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# Generated by Neurodocker and Reproenv.
FROM neurodebian:stretch-non-free
RUN apt-get update -qq \
&& apt-get install -y --quiet \
g++ \
gcc \
octave \
&& rm -rf /var/lib/apt/lists/*
ENV LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/MCR-2017b/v93/runtime/glnxa64:/opt/MCR-2017b/v93/bin/glnxa64:/opt/MCR-2017b/v93/sys/os/glnxa64:/opt/MCR-2017b/v93/extern/bin/glnxa64" \
MATLABCMD="/opt/MCR-2017b/2017b/toolbox/matlab" \
XAPPLRESDIR="/opt//opt/MCR-2017b/v93/x11/app-defaults" \
MCRROOT="/opt/MCR-2017b/2017b"
RUN export TMPDIR="$(mktemp -d)" \
&& apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
bc \
curl \
dbus-x11 \
libncurses5 \
libxext6 \
libxmu6 \
libxpm-dev \
libxt6 \
multiarch-support \
openjdk-8-jre \
unzip \
&& rm -rf /var/lib/apt/lists/* \
&& _reproenv_tmppath="$(mktemp -t tmp.XXXXXXXXXX.deb)" \
&& curl -fsSL --retry 5 -o "${_reproenv_tmppath}" http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
&& apt-get install --yes -q "${_reproenv_tmppath}" \
&& rm "${_reproenv_tmppath}" \
&& apt-get update -qq \
&& apt-get install --yes --quiet --fix-missing \
&& rm -rf /var/lib/apt/lists/* \
&& echo "Downloading MATLAB Compiler Runtime ..." \
&& curl -o "$TMPDIR/mcr.zip" https://ssd.mathworks.com/supportfiles/downloads/R2017b/deployment_files/R2017b/installers/glnxa64/MCR_R2017b_glnxa64_installer.zip \
&& unzip -q "$TMPDIR/mcr.zip" -d "$TMPDIR/mcrtmp" \
&& "$TMPDIR/mcrtmp/install" -destinationFolder /opt/MCR-2017b -mode silent -agreeToLicense yes \
&& rm -rf "$TMPDIR" \
&& unset TMPDIR
ENV FORCE_SPMMCR="1" \
SPM_HTML_BROWSER="0" \
MCR_INHIBIT_CTF_LOCK="1" \
SPMROOT="/opt/CAT12-r1933_R2017b" \
PATH="/opt/CAT12-r1933_R2017b:$PATH"
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
ca-certificates \
curl \
unzip \
&& rm -rf /var/lib/apt/lists/* \
# Install cat12
&& echo "Downloading standalone CAT12 ..." \
&& curl -fL -o /tmp/cat12.zip http://www.neuro.uni-jena.de/cat12/CAT12.8_r1933_R2017b_MCR_Linux.zip \
&& unzip -q /tmp/cat12.zip -d /tmp \
&& rm -rf /tmp/cat12.zip \
&& mkdir -p /opt/CAT12-r1933_R2017b \
&& mv /tmp/*r1933_R2017b*/* /opt/CAT12-r1933_R2017b/ \
&& chmod -R 777 /opt/CAT12-r1933_R2017b \
# Test
&& /opt/CAT12-r1933_R2017b/spm12 function exit
COPY ["test.yml", \
"/tmp/"]
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 "$conda_installer" \
&& conda update -yq -nbase conda \
# Prefer packages in conda-forge
&& conda config --system --prepend channels conda-forge \
# Packages in lower-priority channels not considered if a package with the same
# name exists in a higher priority channel. Can dramatically speed up installations.
# Conda recommends this as a default
# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html
&& conda config --set channel_priority strict \
&& conda config --system --set auto_update_conda false \
&& conda config --system --set show_channel_urls true \
# Enable `conda activate`
&& conda init bash \
&& conda env create --name csp --file /tmp/test.yml \
# Clean up
&& sync && conda clean --all --yes && sync \
&& rm -rf ~/.cache/pip/*
RUN test "$(getent passwd csp)" \
|| useradd --no-user-group --create-home --shell /bin/bash csp
USER csp
RUN mkdir /home/csp/code && chmod -R 777 /home/csp/code
RUN mkdir /home/csp/data && chmod -R 777 /home/csp/data
RUN mkdir /home/csp/cache && chmod -R 777 /home/csp/cache
RUN mkdir /home/csp/output && chmod -R 777 /home/csp/output
RUN mkdir /home/csp/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > home/csp/.jupyter/jupyter_notebook_config.py
