def singleStageBuild(stage):
stage += label(metadata={'MAINTAINER': 'Simeon Ehrig'})
stage += label(metadata={'EMAIL': '*****@*****.**'})
stage += label(metadata={'Version': str(container_version)})
stage += environment(variables={'GOL_VERSION': str(container_version)})
# copy example inside container
stage += copy(src='notebook', dest='/')
# copy and build the pnwriter library
stage += copy(src='pngwriter', dest='/opt')
stage += packages(ospackages=['libpng-dev'])
cmake = CMakeBuild(prefix='/notebook/pngwriter')
stage += shell(commands=[
cmake.configure_step(directory='/opt/pngwriter',
opts=['-DBUILD_SHARED_LIBS=ON']),
cmake.build_step(target='install'), 'rm -rf /opt/pngwriter'
])
# Copy notebook examples and pngwriter lib to the host's /tmp file system to obtain a writable file system.
stage += runscript(commands=[
'if [ ! -d /tmp/GOL-xeus-cling-cuda ]; then \n'
' mkdir /tmp/GOL-xeus-cling-cuda &&'
' cp -r /notebook/ /tmp/GOL-xeus-cling-cuda\n fi',
'cd /tmp/GOL-xeus-cling-cuda/notebook', 'jupyter-lab'
])
print(stage.__str__())
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'])
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 += shell(commands=[
'curl -sL https://deb.nodesource.com/setup_12.x | bash -',
'apt install -y nodejs npm'
])
prefix = '/var/www'
stage0 += shell(commands=[
f'mkdir {prefix} && cd {prefix}',
'git clone --branch 1.16.10-release https://github.com/gmod/jbrowse .',
'./setup.sh',
])
stage0 += environment(variables={
'PATH': f'{prefix}/bin:$PATH'
})
stage0 += runscript(commands=[
f'cd {prefix}',
'npm run start $*'
])
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'{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'])
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 += conda(
eula=True,
packages=['python=3.8.5', 'openjdk', 'pip'],
)
stage0 += environment(variables=from_prefix('/usr/local/anaconda'))
stage0 += shell(commands=['pip install --upgrade minerl'])
stage0 += shell(commands=[
'wget https://launcher.mojang.com/download/Minecraft.deb && dpkg -i Minecraft.deb && rm Minecraft.deb',
])
stage0 += runscript(commands=['source /usr/local/anaconda/etc/profile.d/conda.sh', '/usr/local/anaconda/bin/python3 $*'])
return stage0
def get_stage(container):
# generate baseimage
hpccm.config.set_container_format(container)
# version >3.2 is necessary for multi-stage build
if container == 'singularity':
hpccm.config.set_singularity_version('3.3')
Stage0 = hpccm.Stage()
Stage0 += baseimage(image='ubuntu:bionic')
# copy project from outside in the container
if container == 'singularity':
Stage0 += copy(src='../hello_world_tool', dest='/opt/')
else:
# docker: cannot copy files from outsite the build context
# so, we need to move the build context one level up
Stage0 += copy(src='./hello_world_tool', dest='/opt/hello_world_tool')
# install compiler tools
Stage0 += cmake(eula=True, version='3.14.5')
Stage0 += packages(ospackages=['g++', 'make', 'wget', 'build-essential'])
# build and install project
cmb = CMakeBuild()
cm = []
cm.append(cmb.configure_step(build_directory='/opt/build_hello_world_tool',
directory='/opt/hello_world_tool/'))
cm.append(cmb.build_step(target='install'))
Stage0 += shell(commands=cm)
Stage0 += shell(commands=build_openssl(name='openssl-1.1.1c',
build_dir='/opt/openssl_build'))
# script that runs when
# - singularity uses the run parameter or the image runs directly
# - docker uses the run parameter without arguments
Stage0 += runscript(commands=['hello_world_tool'])
return Stage0
def get_stage(container):
# generate baseimage
hpccm.config.set_container_format(container)
# version >3.2 is necessary for multi-stage build
if container == 'singularity':
