigma', 'kernel', 'absorption', 'nonlinearoptics', 'parabands']
for f in ['real', 'cplx']],
'dirs': []
}

Expand Down
6 changes: 3 additions & 3 deletions easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-2.0.0-intel-2017b.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -47,9 +47,9 @@ preinstallopts = 'sed -i "s/install: all-flavors/install: all/" Makefile && '
installopts = 'INSTDIR=%(installdir)s'

sanity_check_paths = {
'files': ['bin/' + prog + '.' + flavor + '.x'
for prog in ['epsilon', 'sigma', 'kernel', 'absorption', 'nonlinearoptics', 'parabands']
for flavor in ['real', 'cplx']],
'files': ['bin/' + p + '.' + f + '.x'
for p in ['epsilon', 'sigma', 'kernel', 'absorption', 'nonlinearoptics', 'parabands']
for f in ['real', 'cplx']],
'dirs': []
}

Expand Down
6 changes: 3 additions & 3 deletions easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-2.0.0-intel-2018a.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,9 +43,9 @@ preinstallopts = 'sed -i "s/install: all-flavors/install: all/" Makefile && '
installopts = 'INSTDIR=%(installdir)s'

sanity_check_paths = {
'files': ['bin/' + prog + '.' + flavor + '.x'
for prog in ['epsilon', 'sigma', 'kernel', 'absorption', 'nonlinearoptics', 'parabands']
for flavor in ['real', 'cplx']],
'files': ['bin/' + p + '.' + f + '.x'
for p in ['epsilon', 'sigma', 'kernel', 'absorption', 'nonlinearoptics', 'parabands']
for f in ['real', 'cplx']],
'dirs': []
}

Expand Down
6 changes: 3 additions & 3 deletions easybuild/easyconfigs/b/Blender/Blender-2.79b-foss-2018b-Python-3.6.6-CUDA-9.2.88.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = 'Blender'
version = '2.79b'
cuda_ver = '9.2.88'
versionsuffix = '-Python-%%(pyver)s-CUDA-%s' % cuda_ver
local_cuda_ver = '9.2.88'
versionsuffix = '-Python-%%(pyver)s-CUDA-%s' % local_cuda_ver

homepage = 'https://www.blender.org/'
description = """Blender is the free and open source 3D creation suite. It supports
Expand All @@ -24,7 +24,7 @@ dependencies = [
('libGLU', '9.0.0'),
('OpenColorIO', '1.1.0'), # for advanced color management
('OpenImageIO', '1.8.16'), # required for cycles render engine
('CUDA', cuda_ver, '', True),
('CUDA', local_cuda_ver, '', True),
]

builddependencies = [('CMake', '3.12.1')]
Expand Down
8 changes: 4 additions & 4 deletions easybuild/easyconfigs/b/BlobTools/BlobTools-20180528-foss-2018b-Python-2.7.15.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,9 +2,9 @@ easyblock = 'CmdCp'

name = 'BlobTools'
version = '20180528'
commit = 'a14630e'
local_commit = 'a14630e'
versionsuffix = '-Python-%(pyver)s'
taxdump_ver = '2019-03-01'
local_taxdump_ver = '2019-03-01'

homepage = 'https://blobtools.readme.io/docs'
description = """ A modular command-line solution for visualisation,
Expand All @@ -18,12 +18,12 @@ source_urls = [
]
sources = [
{
'download_filename': '%s.tar.gz' % commit,
'download_filename': '%s.tar.gz' % local_commit,
'filename': SOURCE_TAR_GZ,
'extract_cmd': "tar -xzf %s -C %(builddir)s --strip-components 1",
},
{
'filename': 'taxdmp_%s.zip' % taxdump_ver,
'filename': 'taxdmp_%s.zip' % local_taxdump_ver,
'extract_cmd': 'unzip %s && cp -a nodes.dmp names.dmp %(builddir)s/data/',
},
]
Expand Down
6 changes: 2 additions & 4 deletions easybuild/easyconfigs/b/Boost/Boost-1.57.0-gimkl-2.11.5-Python-2.7.10.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
name = 'Boost'
version = '1.57.0'
versionsuffix = '-Python-%(pyver)s'

homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
Expand All @@ -10,13 +11,10 @@ toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]

pythonversion = '2.7.10'
versionsuffix = '-Python-%s' % pythonversion

dependencies = [
('bzip2', '1.0.6'),
('zlib', '1.2.8'),
('Python', pythonversion),
('Python', '2.7.10'),
]

# also build boost_mpi
Expand Down
6 changes: 2 additions & 4 deletions easybuild/easyconfigs/b/Boost/Boost-1.59.0-foss-2016a-Python-2.7.11.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
name = 'Boost'
version = '1.59.0'
versionsuffix = '-Python-%(pyver)s'

homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
Expand All @@ -10,13 +11,10 @@ toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]

pythonversion = '2.7.11'
versionsuffix = '-Python-%s' % pythonversion

dependencies = [
('bzip2', '1.0.6'),
('zlib', '1.2.8'),
('Python', pythonversion),
('Python', '2.7.11'),
]

# also build boost_mpi
Expand Down
6 changes: 2 additions & 4 deletions easybuild/easyconfigs/b/Boost/Boost-1.59.0-intel-2016a-Python-2.7.11.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
name = 'Boost'
version = '1.59.0'
versionsuffix = '-Python-%(pyver)s'

homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
Expand All @@ -10,13 +11,10 @@ toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]

pythonversion = '2.7.11'
versionsuffix = '-Python-%s' % pythonversion

dependencies = [
('bzip2', '1.0.6'),
('zlib', '1.2.8'),
('Python', pythonversion),
('Python', '2.7.11'),
]

# also build boost_mpi
Expand Down
6 changes: 2 additions & 4 deletions easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@

name = 'Boost'
version = "1.60.0"
versionsuffix = '-Python-%(pyver)s'

homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
Expand All @@ -14,12 +15,9 @@ toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%%(namelower)s_%s.tar.bz2' % '_'.join(version.split('.'))]

pythonversion = '2.7.11'
versionsuffix = '-Python-%s' % pythonversion

dependencies = [
('bzip2', '1.0.6'),
('Python', pythonversion),
('Python', '2.7.11'),
]

# also build boost_mpi
Expand Down
6 changes: 2 additions & 4 deletions easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,10 +22,8 @@ parallel = 1
preconfigopts = "./autogen.sh && "

sanity_check_paths = {
'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile
for includefile in ["beagle.h", "platform.h"]] +
["lib/libhmsbeagle%s.so" % libfile
for libfile in ["-cpu", "-cpu-sse", "-jni", ""]],
'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % x for x in ["beagle.h", "platform.h"]] +
["lib/libhmsbeagle%s.so" % x for x in ["-cpu", "-cpu-sse", "-jni", ""]],
'dirs': []
}

Expand Down
6 changes: 2 additions & 4 deletions easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2017a.eb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,10 +23,8 @@ parallel = 1
preconfigopts = "./autogen.sh && "

sanity_check_paths = {
'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile
for includefile in ["beagle.h", "platform.h"]] +
["lib/libhmsbeagle%s.so" % libfile
for libfile in ["-cpu", "-cpu-sse", "-jni", ""]],
'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % x for x in ["beagle.h", "platform.h"]] +
["lib/libhmsbeagle%s.so" % x for x in ["-cpu", "-cpu-sse", "-jni", ""]],
'dirs': []
}

Expand Down
Loading