def build(version='2.1.1'):
stage0 = CVL_ubuntu_stage()
stage0 += generic_build(
repository='https://github.com/DerrickWood/kraken2.git',
branch=f'v{version}',
install=['./install_kraken2.sh /usr/local/kraken2'],
)
stage0 += environment(variables=add_binary('/usr/local/kraken2/bin'))
return stage0
def build(version='1.3'):
stage0 = CVL_ubuntu_stage()
stage0 += generic_build(
repository='https://github.com/lh3/seqtk.git',
branch=f'v{version}',
build=['make'],
install=[
'mkdir -p /usr/local/seqtk/bin && cp seqtk /usr/local/seqtk/bin/'
])
stage0 += environment(variables=add_binary('/usr/local/seqtk/bin'))
return stage0
def build(container_format='singularity', os_release='ubuntu', os_version='20.04'):
config.set_container_format(container_format)
image = f'{os_release}:{os_version}'
stage0 = Stage(name='stage0')
stage0 += baseimage(image=image, _bootstrap='docker')
stage0 += environment(variables={
'LC_ALL': 'en_AU.UTF-8',
'LANGUAGE': 'en_AU.UTF-8',
})
stage0 += label(metadata={'maintainer': 'Luhan Cheng', 'email': '*****@*****.**'})
stage0 += shell(commands=['rm /usr/bin/sh', 'ln -s /usr/bin/bash /usr/bin/sh', '/usr/bin/bash'])
stage0 += packages(apt=['wget', 'git', 'software-properties-common', 'build-essential', 'locales', 'zlib1g-dev',
'perl', 'openssh-server', 'libssl-dev', 'gnuplot', 'globus-gridftp-server-progs', 'rsync', 'acl-dev'])
stage0 += gnu(version='10')
stage0 += shell(commands=[
'yes | cpan Data::MessagePack',
'yes | cpan IO::Socket::SSL'
])
stage0 += generic_build(
repository='https://github.com/eeertekin/bbcp.git',
commit='64af832',
prefix='/usr/local/bbcp/',
build=['make -C src'],
install=['mv bin/amd64_linux/bbcp /usr/local/bbcp/']
)
stage0 += environment(variables=add_binary('/usr/local/bbcp'))
stage0 += generic_build(
repository='https://github.com/pkolano/shift.git',
commit='ffb7f5f',
prefix='/usr/local/shift',
directory='shift/c',
build=['make nolustre'],
install=['mdkir /usr/local/shift/bin && mv c/shift-bin /usr/local/shift/bin']
)
return stage0
def build(container_format='singularity',
os_release='ubuntu',
os_version='20.04'):
config.set_container_format(container_format)
image = f'{os_release}:{os_version}'
stage0 = Stage(name='stage0')
stage0 += baseimage(image=image, _bootstrap='docker')
stage0 += environment(variables={
'LC_ALL': 'en_AU.UTF-8',
'LANGUAGE': 'en_AU.UTF-8',
})
stage0 += label(metadata={
'maintainer': 'Luhan Cheng',
'email': '*****@*****.**'
})
stage0 += shell(commands=[
'rm /usr/bin/sh', 'ln -s /usr/bin/bash /usr/bin/sh', '/usr/bin/bash'
])
stage0 += packages(apt=[
'wget', 'git', 'software-properties-common', 'build-essential',
'locales', 'zlib1g-dev', 'perl', 'ncbi-blast+', 'libx11-dev'
])
stage0 += shell(commands=['locale-gen en_AU.UTF-8'])
stage0 += gnu(version='10')
stage0 += generic_build(
url=
'http://search.cpan.org/CPAN/authors/id/Y/YA/YANICK/Parallel-ForkManager-1.19.tar.gz',
prefix='/usr/local/parallel-forkmanager',
build=['perl Makefile.PL', 'make install'],
install=['mv * /usr/local/parallel-forkmanager/'])
stage0 += environment(
variables=add_binary('/usr/local/parallel-forkmanager'))
stage0 += generic_build(
url=
'ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.1/clustalw-2.1-linux-x86_64-libcppstatic.tar.gz',
prefix='/usr/local/clustalw',
install=['mv clustalw2 /usr/local/clustalw/clustalw'])