hpccm.config.set_singularity_version('3.3')
Stage0 = hpccm.Stage()
# the stages need "names" so that they can reference each other
Stage0 += baseimage(image='ubuntu:bionic', _as='Stage0')
# copy project from outside in the container
if container == 'singularity':
Stage0 += copy(src='../hello_world_tool', dest='/opt/')
else:
# docker: cannot copy files from outsite the build context
# so, we need to move the build context one level up
Stage0 += copy(src='./hello_world_tool', dest='/opt/hello_world_tool')
# install compiler tools
Stage0 += cmake(eula=True, version='3.14.5')
Stage0 += packages(ospackages=['g++', 'make', 'wget', 'build-essential'])
# build and install project
cmb = CMakeBuild(prefix="/opt/hello_install/")
cm = []
cm.append(
cmb.configure_step(build_directory='/opt/build_hello_world_tool',
directory='/opt/hello_world_tool/',
opts=['-DCMAKE_INSTALL_RPATH=/usr/local/lib/']))
cm.append(cmb.build_step(target='install'))
Stage0 += shell(commands=cm)
Stage0 += shell(commands=build_openssl(name='openssl-1.1.1c',
build_dir='/opt/openssl_build'))
# add release stage
Stage1 = hpccm.Stage()
Stage1 += baseimage(image='ubuntu:bionic', _as='Stage1')
Stage1 += copy(_from='Stage0',
src='/opt/hello_install/',
dest='/usr/local/')
Stage1 += copy(_from='Stage0',
src='/opt/openssl_install/',
dest='/usr/local/')
# the commands merge the bin, lib ect. folders of hello_install and openssl_install
# in the /usr/local folder
if container == "singularity":
Stage1 += shell(commands=[
'cp -rl /usr/local/hello_install/* /usr/local/',
'cp -rl /usr/local/openssl_install/* /usr/local/',
'rm -r /usr/local/hello_install/',
'rm -r /usr/local/openssl_install/'
])
# script that runs when
# - singularity uses the run parameter or the image runs directly
# - docker uses the run parameter without arguments
Stage1 += runscript(commands=['hello_world_tool'])
return [Stage0, Stage1]
"cd /usr/local/cuda/lib64/", "ln -s libcufft.so.10.1.168 libcufft.so.8.0"
])
# Relion
Stage1 += copy(_from=Stage0.name,
src='/opt/relion-3.0.7/bin/',
dest='/opt/relion-3.0.7/bin/')
Stage1 += copy(_from=Stage0.name,
src='/opt/relion-3.0.7/lib/',
dest='/opt/relion-3.0.7/lib/')
# MotionCor2
Stage1 += copy(_from=Stage0.name,
src='/opt/MotionCor2_1.2.6',
dest='/opt/MotionCor2_1.2.6')
# Gctf
Stage1 += copy(_from=Stage0.name,
src='/opt/Gctf_v1.06/bin',
dest='/opt/Gctf_v1.06/bin')
# ctffind
Stage1 += copy(_from=Stage0.name,
src='/opt/ctffind-4.1.13/bin',
dest='/opt/ctffind-4.1.13/bin')
# ResMap
Stage1 += copy(_from=Stage0.name, src='/opt/resmap', dest='/opt/resmap')
Stage1 += runscript(commands=["$*"])
def build(container_format='singularity',
flavour="devel",
os_release='ubuntu',
os_version='20.04',
cuda_version='11.3.0',
python_version='3.8',
anaconda_version='4.9.2',
alphafold_path="/opt/alphafold",
version='2.1.2'):
config.set_container_format(container_format)
image = f'nvcr.io/nvidia/cuda:{cuda_version}-{flavour}-{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', 'vim'
])
stage0 += shell(commands=['locale-gen en_AU.UTF-8'])
stage0 += conda(eula=True,
packages=[
f'python={python_version}', "openmm==7.5.1",
"cudnn==8.2.1.32", "cudatoolkit==11.0.3",
"pdbfixer==1.7", "hmmer==3.3.2", "hhsuite==3.3.0",
"kalign2==2.04"
],
channels=['conda-forge', 'bioconda'],
version=anaconda_version)
stage0 += environment(variables=from_prefix('/usr/local/anaconda'))
stage0 += shell(commands=['conda activate base'])
stage0 += shell(commands=[
f"mkdir -p {alphafold_path}",
f'git clone -b v{version} https://github.com/deepmind/alphafold.git {alphafold_path}'
])
stage0 += environment(variables={"ALPHAFOLD_PATH": f"{alphafold_path}"})
