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Dockerfile2
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# Generated by Neurodocker and Reproenv.
FROM neurodebian:stretch-non-free
ARG DEBIAN_FRONTEND=noninteractive
ENV ANTSPATH="/opt/ants-2.3.4/" \
PATH="/opt/ants-2.3.4:$PATH"
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
ca-certificates \
curl \
&& rm -rf /var/lib/apt/lists/* \
&& echo "Downloading ANTs ..." \
&& mkdir -p /opt/ants-2.3.4 \
&& curl -fsSL https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz \
| tar -xz -C /opt/ants-2.3.4 --strip-components 1
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
# ants \
convert3d \
emacs-nox \
fsl \
g++ \
gcc \
git-annex-remote-rclone \
git-annex-standalone \
graphviz \
less \
nano \
ncdu \
netbase \
octave \
tig \
tree \
vim \
&& rm -rf /var/lib/apt/lists/*
ENV FORCE_SPMMCR="1" \
SPM_HTML_BROWSER="0" \
SPMMCRCMD="/opt/spm12-r7771/run_spm12.sh /opt/matlab-compiler-runtime-2010a/v713 script" \
LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlab-compiler-runtime-2010a/v713/runtime/glnxa64:/opt/matlab-compiler-runtime-2010a/v713/bin/glnxa64:/opt/matlab-compiler-runtime-2010a/v713/sys/os/glnxa64:/opt/matlab-compiler-runtime-2010a/v713/extern/bin/glnxa64" \
MATLABCMD="/opt/matlab-compiler-runtime-2010a/v713/toolbox/matlab"
RUN export TMPDIR="$(mktemp -d)" \
&& apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
bc \
ca-certificates \
curl \
libncurses5 \
libxext6 \
libxmu6 \
libxpm-dev \
libxt6 \
multiarch-support \
unzip \
&& rm -rf /var/lib/apt/lists/* \
&& _reproenv_tmppath="$(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 "${_reproenv_tmppath}" \
&& apt-get update -qq \
&& apt-get install --yes --quiet --fix-missing \
&& rm -rf /var/lib/apt/lists/* \
&& echo "Downloading MATLAB Compiler Runtime ..." \
&& curl -fL -o "$TMPDIR/MCRInstaller.bin" https://dl.dropbox.com/s/zz6me0c3v4yq5fd/MCR_R2010a_glnxa64_installer.bin \
&& chmod +x "$TMPDIR/MCRInstaller.bin" \
&& "$TMPDIR/MCRInstaller.bin" -silent -P installLocation="/opt/matlab-compiler-runtime-2010a" \
&& rm -rf "$TMPDIR" \
&& unset TMPDIR \
# Install spm12
&& echo "Downloading standalone SPM12 ..." \
&& curl -fL -o /tmp/spm12.zip https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/previous/spm12_r7771_R2010a.zip \
&& unzip -q /tmp/spm12.zip -d /tmp \
&& mkdir -p /opt/spm12-r7771 \
&& mv /tmp/spm12/* /opt/spm12-r7771/ \
&& chmod -R 777 /opt/spm12-r7771 \
&& rm -rf /tmp/spm* \
# Test
&& /opt/spm12-r7771/run_spm12.sh /opt/matlab-compiler-runtime-2010a/v713 quit
ENV CONDA_DIR="/opt/miniconda-latest" \
PATH="/opt/miniconda-latest/bin:$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 install -y --name base \
