Commit 506f8286 authored by Lukáš Krupčík's avatar Lukáš Krupčík

modified: b/BCFtools/BCFtools-1.6-intel-2017a.eb

	new file:   b/Boost/Boost-1.68.0-intel-2017a.eb
	new file:   b/Boost/Boost-1.68.0-intel-2017c.eb
	new file:   "b/bcl2fastq2/\\"
	new file:   b/bcl2fastq2/bcl2fastq2-2.20.0-intel-2017a-Py-2.7.eb
	new file:   b/bcl2fastq2/bcl2fastq2-2.20.0-intel-2017a-Py-3.6.eb
	modified:   d/DIRAC/DIRAC-18.0-intel-2017c-Py-2.7-test.eb
	new file:   f/FastQC/FastQC-0.11.3.eb
	new file:   f/FastQC/FastQC-0.11.8.eb
	new file:   f/fontconfig/fontconfig-2.13.0-libpng-1.6.34.eb
	new file:   g/GATK/GATK-4.1.2.0-Java-1.8.0_202.eb
	new file:   g/GDAL/GDAL-2.4.0-intel-2017a-Py-3.6.eb
	new file:   g/GEOS/GEOS-3.7.2-Py-3.6.eb
	new file:   g/gnuplot/gnuplot-5.2.7-GCC-6.3.0-2.27.eb
	modified:   h/HTSlib/HTSlib-1.6-intel-2017a.eb
	new file:   l/libMesh/libMesh-1.4.1-intel-2017a.eb
	new file:   l/libMesh/libMesh-1.4.1-intel-2017c.eb
	new file:   m/MUMPS/MUMPS-5.2.0-intel-2017c-parmetis.eb
	modified:   p/Python/Python-3.6.8-GCC-6.3.0-2.27-base.eb
	new file:   r/R/R-3.5.3-intel-2017a-Py-3.6.eb
	modified:   s/SAMtools/SAMtools-1.6-intel-2017a.eb
	new file:   s/SWIG/SWIG-3.0.12-Py-3.6.eb
	deleted:    b/bcl2fastq2/bcl2fastq2-2.20.0-intel-2017a-Python-2.7.13.eb
parent 647491a9
# IT4Innovations 2019
easyblock = 'ConfigureMake'
name = 'BCFtools'
......@@ -19,8 +21,8 @@ source_urls = [
dependencies = [
('zlib', '1.2.11', '', True),
('HTSlib', '1.6'),
('GSL', '2.3'),
('XZ', '5.2.3', '', True),
('GSL', '2.5'),
('XZ', '5.2.4', '', True),
]
parallel = 1
......
# IT4Innovations 201
name = 'Boost'
version = '1.68.0'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'intel', 'version': '2017a'}
toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
dependencies = [
('bzip2', '1.0.6', '', True),
('zlib', '1.2.11', '', True),
]
configopts = '--without-libraries=python'
# also build boost_mpi
boost_mpi = True
moduleclass = 'devel'
# IT4Innovations 2018
name = 'Boost'
version = '1.68.0'
homepage = 'http://www.boost.org/'
description = """Boost provides free peer-reviewed portable C++ source libraries."""
toolchain = {'name': 'intel', 'version': '2017c'}
toolchainopts = {'pic': True, 'usempi': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
dependencies = [
('bzip2', '1.0.6', '', True),
('zlib', '1.2.11', '', True),
]
configopts = '--without-libraries=python'
# also build boost_mpi
boost_mpi = True
moduleclass = 'devel'
# IT4Innovations 2019
easyblock = 'ConfigureMake'
name = 'bcl2fastq2'
version = '2.20.0'
versionsuffix = '-Python-%(pyver)s'
versionsuffix = '-Py-3.6'
homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html'
description = """bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by
......@@ -13,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2017a'}
source_urls = [
'ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/']
sources = [{
'filename': '%(name)s-v%(version)s-tar.zip',
'filename': '%(name)s-v2-20-0-tar.zip',
# source file is a .zip that contains a .tar.gz
'extract_cmd': 'unzip -p %s | tar -xzvf -',
}]
......@@ -22,11 +24,11 @@ start_dir = 'src'
configopts = '--force-builddir --with-cmake=cmake '
builddependencies = [
('CMake', '3.9.1', '', True),
('CMake', '3.8.1', '', True),
]
dependencies = [
('Python', '2.7.13', '', True),
('Py', '3.6', '', True),
]
sanity_check_paths = {
......