stage0 += shell(commands=[
f'wget -q -P {alphafold_path}/alphafold/common/ https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt'
])
stage0 += pip(packages=[
"absl-py==0.13.0", "biopython==1.79", "chex==0.0.7", "dm-haiku==0.0.4",
"dm-tree==0.1.6", "immutabledict==2.0.0", "ml-collections==0.1.0",
"numpy==1.19.5", "scipy==1.7.0", "tensorflow==2.5.0", "pandas==1.3.4",
"tensorflow-cpu==2.5.0"
],
pip='pip3')
stage0 += pip(packages=[
"jax",
"jaxlib==0.1.69+cuda111 -f https://storage.googleapis.com/jax-releases/jax_releases.html"
],
upgrade=True,
pip='pip3')
stage0 += pip(packages=[f'-r {alphafold_path}/requirements.txt'],
pip='pip3')
stage0 += shell(commands=[
f'cd /usr/local/anaconda/lib/python{python_version}/site-packages/ && patch -p0 < {alphafold_path}/docker/openmm.patch'
])
stage0 += shell(commands=[
f'cd {alphafold_path}',
'wget https://raw.githubusercontent.com/0luhancheng0/hpccm-containers/main/src/hpccm_containers/alphafold/run_alphafold.sh && chmod a+x run_alphafold.sh'
])
stage0 += runscript(commands=[
'source /usr/local/anaconda/etc/profile.d/conda.sh',
f"cd {alphafold_path}", f'{alphafold_path}/run_alphafold.sh $@'
])
return stage0
def build(container_format='singularity',
image='ubuntu:20.04',
version='3.8.7',
gnu_version='10',
mkl_version='2020.0-088',
numpy_version='1.20.0rc2'):
config.set_container_format(container_format)
stage0 = Stage(name='stage0')
stage0 += baseimage(image=image, _bootstrap='docker')
stage0 += label(metadata={
'maintainer': 'Luhan Cheng',
'email': '*****@*****.**'
})
stage0 += shell(
commands=['rm /bin/sh && ln -s /bin/bash /bin/sh', '/bin/bash'])
stage0 += packages(apt=[
'wget', 'git', 'software-properties-common', 'build-essential',
'locales'
])
stage0 += shell(commands=['locale-gen en_AU.UTF-8'])
stage0 += environment(variables={
'LC_ALL': 'en_AU.UTF-8',
'LANGUAGE': 'en_AU.UTF-8',
})
filename = f'Python-{version}.tar.xz'
url = f'https://www.python.org/ftp/python/{version}/{filename}'
stage0 += packages(apt=[
'wget', 'xz-utils', 'build-essential', 'software-properties-common',
'libsqlite3-dev', 'libssl-dev', 'libbz2-dev', 'libgdbm-compat-dev',
'libssl-dev', 'liblzma-dev', 'tk-dev', 'uuid-dev', 'libreadline-dev',
'zlib1g-dev', 'python-dev', 'libncurses*-dev', 'libgdbm-dev',
'libsqlite3-dev', 'libffi-dev', 'git'
])
compiler = gnu(version=gnu_version)
stage0 += compiler
# stage0 += shell(commands=[
# 'export LDFLAGS="-rpath /usr/local/python/bin $LDFLAGS"'
# ])
stage0 += generic_autotools(
url=url,
directory=f'Python-{version}',
prefix='/usr/local/python',
with_computed_goto=True,
with_threads=True,
enable_shared=True,
enable_profiling=True,
enable_optimizations=True,
with_pydebug=True,
enable_ipv6=True,
toolchain=compiler.toolchain,
# build_environment={
# 'CPPFLAGS': '"-Wl,-rpath=/usr/local/python/lib $CPPFLAGS"'
# }
)
stage0 += packages(apt=['patchelf'])
stage0 += shell(commands=[
# 'snap install patchelf --edge --classic',
'patchelf --set-rpath /usr/local/python/lib /usr/local/python/bin/python3',
])
stage0 += environment(variables=from_prefix('/usr/local/python'))
stage0 += mkl(version=mkl_version, eula=True)
stage0 += shell(commands=['source /opt/intel/mkl/bin/mklvars.sh intel64'])
stage0 += pip(
packages=['Cython>0.29.21', 'pytest>1.15', 'Hypothesis>5.3.0'],
pip='pip3')
stage0 += shell(commands=[
f'git clone --branch v{numpy_version} https://github.com/numpy/numpy.git',
'apt remove -y python-numpy python-scipy', 'rm -rf /numpy'
])
stage0 += runscript(commands=['/usr/local/python/bin/python3 $*'])
return stage0
def main():
parser = argparse.ArgumentParser(
description=
'Simple script for generating a singularity recipe for the GOL example.'
