Commit 7fb68d5b authored by Josef Hrabal's avatar Josef Hrabal

new file: g/GATK/GATK-4.1.4.0-Java-1.8.0_202.eb

	new file:   g/Go/Go-1.13.1.eb
	new file:   s/Singularity/Singularity-3.4.1.eb
parent 47d23b55
Pipeline #9008 passed with stage
in 14 seconds
# IT4Innovations 2019
easyblock = 'Tarball'
name = 'GATK'
version = '4.1.4.0'
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': 'system', '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'
# It4Innovations 2019
easyblock = 'Tarball'
name = 'Go'
version = '1.13.1'
homepage = 'http://www.golang.org'
description = """Go is an open source programming language that makes it easy to build
simple, reliable, and efficient software."""
toolchain = {'name': 'system', 'version': ''}
source_urls = ['https://dl.google.com/go/']
sources = ['%(namelower)s%(version)s.linux-amd64.tar.gz']
checksums = ['b7df1f54d4d176a19bc416643c63738e']
sanity_check_paths = {
'files': ['bin/go', 'bin/gofmt'],
'dirs': ['api', 'doc', 'lib', 'pkg'],
}
modextravars = {'GOROOT': '%(installdir)s'}
moduleclass = 'compiler'
# IT4Innovations 2019
easyblock = 'ConfigureMake'
name = 'Singularity'
version = '3.4.1'
homepage = 'https://github.com/sylabs/singularity'
description = "Singularity is an open source container platform designed to be simple, fast, and secure. Singularity is optimized for EPC and HPC workloads, allowing untrusted users to run untrusted containers in a trusted way."
toolchain = {'name': 'system', 'version': ''}
source_urls = ['https://github.com/sylabs/singularity/releases/download/v%s/' % version]
sources = ['singularity-%(version)s.tar.gz']
checksums = ['27ea29349ba6f5f467a6d256580ea21f']
builddependencies = [
('Go', '1.13.1'),
]
dependencies = [
('squashfs-tools', '4.3'),
]
osdependencies = [
('openssl-devel', 'libssl-dev', 'libopenssl-devel'),
]
skipsteps = ['configure']
#prebuildopts = 'export GOPATH=$(pwd):$GOPATH && '
skipsteps = ['configure']
prebuildopts = 'mkdir -p src/github.com/sylabs && '
prebuildopts += 'ln -sf %(builddir)s/singularity src/github.com/sylabs/singularity && '
prebuildopts += './mconfig -p %(installdir)s -b build && '
prebuildopts += 'cd build && '
preinstallopts = 'cd build && '
postinstallcmds = [
'echo "mksquashfs path = /apps/all/squashfs-tools/4.3/bin" >> %(installdir)s/etc/singularity/singularity.conf',
]
# next steps after installation
# INSTALLATION_PATH=your_installation_path
# chown root:root $INSTALLATION_PATH/Singularity/*/etc/singularity/singularity.conf
# chown root:root $INSTALLATION_PATH/Singularity/*/etc/singularity/capability.json
# chown root:root $INSTALLATION_PATH/Singularity/*/etc/singularity/ecl.toml
# chown root:root $INSTALLATION_PATH/Singularity/*/libexec/singularity/bin/*-suid
# chmod 4755 $INSTALLATION_PATH/Singularity/*/libexec/singularity/bin/*-suid
# chmod +s $INSTALLATION_PATH/Singularity/*/libexec/singularity/bin/*-suid
sanity_check_paths = {
'files': ['bin/singularity'],
'dirs': ['bin', 'etc', 'libexec', 'var'],
}
moduleclass = 'tools'
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