# IT4Innovations 2019
easyblock = 'ConfigureMake'
name = 'bcl2fastq2'
version = '2.20.0'
versionsuffix = '-Py-2.7'
homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html'
description = """bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by
Illumina sequencing systems to standard FASTQ file formats for downstream analysis."""
toolchain = {'name': 'intel', 'version': '2017a'}
source_urls = [
'ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/']
sources = [{
'filename': '%(name)s-v2-20-0-tar.zip',
# source file is a .zip that contains a .tar.gz
'extract_cmd': 'unzip -p %s | tar -xzvf -',
}]
start_dir = 'src'
configopts = '--force-builddir --with-cmake=cmake '
builddependencies = [
('CMake', '3.8.1', '', True),
]
dependencies = [
('Py', '2.7', '', True),
]
sanity_check_paths = {
'files': ['bin/bcl2fastq'],
'dirs': ['lib']
}
moduleclass = 'bio'
# IT4Innovations 2019
easyblock = 'ConfigureMake'
name = 'bcl2fastq2'
version = '2.20.0'
versionsuffix = '-Py-3.6'
homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html'
description = """bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by
Illumina sequencing systems to standard FASTQ file formats for downstream analysis."""
toolchain = {'name': 'intel', 'version': '2017a'}
source_urls = [
'ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/']
sources = [{
'filename': '%(name)s-v2-20-0-tar.zip',
# source file is a .zip that contains a .tar.gz
'extract_cmd': 'unzip -p %s | tar -xzvf -',
}]
start_dir = 'src'
configopts = '--force-builddir --with-cmake=cmake '
builddependencies = [
('CMake', '3.8.1', '', True),
]
dependencies = [
('Py', '3.6', '', True),
]
sanity_check_paths = {
'files': ['bin/bcl2fastq'],
'dirs': ['lib']
}
moduleclass = 'bio'
# IT4Innovations 2019
easyblock = 'ConfigureMake'
name = 'DIRAC'
version = '18.0'
versionsuffix = '-Py-2.7-test'
......@@ -26,12 +24,12 @@ builddependencies = [
('CMake', '3.14.1', '', True)
]
skipsteps = ['configure']
#skipsteps = ['configure']
prebuildopts = './setup --fc=mpiifort --mpi --cc=mpiicc --cxx=mpicxx --prefix=/apps/all/DIRAC/%(version)s-intel-2017c-Py-2.7 && '
prebuildopts += 'cd build && '
preinstallopts = 'cd build && '
preinstallopts += 'make install && '
#prebuildopts = './setup --fc=mpiifort --mpi --cc=mpiicc --cxx=mpicxx --prefix=/apps/all/DIRAC/%(version)s-intel-2017c-Py-2.7 && '
#prebuildopts += 'cd build && '
#preinstallopts = 'cd build && '
#preinstallopts += 'make install && '
sanity_check_paths = {
'files': [],
......
# IT4Innovations 2019
easyblock = 'PackedBinary'
name = 'FastQC'
version = '0.11.3'
homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'
description = """FastQC is a quality control application for high throughput sequence data.