)
parser.add_argument(
'--build_prefix',
type=str,
default='/tmp/GOL_example',
help=
'Define the path in which all projects will be built (default: /tmp/GOL_example).'
)
parser.add_argument('-v ',
'--version',
action='store_true',
help='print version of the container')
args = parser.parse_args()
if args.version:
print(container_version)
sys.exit(0)
hpccm.config.set_container_format('singularity')
hpccm.config.set_singularity_version('3.3')
stage = hpccm.Stage()
stage += label(metadata={'GOL_MAINTAINER': 'Simeon Ehrig'})
stage += label(metadata={'GOL_EMAIL': '*****@*****.**'})
stage += label(metadata={'GOL_Version': str(container_version)})
# copy example inside container
stage += copy(src='notebook', dest='/')
stage += copy(src='jupyter_notebook_config.py', dest='/')
# copy and build the pnwriter library
stage += packages(ospackages=['libpng-dev'])
png = []
png_git = git()
png.append(
png_git.clone_step(
repository='https://github.com/pngwriter/pngwriter.git',
branch='dev',
path='/opt/'))
png_cmake = CMakeBuild(prefix='/notebook/pngwriter')
png.append(
png_cmake.configure_step(directory='/opt/pngwriter',
opts=['-DBUILD_SHARED_LIBS=ON']))
png.append(png_cmake.build_step(target='install'))
png.append('rm -rf /opt/pngwriter')
stage += shell(commands=png)
# Copy notebook examples and pngwriter lib to the host's /tmp file system to obtain a writable file system.
stage += runscript(commands=[
'if [ ! -d /tmp/GOL-xeus-cling-cuda ]; then \n'
' mkdir /tmp/GOL-xeus-cling-cuda &&'
' cp -r /notebook/ /tmp/GOL-xeus-cling-cuda &&'
' ln -s /tmp/GOL-xeus-cling-cuda/notebook/pngwriter'
' /tmp/GOL-xeus-cling-cuda/notebook/GTC_presentations/simulation/ \n fi',
'cd /tmp/GOL-xeus-cling-cuda/notebook',
'jupyter-notebook --config=/jupyter_notebook_config.py'
])
# Add the bootstrap manually because hpccm does not support .sregistry,
recipe = stage.__str__()
recipe = 'Bootstrap: library\nFrom: sehrig/default/xeus-cling-cuda:2.3\n\n' + recipe
print(recipe)
def build(python_version='3.6', freesurfer_version='6.0.1'):
stage0 = Stage()
config.set_container_format('singularity')
stage0 += baseimage(image='nvidia/cuda:10.0-cudnn7-runtime-ubuntu16.04',
_bootstrap='docker')
stage0 += shell(
commands=['rm /bin/sh', 'ln -s /bin/bash /bin/sh', '/bin/bash'])
stage0 += packages(apt=[
'build-essential', 'cmake', 'git', 'vim', 'wget', 'ca-certificates',
'bzip2', 'libx11-6', 'libjpeg-dev', 'libpng-dev', 'bc', 'tar', 'zip',
'gawk', 'tcsh', 'time', 'libgomp1', 'libglu1-mesa', 'libglu1-mesa-dev',
'perl-modules'
])
stage0 += comment(
"https://github.com/Deep-MI/FastSurfer/blob/master/Docker/Dockerfile")
stage0 += shell(commands=[
f"wget -qO- https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/{freesurfer_version}/freesurfer-Linux-centos6_x86_64-stable-pub-v{freesurfer_version}.tar.gz | tar zxv --no-same-owner -C /opt \
--exclude='freesurfer/trctrain' \
--exclude='freesurfer/subjects/fsaverage_sym' \
--exclude='freesurfer/subjects/fsaverage3' \
--exclude='freesurfer/subjects/fsaverage4' \
--exclude='freesurfer/subjects/fsaverage5' \
--exclude='freesurfer/subjects/fsaverage6' \
--exclude='freesurfer/subjects/cvs_avg35' \
--exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
--exclude='freesurfer/subjects/bert' \
--exclude='freesurfer/subjects/V1_average' \
--exclude='freesurfer/average/mult-comp-cor' \
--exclude='freesurfer/lib/cuda' \
--exclude='freesurfer/lib/qt'",
])
stage0 += conda(
channels=['pytorch', 'conda-forge'],
packages=[
f'python={python_version}', 'scipy', 'numpy', 'matplotlib', 'h5py',