stage0 += environment(variables=add_binary('/usr/local/clustalw'))
stage0 += generic_autotools(
url='ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz',
prefix='/usr/local/emboss',
)
stage0 += environment(variables=from_prefix('/usr/local/emboss'))
stage0 += generic_autotools(
url=
'https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.17.tar.gz',
prefix='/usr/local/viennarna')
stage0 += environment(variables=from_prefix('/usr/local/viennarna'))
stage0 += generic_build(
url='https://github.com/weizhongli/cdhit/archive/V4.8.1.tar.gz',
prefix='/usr/local/cdhit',
directory='cdhit-4.8.1',
build=['make'],
install=['mv * /usr/local/cdhit/'])
stage0 += environment(variables=add_binary('/usr/local/cdhit'))
stage0 += generic_build(
repository='https://github.com/ambarishbiswas/CRISPRDetect_2.2.git',
commit='0f8249f',
prefix='/usr/local/crisprdetect',
install=['mv * /usr/local/crisprdetect/'])
stage0 += environment(variables=add_binary('/usr/local/crisprdetect'))
return stage0
def build(container_format='singularity',
os_release='ubuntu',
os_version='20.04',
cuda_version='11.0'):
config.set_container_format(container_format)
image = f'nvcr.io/nvidia/cuda:{cuda_version}-devel-{os_release}{os_version}'
stage0 = Stage(name='stage0')
stage0 += baseimage(image=image, _bootstrap='docker')
stage0 += environment(variables={
'LC_ALL': 'en_AU.UTF-8',
'LANGUAGE': 'en_AU.UTF-8',
})
stage0 += label(metadata={
'maintainer': 'Luhan Cheng',
'email': '*****@*****.**'
})
stage0 += shell(commands=[
'rm -f /bin/sh && ln -s /bin/bash /bin/sh',
'rm -f /usr/bin/sh && ln -s /usr/bin/bash /usr/bin/sh',
'/bin/bash',
])
stage0 += environment(variables=from_prefix('/usr/local/cuda'))
stage0 += packages(apt=[
'wget', 'git', 'software-properties-common', 'build-essential',
'locales', 'zlib1g-dev'
])
stage0 += shell(commands=['locale-gen en_AU.UTF-8'])
stage0 += comment('Installing vglrun and TurboVNC')
stage0 += packages(apt=[
'ubuntu-desktop', 'vim', 'mesa-utils', 'python3-pip', 'python3-pyqt5',
'pyqt5-dev', 'python3-tk'
])
stage0 += shell(commands=[
'wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/turbovnc_2.2.5_amd64.deb && dpkg -i turbovnc_2.2.5_amd64.deb && rm turbovnc_2.2.5_amd64.deb',
'wget https://swift.rc.nectar.org.au/v1/AUTH_810/CVL-Singularity-External-Files/virtualgl_2.6.4_amd64.deb && dpkg -i virtualgl_2.6.4_amd64.deb && rm virtualgl_2.6.4_amd64.deb',
'apt update', 'apt -y upgrade'
])
stage0 += comment('Installing pre-requisites')
stage0 += primitives.copy(
src="./ccp4-7.1.014-shelx-arpwarp-linux64.tar.gz",
dest="/opt/ccp4-7.1.014-shelx-arpwarp-linux64.tar.gz")
stage0 += shell(commands=[
'cd /opt && tar -xf ccp4-7.1.014-shelx-arpwarp-linux64.tar.gz && rm ccp4-7.1.014-shelx-arpwarp-linux64.tar.gz',
'touch $HOME/.agree2ccp4v6',
'cd ccp4-7.1',
'./BINARY.setup',
])
stage0 += environment(variables=add_binary('/opt/ccp4-7.1/bin'))
stage0 += comment('Installing CCP-EM')
stage0 += primitives.copy(src="./ccpem-1.5.0-linux-x86_64.tar.gz",
dest="/opt/ccpem-1.5.0-linux-x86_64.tar.gz")
stage0 += primitives.copy(src="./input.txt", dest="/opt/input.txt")
stage0 += shell(commands=[
'touch $HOME/.agree2ccpemv1',
'cd /opt && tar -xf ccpem-1.5.0-linux-x86_64.tar.gz && rm ccpem-1.5.0-linux-x86_64.tar.gz',
'cd ccpem-1.5.0', './install_ccpem.sh',
'cat /opt/input.txt | bash install_modeller.sh'
])
return stage0