It reads in sequence data in a variety of formats and can either provide an interactive
application to review the results of several different QC checks, or create an HTML based
report which can be integrated into a pipeline."""
toolchain = {'name': 'dummy', 'version': ''}
source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s/']
sources = ['%(namelower)s_v%(version)s.zip']
dependencies = [('Java', '1.7.0_79')]
install_cmd = "cp -a FastQC/* %(installdir)s && chmod +x %(installdir)s/fastqc"
sanity_check_paths = {
'files': ["fastqc", "fastqc_icon.ico", "INSTALL.txt", "jbzip2-0.9.jar", "LICENSE.txt",
"README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.103.jar"],
'dirs': ["Configuration", "Help", "Templates", "uk"],
}
# How to create working alias?
moduleclass = 'bio'
# IT4Innovations 2019
easyblock = 'PackedBinary'
name = 'FastQC'
version = '0.11.8'
homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'
description = """FastQC is a quality control application for high throughput sequence data.
It reads in sequence data in a variety of formats and can either provide an interactive
application to review the results of several different QC checks, or create an HTML based
report which can be integrated into a pipeline."""
toolchain = {'name': 'dummy', 'version': ''}
source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s/']
sources = ['%(namelower)s_v%(version)s.zip']
dependencies = [('Java', '1.8.0_202')]
install_cmd = "cp -a FastQC/* %(installdir)s && chmod +x %(installdir)s/fastqc"
sanity_check_paths = {
'files': ["fastqc", "fastqc_icon.ico", "INSTALL.txt", "jbzip2-0.9.jar", "LICENSE.txt",
"README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.103.jar"],
'dirs': ["Configuration", "Help", "Templates", "uk"],
}
# How to create working alias?
moduleclass = 'bio'
easyblock = 'ConfigureMake'
name = 'fontconfig'
version = '2.13.0'
versionsuffix = '-libpng-1.6.34'
homepage = 'http://www.freedesktop.org/software/fontconfig'
description = """Fontconfig is a library designed to provide system-wide font configuration, customization and
application access."""
toolchain = {'name': 'dummy', 'version': ''}
source_urls = ['http://www.freedesktop.org/software/fontconfig/release/']
sources = [SOURCE_TAR_GZ]
dependencies = [
('freetype', '2.9.1', versionsuffix),
('util-linux', '2.32'),
('expat', '2.2.0'),
]
builddependencies = [
('gperf', '3.1'),
]
configopts = '--disable-docs '
moduleclass = 'vis'
# IT4Innovations 2019
easyblock = 'Tarball'
name = 'GATK'
version = '4.1.2.0'
versionsuffix = '-Java-%(javaver)s'
homepage = 'http://www.broadinstitute.org/gatk/'
description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute
to analyse next-generation resequencing data. The toolkit offers a wide variety of tools,
with a primary focus on variant discovery and genotyping as well as strong emphasis on
data quality assurance. Its robust architecture, powerful processing engine and
high-performance computing features make it capable of taking on projects of any size."""
toolchain = {'name': 'dummy', 'version': ''}
# download manually from http://www.broadinstitute.org/gatk/download
source_urls = [
' https://github.com/broadinstitute/gatk/releases/download/%(version)s/']
sources = ['gatk-%(version)s.zip']
dependencies = [('Java', '1.8.0_202')]
postinstallcmds = [
'mkdir %(installdir)s/bin',
'mv %(installdir)s/gatk %(installdir)s/bin',
]
modextravars = {
'export GATK_LOCAL_JAR': '%(installdir)s/gatk-package-%(version)s-local.jar'
}
sanity_check_paths = {
'files': [
'gatk-package-%(version)s-local.jar',
'gatk-package-%(version)s-spark.jar'],
'dirs': ['bin'],
}
moduleclass = 'bio'
# ITInnovations 2018
#
# Error in SWIG build, finished by hand
easyblock = 'ConfigureMake'
name = 'GDAL'
version = '2.4.0'
versionsuffix = '-Py-3.6'
homepage = 'http://www.gdal.org/'
description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style
Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model
to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for
data translation and processing."""
