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Dockerfile_ps7
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# Generated by Neurodocker and Reproenv.
FROM ubuntu:jammy
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
bc \
curl \
libglu1-mesa \
libgomp1 \
libpython2.7-stdlib \
libsm-dev \
libx11-dev \
libxext-dev \
libxt-dev \
perl-modules \
python2 \
tar \
tcsh \
wget \
&& rm -rf /var/lib/apt/lists/*
ENV OS="Linux" \
PATH="/opt//bin:/opt//fsfast/bin:/opt//tktools:/opt//mni/bin:$PATH" \
FREESURFER_HOME="/opt/" \
FREESURFER="/opt/" \
SUBJECTS_DIR="/opt//subjects" \
LOCAL_DIR="/opt//local" \
FSFAST_HOME="/opt//fsfast" \
FMRI_ANALYSIS_DIR="/opt//fsfast" \
FUNCTIONALS_DIR="/opt//sessions" \
FS_OVERRIDE="0" \
FIX_VERTEX_AREA="" \
FSF_OUTPUT_FORMAT="nii.gz# mni env requirements" \
MINC_BIN_DIR="/opt//mni/bin" \
MINC_LIB_DIR="/opt//mni/lib" \
MNI_DIR="/opt//mni" \
MNI_DATAPATH="/opt//mni/data" \
MNI_PERL5LIB="/opt//mni/share/perl5" \
PERL5LIB="/opt//mni/share/perl5"
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
bc \
ca-certificates \
curl \
libgomp1 \
libxmu6 \
libxt6 \
perl \
tcsh \
&& rm -rf /var/lib/apt/lists/* \
&& echo "Downloading FreeSurfer ..." \
&& mkdir -p /opt/ \
&& curl -fL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-linux-centos7_x86_64-7.4.1.tar.gz \
| tar -xz -C /opt/ --owner root --group root --no-same-owner --strip-components 1 \
--exclude='average/mult-comp-cor' \
--exclude='lib/cuda' \
--exclude='lib/qt' \
--exclude='subjects/V1_average' \
--exclude='subjects/bert' \
--exclude='subjects/cvs_avg35' \
--exclude='subjects/cvs_avg35_inMNI152' \
--exclude='subjects/fsaverage3' \
--exclude='subjects/fsaverage4' \
--exclude='subjects/fsaverage5' \
--exclude='subjects/fsaverage6' \
--exclude='subjects/fsaverage_sym' \
--exclude='trctrain'
ENV CONDA_DIR="/opt/miniconda-latest" \
PATH="/opt/miniconda-latest/bin:$PATH"
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
bzip2 \
ca-certificates \
curl \
&& rm -rf /var/lib/apt/lists/* \
# Install dependencies.
&& export PATH="/opt/miniconda-latest/bin:$PATH" \
&& echo "Downloading Miniconda installer ..." \
&& conda_installer="/tmp/miniconda.sh" \
&& curl -fsSL -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
&& bash "$conda_installer" -b -p /opt/miniconda-latest \
&& rm -f "$conda_installer" \
&& conda update -yq -nbase conda \
&& conda install -yq -nbase conda-libmamba-solver \
&& conda config --set solver libmamba \
# Prefer packages in conda-forge
&& conda config --system --prepend channels conda-forge \
# Packages in lower-priority channels not considered if a package with the same
# name exists in a higher priority channel. Can dramatically speed up installations.
# Conda recommends this as a default
# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html
&& conda config --set channel_priority strict \
&& conda config --system --set auto_update_conda false \
&& conda config --system --set show_channel_urls true \
# Enable `conda activate`
&& conda init bash \
&& conda install -y --name base \
"pandas=1.5.3" \
&& bash -c "source activate base \
&& python -m pip install --no-cache-dir \
"nibabel"" \
# Clean up
&& sync && conda clean --all --yes && sync \
&& rm -rf ~/.cache/pip/*
RUN bash -c 'curl -sL https://deb.nodesource.com/setup_18.x | bash -'
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
nodejs \
&& rm -rf /var/lib/apt/lists/*
RUN bash -c 'npm install -g bids-validator@1.12.0'
ENV FSLDIR="/usr/share/fsl/5.0" \
FSLOUTPUTTYPE="NIFTI_GZ" \
FSLMULTIFILEQUIT="TRUE" \
POSSUMDIR="/usr/share/fsl/5.0" \
LD_LIBRARY_PATH="/usr/lib/fsl/5.0:" \
FSLTCLSH="/usr/bin/tclsh" \
FSLWISH="/usr/bin/wish"
ENV 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" \
MINC_BIN_DIR="/opt/freesurfer/mni/bin" \
MINC_LIB_DIR="/opt/freesurfer/mni/lib" \
MNI_DATAPATH="/opt/freesurfer/mni/data" \
FMRI_ANALYSIS_DIR="/opt/freesurfer/fsfast" \
PERL5LIB="/opt/freesurfer/mni/share/perl5" \
MNI_PERL5LIB="/opt/freesurfer/mni/share/perl5/" \
PATH="/opt/miniconda-latest/bin:/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/lib/fsl/5.0:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin" \
PYTHONPATH=""
RUN mkdir root/matlab && touch root/matlab/startup.m
RUN mkdir /scratch
RUN mkdir /local-scratch
COPY ["run_pet.py", \
"/run_pet.py"]
RUN chmod +x /run_pet.py
COPY ["version", \
"/version"]
ENTRYPOINT ["python", "/run_pet.py"]
