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Dockerfile.neuro
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Dockerfile.neuro
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# Generated by Neurodocker and Reproenv.
FROM neurodebian:bullseye
ENV FSLDIR="/opt/fsl-6.0.5.1" \
PATH="/opt/fsl-6.0.5.1/bin:$PATH" \
FSLOUTPUTTYPE="NIFTI_GZ" \
FSLMULTIFILEQUIT="TRUE" \
FSLTCLSH="/opt/fsl-6.0.5.1/bin/fsltclsh" \
FSLWISH="/opt/fsl-6.0.5.1/bin/fslwish" \
FSLLOCKDIR="" \
FSLMACHINELIST="" \
FSLREMOTECALL="" \
FSLGECUDAQ="cuda.q"
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
bc \
ca-certificates \
curl \
dc \
file \
libfontconfig1 \
libfreetype6 \
libgl1-mesa-dev \
libgl1-mesa-dri \
libglu1-mesa-dev \
libgomp1 \
libice6 \
libopenblas-base \
libxcursor1 \
libxft2 \
libxinerama1 \
libxrandr2 \
libxrender1 \
libxt6 \
nano \
sudo \
wget \
&& rm -rf /var/lib/apt/lists/* \
&& echo "Downloading FSL ..." \
&& mkdir -p /opt/fsl-6.0.5.1 \
&& curl -fL https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.5.1-centos7_64.tar.gz \
| tar -xz -C /opt/fsl-6.0.5.1 --strip-components 1 \
&& echo "Installing FSL conda environment ..." \
&& bash /opt/fsl-6.0.5.1/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.5.1
ENV ANTSPATH="/opt/ants-2.4.1/" \
PATH="/opt/ants-2.4.1:$PATH"
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
ca-certificates \
curl \
unzip \
&& rm -rf /var/lib/apt/lists/* \
&& echo "Downloading ANTs ..." \
&& curl -fsSL -o ants.zip https://github.com/ANTsX/ANTs/releases/download/v2.4.1/ants-2.4.1-centos7-X64-gcc.zip \
&& unzip ants.zip -d /opt \
&& mv /opt/ants-2.4.1/bin/* /opt/ants-2.4.1 \
&& rm ants.zip
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 "$conda_installer" \
&& conda update -yq -nbase conda \
# Prefer packages in conda-forge
&& conda config --system --prepend channels conda-forge \
# Packages in lower-priority channels not considered if a package with the same
# name exists in a higher priority channel. Can dramatically speed up installations.
# Conda recommends this as a default
# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html
&& conda config --set channel_priority strict \
&& conda config --system --set auto_update_conda false \
&& conda config --system --set show_channel_urls true \
# Enable `conda activate`
&& conda init bash \
&& conda install -y --name base \
"nipype" \
"notebook" \
# Clean up
&& sync && conda clean --all --yes && sync \
&& rm -rf ~/.cache/pip/*
# Save specification to JSON.
RUN printf '{ \
"pkg_manager": "apt", \
"existing_users": [ \
"root" \
], \
"instructions": [ \
{ \
"name": "from_", \
"kwds": { \
"base_image": "neurodebian:bullseye" \
} \
}, \
{ \
"name": "env", \
"kwds": { \
"FSLDIR": "/opt/fsl-6.0.5.1", \
"PATH": "/opt/fsl-6.0.5.1/bin:$PATH", \
"FSLOUTPUTTYPE": "NIFTI_GZ", \
"FSLMULTIFILEQUIT": "TRUE", \
"FSLTCLSH": "/opt/fsl-6.0.5.1/bin/fsltclsh", \
"FSLWISH": "/opt/fsl-6.0.5.1/bin/fslwish", \
"FSLLOCKDIR": "", \
"FSLMACHINELIST": "", \
"FSLREMOTECALL": "", \
"FSLGECUDAQ": "cuda.q" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n bc \\\\\\n ca-certificates \\\\\\n curl \\\\\\n dc \\\\\\n file \\\\\\n libfontconfig1 \\\\\\n libfreetype6 \\\\\\n libgl1-mesa-dev \\\\\\n libgl1-mesa-dri \\\\\\n libglu1-mesa-dev \\\\\\n libgomp1 \\\\\\n libice6 \\\\\\n libopenblas-base \\\\\\n libxcursor1 \\\\\\n libxft2 \\\\\\n libxinerama1 \\\\\\n libxrandr2 \\\\\\n libxrender1 \\\\\\n libxt6 \\\\\\n nano \\\\\\n sudo \\\\\\n wget\\nrm -rf /var/lib/apt/lists/*\\necho \\"Downloading FSL ...\\"\\nmkdir -p /opt/fsl-6.0.5.1\\ncurl -fL https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.5.1-centos7_64.tar.gz \\\\\\n| tar -xz -C /opt/fsl-6.0.5.1 --strip-components 1 \\necho \\"Installing FSL conda environment ...\\"\\nbash /opt/fsl-6.0.5.1/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.5.1" \
} \
}, \
{ \
"name": "env", \
"kwds": { \
"ANTSPATH": "/opt/ants-2.4.1/", \
"PATH": "/opt/ants-2.4.1:$PATH" \
} \
}, \
{ \
"name": "run", \
"kwds": { \
"command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n ca-certificates \\\\\\n curl \\\\\\n unzip\\nrm -rf /var/lib/apt/lists/*\\necho \\"Downloading ANTs ...\\"\\ncurl -fsSL -o ants.zip https://github.com/ANTsX/ANTs/releases/download/v2.4.1/ants-2.4.1-centos7-X64-gcc.zip\\nunzip ants.zip -d /opt\\nmv /opt/ants-2.4.1/bin/* /opt/ants-2.4.1\\nrm ants.zip" \
} \
}, \
{ \
"name": "env", \
"kwds": { \
"CONDA_DIR": "/opt/miniconda-latest", \
"PATH": "/opt/miniconda-latest/bin:$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 \\"nipype\\" \\\\\\n \\"notebook\\"\\n# Clean up\\nsync && conda clean --all --yes && sync\\nrm -rf ~/.cache/pip/*" \
} \
} \
] \
}' > /.reproenv.json
# End saving to specification to JSON.