toolchain = {'name': 'intel', 'version': '2017a'}
toolchainopts = {'usempi': True}
source_urls = ['http://download.osgeo.org/gdal/%(version)s/']
sources = [SOURCELOWER_TAR_XZ]
dependencies = [
('Py', '3.6', '', True),
('netCDF', '4.6.3'),
('expat', '2.2.6', '', True),
('GEOS', '3.7.2', '', ('Py', '3.6')),
('SQLite', '3.27.1', '', True),
('libxml2', '2.9.9', '', True),
('libpng', '1.6.34', '', True),
('libjpeg-turbo', '1.5.3', '', True),
('JasPer', '2.0.14', '', True),
('LibTIFF', '4.0.7', '', True),
('zlib', '1.2.11', '', True),
('cURL', '7.56.1', '', True),
('PCRE', '8.42','', True),
('PROJ', '5.0.0'),
]
configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF'
configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO'
configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER'
configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python'
modextrapaths = {'PYTHONPATH': 'lib/python2.7/site-packages'}
sanity_check_paths = {
'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT],
'dirs': ['bin', 'include', 'lib/python3.6/site-packages']
}
moduleclass = 'data'
# IT4Innovations 2019
easyblock = 'ConfigureMake'
name = 'GEOS'
version = '3.7.2'
homepage = 'http://trac.osgeo.org/geos'
description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)"""
toolchain = {'name': 'Py', 'version': '3.6'}
source_urls = ['http://download.osgeo.org/geos/']
sources = [SOURCELOWER_TAR_BZ2]
patches = ['GEOS-%(version)s_fix-Python3.patch']
builddependencies = [('SWIG', '3.0.12')]
configopts = '--enable-python'
modextrapaths = {'PYTHONPATH': 'lib/python3.6/site-packages'}
sanity_check_paths = {
'files': [
'bin/geos-config',
'lib/libgeos.%s' %
SHLIB_EXT,
'lib/libgeos.a',
'include/geos.h'],
'dirs': [
'lib/python3.6/site-packages/geos']
}
moduleclass = 'math'
# IT4Innovations 2018
easyblock = 'ConfigureMake'
name = 'gnuplot'
version = '5.2.7'
homepage = 'http://gnuplot.sourceforge.net/'
description = """Portable interactive, function plotting utility"""
toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
sources = [SOURCE_TAR_GZ]
source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')]
dependencies = [
('cairo', '1.14.12', '', True),
('libjpeg-turbo', '1.5.3', '', True),
('libpng', '1.6.34', '', True),
('libgd', '2.2.5', '', True),
('Pango', '1.42.1'),
('libcerf', '1.5', '', True),
('Qt', '4.8.7', '', True),
('LibTIFF', '4.0.7', '', True),
]
configopts = '--with-qt=qt4 '
sanity_check_paths = {
'files': ['bin/gnuplot'],
'dirs': []
}
moduleclass = 'vis'
# IT4Innovations 2019
easyblock = 'ConfigureMake'
name = 'HTSlib'
......@@ -15,7 +17,8 @@ sources = [SOURCELOWER_TAR_BZ2]
dependencies = [
('zlib', '1.2.11', '', True),
('XZ', '5.2.3', '', True),
('XZ', '5.2.4', '', True),
('bzip2', '1.0.6', '', True),
]
sanity_check_paths = {
......