# Save specification to JSON.
RUN printf '{ \
"pkg_manager": "apt", \
"existing_users": [ \
"root" \
], \
"instructions": [ \
{ \
"name": "from_", \
"kwds": { \
"base_image": "ubuntu:jammy" \
} \
}, \
{ \
"name": "install", \
"kwds": { \
"pkgs": [ \
"tcsh", \
"bc", \
"tar", \
"libgomp1", \
"perl-modules", \
"wget", \
"curl", \
"libsm-dev", \
"libx11-dev", \
"libxt-dev", \
"libxext-dev", \
"libglu1-mesa", \
"libpython2.7-stdlib", \
"python2" \
], \
"opts": null \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "apt-get update -qq \\\\\\n && apt-get install -y -q --no-install-recommends \\\\\\n bc \\\\\\n curl \\\\\\n libglu1-mesa \\\\\\n libgomp1 \\\\\\n libpython2.7-stdlib \\\\\\n libsm-dev \\\\\\n libx11-dev \\\\\\n libxext-dev \\\\\\n libxt-dev \\\\\\n perl-modules \\\\\\n python2 \\\\\\n tar \\\\\\n tcsh \\\\\\n wget \\\\\\n && rm -rf /var/lib/apt/lists/*" \
} \
}, \
{ \
"name": "env", \
"kwds": { \
"OS": "Linux", \
"PATH": "/opt//bin:/opt//fsfast/bin:/opt//tktools:/opt//mni/bin:$PATH", \
"FREESURFER_HOME": "/opt/", \
"FREESURFER": "/opt/", \
"SUBJECTS_DIR": "/opt//subjects", \
"LOCAL_DIR": "/opt//local", \
"FSFAST_HOME": "/opt//fsfast", \
"FMRI_ANALYSIS_DIR": "/opt//fsfast", \
"FUNCTIONALS_DIR": "/opt//sessions", \
"FS_OVERRIDE": "0", \
"FIX_VERTEX_AREA": "", \
"FSF_OUTPUT_FORMAT": "nii.gz# mni env requirements", \
"MINC_BIN_DIR": "/opt//mni/bin", \
"MINC_LIB_DIR": "/opt//mni/lib", \
"MNI_DIR": "/opt//mni", \
"MNI_DATAPATH": "/opt//mni/data", \
"MNI_PERL5LIB": "/opt//mni/share/perl5", \
"PERL5LIB": "/opt//mni/share/perl5" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n bc \\\\\\n ca-certificates \\\\\\n curl \\\\\\n libgomp1 \\\\\\n libxmu6 \\\\\\n libxt6 \\\\\\n perl \\\\\\n tcsh\\nrm -rf /var/lib/apt/lists/*\\necho \\"Downloading FreeSurfer ...\\"\\nmkdir -p /opt/\\ncurl -fL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-linux-centos7_x86_64-7.4.1.tar.gz \\\\\\n| tar -xz -C /opt/ --owner root --group root --no-same-owner --strip-components 1 \\\\\\n --exclude='"'"'average/mult-comp-cor'"'"' \\\\\\n --exclude='"'"'lib/cuda'"'"' \\\\\\n --exclude='"'"'lib/qt'"'"' \\\\\\n --exclude='"'"'subjects/V1_average'"'"' \\\\\\n --exclude='"'"'subjects/bert'"'"' \\\\\\n --exclude='"'"'subjects/cvs_avg35'"'"' \\\\\\n --exclude='"'"'subjects/cvs_avg35_inMNI152'"'"' \\\\\\n --exclude='"'"'subjects/fsaverage3'"'"' \\\\\\n --exclude='"'"'subjects/fsaverage4'"'"' \\\\\\n --exclude='"'"'subjects/fsaverage5'"'"' \\\\\\n --exclude='"'"'subjects/fsaverage6'"'"' \\\\\\n --exclude='"'"'subjects/fsaverage_sym'"'"' \\\\\\n --exclude='"'"'trctrain'"'"'" \
} \
}, \
{ \
"name": "env", \
"kwds": { \
"CONDA_DIR": "/opt/miniconda-latest", \