'scikit-image', 'pytorch', 'cudatoolkit=10.0',
'pytorch=1.2.0=py3.6_cuda10.0.130_cudnn7.6.2_0',
'torchvision=0.4.0', 'scikit-sparse', 'nibabel=2.5.1',
'pillow=7.1.1'
],
eula=True,
)
stage0 += generic_build(
repository='https://github.com/Deep-MI/FastSurfer.git',
# branch='c5894bd',
build=['git checkout c5894bd'],
install=['mkdir /fastsurfer && mv * /fastsurfer/'])
stage0 += environment(
variables={
'OS': 'Linux',
'FS_OVERRIDE': 0,
'FIX_VERTEX_AREA': '',
'SUBJECTS_DIR': '/opt/freesurfer/subjects',
'FSF_OUTPUT_FORMAT': 'nii.gz',
'MNI_DIR': '/opt/freesurfer/mni',
'LOCAL_DIR': '/opt/freesurfer/local',
'FREESURFER_HOME': '/opt/freesurfer',
'FSFAST_HOME': '/opt/freesurfer/fsfast',
'PERL5LIB': '/opt/freesurfer/mni/lib/perl5/5.8.5',
'MNI_PERL4LIB': '/opt/freesurfer/mni/lib/perl5/5.8.5',
'PYTHONNUMBUFFERED': 0,
'PATH':
'/fastsurfer/recon_surf:/fastsurfer:/usr/local/anaconda/bin:/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:$PATH',
**from_prefix('/usr/local/cuda')
})
stage0 += runscript(commands=[
'cd /fastsurfer', 'source /usr/local/anaconda/etc/profile.d/conda.sh',
'source $FREESURFER_HOME/SetUpFreeSurfer.sh', "$*"
])
return stage0
def main():
parser = argparse.ArgumentParser(
description=
'Simple script for generating a singularity recipe for the GOL exercise.'
)
parser.add_argument(
'--build_prefix',
type=str,
default='/tmp/GOL_example',
help=
'Define the path in which all projects will be built (default: /tmp/GOL_example).'
)
parser.add_argument('-j',
type=str,
help='number of build threads for make (default: -j)')
parser.add_argument(
'-l',
type=str,
help='number of linker threads for the cling build (default: -j)')
parser.add_argument('-v ',
'--version',
action='store_true',
help='print version of the container')
args = parser.parse_args()
if args.version:
print(container_version)
sys.exit(0)
if args.j:
threads = int(args.j)
if threads < 1:
raise ValueError('-j have to be greater than 0')
else:
threads = None
if args.l:
linker_threads = int(args.l)
if linker_threads < 1:
raise ValueError('-l have to be greater than 0')
else:
linker_threads = None
xcc_gen = gn.XCC_gen(build_prefix=args.build_prefix,
threads=threads,
linker_threads=linker_threads)
stage = xcc_gen.gen_release_single_stage()
stage += label(metadata={'EXAMPLE_CONTAINER_MAINTAINER': 'Simeon Ehrig'})
stage += label(metadata={'EXAMPLE_CONTAINER_EMAIL': '*****@*****.**'})
stage += label(
metadata={'EXAMPLE_CONTAINER_Version': str(container_version)})
# disable the xsrf check, which avoid some problems in Firefox
stage += copy(src='jupyter_notebook_config.py', dest='/')
# copy and build the pnwriter library
stage += packages(ospackages=['libpng-dev'])
png_git = git()
stage += png_git.clone_step(
repository='https://github.com/pngwriter/pngwriter.git',
branch='dev',
path='/opt/')
png_cmake = CMakeBuild()
stage += shell(commands=[
png_cmake.configure_step(directory='/opt/pngwriter',
opts=['-DBUILD_SHARED_LIBS=ON']),
png_cmake.build_step(target='install')
])
# copy and install jitify
jitify_git = git()
stage += jitify_git.clone_step(
repository='https://github.com/NVIDIA/jitify.git', path='/opt/')
png_cmake = CMakeBuild()
stage += shell(commands=['cp /opt/jitify/jitify.hpp /usr/local/include'])
stage += shell(commands=['rm -rf /opt/pngwriter', 'rm -rf /opt/jitify'])
# check if the path to the notebook is specified, otherwise use the current directory
stage += runscript(commands=[
'if [ $# -gt 0 ]', 'then', 'cd $1', 'fi',
'jupyter-notebook --config=/jupyter_notebook_config.py'
])
print(stage.__str__())