# IT4Innovations 2019
easyblock = 'ConfigureMake'
name = 'libMesh'
version = '1.4.1'
homepage = 'http://libmesh.github.io/'
description = """The libMesh library provides a framework for the numerical simulation of partial differential equations
using arbitrary unstructured discretizations on serial and parallel platforms. A major goal of the library is to
provide support for adaptive mesh refinement (AMR) computations in parallel while allowing a research scientist
to focus on the physics they are modeling."""
toolchain = {'name': 'intel', 'version': '2017a'}
toolchainopts = {'pic': True, 'usempi': True}
source_urls = [
'https://github.com/libMesh/libmesh/releases/download/v%(version)s/',
]
sources = [SOURCELOWER_TAR_GZ]
configopts = "--with-parmetis"
dependencies = [
('ParMETIS', '4.0.3'),
('Boost', '1.68.0'),
]
sanity_check_paths = {
'files': ['bin/meshtool-opt'],
'dirs': ['bin'],
}
moduleclass = 'lib'
# IT4Innovations 2019
easyblock = 'ConfigureMake'
name = 'libMesh'
version = '1.4.1'
homepage = 'http://libmesh.github.io/'
description = """The libMesh library provides a framework for the numerical simulation of partial differential equations
using arbitrary unstructured discretizations on serial and parallel platforms. A major goal of the library is to
provide support for adaptive mesh refinement (AMR) computations in parallel while allowing a research scientist
to focus on the physics they are modeling."""
toolchain = {'name': 'intel', 'version': '2017c'}
toolchainopts = {'pic': True, 'usempi': True}
source_urls = [
'https://github.com/libMesh/libmesh/releases/download/v%(version)s/',
]
sources = [SOURCELOWER_TAR_GZ]
configopts = "--with-parmetis"
dependencies = [
('ParMETIS', '4.0.3'),
('Boost', '1.68.0'),
]
sanity_check_paths = {
'files': ['bin/meshtool-opt'],
'dirs': ['bin'],
}
moduleclass = 'lib'
# IT4Innovations 2019
name = 'MUMPS'
version = '5.2.0'
versionsuffix = '-parmetis'
homepage = 'http://graal.ens-lyon.fr/MUMPS/'
description = "A parallel sparse direct solver"
toolchain = {'name': 'intel', 'version': '2017c'}
toolchainopts = {'pic': True, 'usempi': True}
source_urls = ['http://mumps.enseeiht.fr/']
sources = ['%(name)s_%(version)s.tar.gz']
dependencies = [
('SCOTCH', '6.0.6'),
('ParMETIS', '4.0.3'),
]
parallel = 1
buildopts = 'all'
moduleclass = 'math'
......@@ -15,7 +15,7 @@ sources = [SOURCE_TGZ]
prebuildopts = 'export CFLAGS="-I${EBROOTXZ}/include" && '
prebuildopts += 'export LDFLAGS="-L${EBROOTXZ}/lib" && '
configopts = "--enable-optimizations"
configopts = "--enable-optimizations --enable-shared"
# python needs bzip2 to build the bz2 package
dependencies = [
......@@ -24,7 +24,7 @@ dependencies = [
('SQLite', '3.27.1', '', True),
('Tk', '8.6.9', '', True),
('GMP', '6.1.2', '', True),
('XZ', '5.2.3', '', True),
('XZ', '5.2.4', '', True),
('zlib', '1.2.11', '', True),
('ncurses', '6.0', '', True),
# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's
......
This diff is collapsed.
......@@ -18,7 +18,8 @@ sources = [SOURCELOWER_TAR_BZ2]
dependencies = [
('ncurses', '6.0', '', True),
('zlib', '1.2.11', '', True),
('XZ', '5.2.3', '', True),
('XZ', '5.2.4', '', True),
('bzip2', '1.0.6', '', True),
]
moduleclass = 'bio'
# IT4Innovations
name = 'SWIG'
version = '3.0.12'
homepage = 'http://www.swig.org/'
description = """SWIG is a software development tool that connects programs written in C and C++ with
a variety of high-level programming languages."""
toolchain = {'name': 'Py', 'version': '3.6'}
toolchainopts = {'pic': True, 'opt': True, 'optarch': True}
source_urls = [SOURCEFORGE_SOURCE]
sources = [SOURCELOWER_TAR_GZ]
dependencies = [
('PCRE', '8.42', '', True),
]
moduleclass = 'devel'
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