"PATH": "/opt/miniconda-latest/bin:$PATH" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n bzip2 \\\\\\n ca-certificates \\\\\\n curl\\nrm -rf /var/lib/apt/lists/*\\n# Install dependencies.\\nexport PATH=\\"/opt/miniconda-latest/bin:$PATH\\"\\necho \\"Downloading Miniconda installer ...\\"\\nconda_installer=\\"/tmp/miniconda.sh\\"\\ncurl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh\\nbash \\"$conda_installer\\" -b -p /opt/miniconda-latest\\nrm -f \\"$conda_installer\\"\\nconda update -yq -nbase conda\\nconda install -yq -nbase conda-libmamba-solver\\nconda config --set solver libmamba\\n# Prefer packages in conda-forge\\nconda config --system --prepend channels conda-forge\\n# Packages in lower-priority channels not considered if a package with the same\\n# name exists in a higher priority channel. Can dramatically speed up installations.\\n# Conda recommends this as a default\\n# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html\\nconda config --set channel_priority strict\\nconda config --system --set auto_update_conda false\\nconda config --system --set show_channel_urls true\\n# Enable `conda activate`\\nconda init bash\\nconda install -y --name base \\\\\\n \\"pandas=1.5.3\\"\\nbash -c \\"source activate base\\n python -m pip install --no-cache-dir \\\\\\n \\"nibabel\\"\\"\\n# Clean up\\nsync && conda clean --all --yes && sync\\nrm -rf ~/.cache/pip/*" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "bash -c '"'"'curl -sL https://deb.nodesource.com/setup_18.x | bash -'"'"'" \
} \
}, \
{ \
"name": "install", \
"kwds": { \
"pkgs": [ \
"nodejs" \
], \
"opts": null \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "apt-get update -qq \\\\\\n && apt-get install -y -q --no-install-recommends \\\\\\n nodejs \\\\\\n && rm -rf /var/lib/apt/lists/*" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "bash -c '"'"'npm install -g bids-validator@1.12.0'"'"'" \
} \
}, \
{ \
"name": "env", \
"kwds": { \
"FSLDIR": "/usr/share/fsl/5.0", \
"FSLOUTPUTTYPE": "NIFTI_GZ", \
"FSLMULTIFILEQUIT": "TRUE", \
"POSSUMDIR": "/usr/share/fsl/5.0", \
"LD_LIBRARY_PATH": "/usr/lib/fsl/5.0:", \
"FSLTCLSH": "/usr/bin/tclsh", \
"FSLWISH": "/usr/bin/wish" \
} \
}, \
{ \
"name": "env", \
"kwds": { \
"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", \
"MINC_BIN_DIR": "/opt/freesurfer/mni/bin", \
"MINC_LIB_DIR": "/opt/freesurfer/mni/lib", \
"MNI_DATAPATH": "/opt/freesurfer/mni/data", \
"FMRI_ANALYSIS_DIR": "/opt/freesurfer/fsfast", \
"PERL5LIB": "/opt/freesurfer/mni/share/perl5", \
"MNI_PERL5LIB": "/opt/freesurfer/mni/share/perl5/", \
"PATH": "/opt/miniconda-latest/bin:/opt/freesurfer/bin:/opt/freesurfer/fsfast/bin:/opt/freesurfer/tktools:/opt/freesurfer/mni/bin:/usr/lib/fsl/5.0:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin", \
"PYTHONPATH": "" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "mkdir root/matlab && touch root/matlab/startup.m" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "mkdir /scratch" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "mkdir /local-scratch" \
} \
}, \
{ \
"name": "copy", \
"kwds": { \
"source": [ \
"run.py", \
"/run.py" \
], \
"destination": "/run.py" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "chmod +x /run.py" \
} \
}, \
{ \
"name": "copy", \
"kwds": { \
"source": [ \
"version", \
"/version" \
], \
"destination": "/version" \
} \
}, \
{ \
"name": "entrypoint", \
"kwds": { \
"args": [ \
"python", \
"/run.py" \
] \
} \
} \
] \
}' > /.reproenv.json
# End saving to specification to JSON.