WORKDIR /home/csp/code
RUN echo source activate csp >> /home/csp/.bashrc
# Save specification to JSON.
USER root
RUN printf '{ \
"pkg_manager": "apt", \
"existing_users": [ \
"root" \
], \
"instructions": [ \
{ \
"name": "from_", \
"kwds": { \
"base_image": "neurodebian:stretch-non-free" \
} \
}, \
{ \
"name": "install", \
"kwds": { \
"pkgs": [ \
"gcc", \
"g++", \
"octave" \
], \
"opts": "--quiet" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "apt-get update -qq \\\\\\n && apt-get install -y --quiet \\\\\\n g++ \\\\\\n gcc \\\\\\n octave \\\\\\n && rm -rf /var/lib/apt/lists/*" \
} \
}, \
{ \
"name": "env", \
"kwds": { \
"LD_LIBRARY_PATH": "$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/MCR-2017b/v93/runtime/glnxa64:/opt/MCR-2017b/v93/bin/glnxa64:/opt/MCR-2017b/v93/sys/os/glnxa64:/opt/MCR-2017b/v93/extern/bin/glnxa64", \
"MATLABCMD": "/opt/MCR-2017b/2017b/toolbox/matlab", \
"XAPPLRESDIR": "/opt//opt/MCR-2017b/v93/x11/app-defaults", \
"MCRROOT": "/opt/MCR-2017b/2017b" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "export TMPDIR=\\"$\(mktemp -d\)\\"\\napt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n bc \\\\\\n curl \\\\\\n dbus-x11 \\\\\\n libncurses5 \\\\\\n libxext6 \\\\\\n libxmu6 \\\\\\n libxpm-dev \\\\\\n libxt6 \\\\\\n multiarch-support \\\\\\n openjdk-8-jre \\\\\\n unzip\\nrm -rf /var/lib/apt/lists/*\\n_reproenv_tmppath=\\"$\(mktemp -t tmp.XXXXXXXXXX.deb\)\\"\\ncurl -fsSL --retry 5 -o \\"${_reproenv_tmppath}\\" http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb\\napt-get install --yes -q \\"${_reproenv_tmppath}\\"\\nrm \\"${_reproenv_tmppath}\\"\\napt-get update -qq\\napt-get install --yes --quiet --fix-missing\\nrm -rf /var/lib/apt/lists/*\\necho \\"Downloading MATLAB Compiler Runtime ...\\"\\ncurl -o \\"$TMPDIR/mcr.zip\\" https://ssd.mathworks.com/supportfiles/downloads/R2017b/deployment_files/R2017b/installers/glnxa64/MCR_R2017b_glnxa64_installer.zip\\nunzip -q \\"$TMPDIR/mcr.zip\\" -d \\"$TMPDIR/mcrtmp\\"\\n\\"$TMPDIR/mcrtmp/install\\" -destinationFolder /opt/MCR-2017b -mode silent -agreeToLicense yes\\nrm -rf \\"$TMPDIR\\"\\nunset TMPDIR" \
} \
}, \
{ \
"name": "env", \
"kwds": { \
"FORCE_SPMMCR": "1", \
"SPM_HTML_BROWSER": "0", \
"MCR_INHIBIT_CTF_LOCK": "1", \
"SPMROOT": "/opt/CAT12-r1933_R2017b", \
"PATH": "/opt/CAT12-r1933_R2017b:$PATH" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n ca-certificates \\\\\\n curl \\\\\\n unzip\\nrm -rf /var/lib/apt/lists/*\\n# Install cat12\\necho \\"Downloading standalone CAT12 ...\\"\\ncurl -fL -o /tmp/cat12.zip http://www.neuro.uni-jena.de/cat12/CAT12.8_r1933_R2017b_MCR_Linux.zip\\nunzip -q /tmp/cat12.zip -d /tmp\\nrm -rf /tmp/cat12.zip\\nmkdir -p /opt/CAT12-r1933_R2017b\\nmv /tmp/*r1933_R2017b*/* /opt/CAT12-r1933_R2017b/\\nchmod -R 777 /opt/CAT12-r1933_R2017b\\n# Test\\n/opt/CAT12-r1933_R2017b/spm12 function exit" \
} \
}, \
{ \
"name": "copy", \
"kwds": { \
"source": [ \
"test.yml", \
"/tmp/" \
], \
"destination": "/tmp/" \
} \
}, \
{ \
"name": "env", \
"kwds": { \
"CONDA_DIR": "/opt/miniconda-latest", \
"PATH": "/opt/miniconda-latest/bin:$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\\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 env create --name csp --file /tmp/test.yml\\n# Clean up\\nsync && conda clean --all --yes && sync\\nrm -rf ~/.cache/pip/*" \
} \
}, \
{ \
"name": "user", \
"kwds": { \
"user": "csp" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "mkdir /home/csp/code && chmod -R 777 /home/csp/code" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "mkdir /home/csp/data && chmod -R 777 /home/csp/data" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "mkdir /home/csp/cache && chmod -R 777 /home/csp/cache" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "mkdir /home/csp/output && chmod -R 777 /home/csp/output" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "mkdir /home/csp/.jupyter && echo c.NotebookApp.ip = \\\\\\"0.0.0.0\\\\\\" > home/csp/.jupyter/jupyter_notebook_config.py" \
} \
}, \
{ \
"name": "workdir", \
"kwds": { \
"path": "/home/csp/code" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "echo source activate csp >> /home/csp/.bashrc" \
} \
} \
] \
}' > /.reproenv.json
USER csp
# End saving to specification to JSON.