"python=3.8" \
"pytest" \
"jupyter" \
"jupyterlab" \
"jupyter_contrib_nbextensions" \
"traits" \
"pandas" \
"matplotlib" \
"scikit-learn" \
"scikit-image" \
"seaborn" \
"nbformat" \
"nb_conda" \
&& bash -c "source activate base \
&& python -m pip install --no-cache-dir \
"https://github.com/nipy/nipype/tarball/master" \
"https://github.com/INCF/pybids/tarball/master" \
"nilearn" \
"nipy" \
"duecredit" \
"nbval"" \
# Clean up
&& sync && conda clean --all --yes && sync \
&& rm -rf ~/.cache/pip/*
# Save specification to JSON.
RUN printf '{ \
"pkg_manager": "apt", \
"existing_users": [ \
"root" \
], \
"instructions": [ \
{ \
"name": "from_", \
"kwds": { \
"base_image": "neurodebian:stretch-non-free" \
} \
}, \
{ \
"name": "arg", \
"kwds": { \
"key": "DEBIAN_FRONTEND", \
"value": "noninteractive" \
} \
}, \
{ \
"name": "install", \
"kwds": { \
"pkgs": [ \
"convert3d", \
"ants", \
"fsl", \
"gcc", \
"g++", \
"graphviz", \
"tree", \
"git-annex-standalone", \
"vim", \
"emacs-nox", \
"nano", \
"less", \
"ncdu", \
"tig", \
"git-annex-remote-rclone", \
"octave", \
"netbase" \
], \
"opts": null \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "apt-get update -qq \\\\\\n && apt-get install -y -q --no-install-recommends \\\\\\n ants \\\\\\n convert3d \\\\\\n emacs-nox \\\\\\n fsl \\\\\\n g++ \\\\\\n gcc \\\\\\n git-annex-remote-rclone \\\\\\n git-annex-standalone \\\\\\n graphviz \\\\\\n less \\\\\\n nano \\\\\\n ncdu \\\\\\n netbase \\\\\\n octave \\\\\\n tig \\\\\\n tree \\\\\\n vim \\\\\\n && rm -rf /var/lib/apt/lists/*" \
} \
}, \
{ \
"name": "env", \
"kwds": { \
"FORCE_SPMMCR": "1", \
"SPM_HTML_BROWSER": "0", \
"SPMMCRCMD": "/opt/spm12-r7771/run_spm12.sh /opt/matlab-compiler-runtime-2010a/v713 script", \
"LD_LIBRARY_PATH": "$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlab-compiler-runtime-2010a/v713/runtime/glnxa64:/opt/matlab-compiler-runtime-2010a/v713/bin/glnxa64:/opt/matlab-compiler-runtime-2010a/v713/sys/os/glnxa64:/opt/matlab-compiler-runtime-2010a/v713/extern/bin/glnxa64", \
"MATLABCMD": "/opt/matlab-compiler-runtime-2010a/v713/toolbox/matlab" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "export TMPDIR=\\"$\(mktemp -d\)\\"\\napt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n bc \\\\\\n ca-certificates \\\\\\n curl \\\\\\n libncurses5 \\\\\\n libxext6 \\\\\\n libxmu6 \\\\\\n libxpm-dev \\\\\\n libxt6 \\\\\\n multiarch-support \\\\\\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 \\"${_reproenv_tmppath}\\"\\napt-get update -qq\\napt-get install --yes --quiet --fix-missing\\nrm -rf /var/lib/apt/lists/*\\necho \\"Downloading MATLAB Compiler Runtime ...\\"\\ncurl -fL -o \\"$TMPDIR/MCRInstaller.bin\\" https://dl.dropbox.com/s/zz6me0c3v4yq5fd/MCR_R2010a_glnxa64_installer.bin\\nchmod +x \\"$TMPDIR/MCRInstaller.bin\\"\\n\\"$TMPDIR/MCRInstaller.bin\\" -silent -P installLocation=\\"/opt/matlab-compiler-runtime-2010a\\"\\nrm -rf \\"$TMPDIR\\"\\nunset TMPDIR\\n# Install spm12\\necho \\"Downloading standalone SPM12 ...\\"\\ncurl -fL -o /tmp/spm12.zip https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/previous/spm12_r7771_R2010a.zip\\nunzip -q /tmp/spm12.zip -d /tmp\\nmkdir -p /opt/spm12-r7771\\nmv /tmp/spm12/* /opt/spm12-r7771/\\nchmod -R 777 /opt/spm12-r7771\\nrm -rf /tmp/spm*\\n# Test\\n/opt/spm12-r7771/run_spm12.sh /opt/matlab-compiler-runtime-2010a/v713 quit" \
} \
}, \
{ \
"name": "env", \
"kwds": { \
"CONDA_DIR": "/opt/miniconda-latest", \
"PATH": "/opt/miniconda-latest/bin:$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 install -y --name base \\\\\\n \\"python=3.8\\" \\\\\\n \\"pytest\\" \\\\\\n \\"jupyter\\" \\\\\\n \\"jupyterlab\\" \\\\\\n \\"jupyter_contrib_nbextensions\\" \\\\\\n \\"traits\\" \\\\\\n \\"pandas\\" \\\\\\n \\"matplotlib\\" \\\\\\n \\"scikit-learn\\" \\\\\\n \\"scikit-image\\" \\\\\\n \\"seaborn\\" \\\\\\n \\"nbformat\\" \\\\\\n \\"nb_conda\\"\\nbash -c \\"source activate base\\n python -m pip install --no-cache-dir \\\\\\n \\"https://github.com/nipy/nipype/tarball/master\\" \\\\\\n \\"https://github.com/INCF/pybids/tarball/master\\" \\\\\\n \\"nilearn\\" \\\\\\n \\"nipy\\" \\\\\\n \\"duecredit\\" \\\\\\n \\"nbval\\"\\"\\n# Clean up\\nsync && conda clean --all --yes && sync\\nrm -rf ~/.cache/pip/*" \
} \
} \
] \
}' > /.reproenv.json
# End saving to specification to JSON.