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Dockerfile
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# NiWorkflows Docker Container Image distribution
#
# MIT License
#
# Copyright (c) 2022 The NiPreps Developers
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
FROM nipreps/miniconda:py39_2205.0
ARG DEBIAN_FRONTEND=noninteractive
ENV LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:${CONDA_PATH}/lib"
# Installing freesurfer
RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz | tar zxv --no-same-owner -C /opt \
--exclude='freesurfer/average' \
--exclude='freesurfer/diffusion' \
--exclude='freesurfer/docs' \
--exclude='freesurfer/fsfast' \
--exclude='freesurfer/lib/cuda' \
--exclude='freesurfer/lib/qt' \
--exclude='freesurfer/matlab' \
--exclude='freesurfer/mni/share/man' \
--exclude='freesurfer/subjects/fsaverage_sym' \
--exclude='freesurfer/subjects/fsaverage3' \
--exclude='freesurfer/subjects/fsaverage4' \
--exclude='freesurfer/subjects/cvs_avg35' \
--exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
--exclude='freesurfer/subjects/bert' \
--exclude='freesurfer/subjects/lh.EC_average' \
--exclude='freesurfer/subjects/rh.EC_average' \
--exclude='freesurfer/subjects/sample-*.mgz' \
--exclude='freesurfer/subjects/V1_average' \
--exclude='freesurfer/trctrain'
# Simulate SetUpFreeSurfer.sh
ENV FSL_DIR="/opt/fsl" \
OS="Linux" \
FS_OVERRIDE=0 \
FIX_VERTEX_AREA="" \
FSF_OUTPUT_FORMAT="nii.gz" \
FREESURFER_HOME="/opt/freesurfer"
ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \
MNI_DIR="$FREESURFER_HOME/mni" \
LOCAL_DIR="$FREESURFER_HOME/local" \
MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
MNI_DATAPATH="$FREESURFER_HOME/mni/data"
ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
PATH="$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
# Install AFNI latest (neurodocker build)
ENV AFNI_DIR="/opt/afni"
RUN echo "Downloading AFNI ..." \
&& mkdir -p ${AFNI_DIR} \
&& curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
| tar -xz -C ${AFNI_DIR} --strip-components 1 \
# Keep only what we use
&& find ${AFNI_DIR} -type f -not \( \
-name "3dTshift" -or \
-name "3dUnifize" -or \
-name "3dAutomask" -or \
-name "3dvolreg" \) -delete
ENV PATH="${AFNI_DIR}:$PATH" \
AFNI_IMSAVE_WARNINGS="NO" \
AFNI_MODELPATH="${AFNI_DIR}/models" \
AFNI_TTATLAS_DATASET="${AFNI_DIR}/atlases" \
AFNI_PLUGINPATH="${AFNI_DIR}/plugins"
# Install AFNI's dependencies
RUN ${CONDA_PATH}/bin/conda install -c conda-forge -c anaconda \
gsl \
xorg-libxp \
scipy=1.8 \
&& ${CONDA_PATH}/bin/conda install -c sssdgc png \
&& sync \
&& ${CONDA_PATH}/bin/conda clean -afy; sync \
&& rm -rf ~/.conda ~/.cache/pip/*; sync \
&& ln -s ${CONDA_PATH}/lib/libgsl.so.25 /usr/lib/x86_64-linux-gnu/libgsl.so.19 \
&& ln -s ${CONDA_PATH}/lib/libgsl.so.25 /usr/lib/x86_64-linux-gnu/libgsl.so.0 \
&& ldconfig
RUN apt-get update \
&& apt-get install -y -q --no-install-recommends \
libcurl4-openssl-dev \
libgdal-dev \
libgfortran-8-dev \
libgfortran4 \
libglw1-mesa \
libgomp1 \
libjpeg62 \
libnode-dev \
libssl-dev \
libudunits2-dev \
libxm4 \
libxml2-dev \
netpbm \
tcsh \
xfonts-base \
&& apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
&& ldconfig
# Installing ANTs 2.3.4 (NeuroDocker build)
ENV ANTSPATH="/opt/ants"
WORKDIR $ANTSPATH
RUN curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" \
| tar -xzC $ANTSPATH --strip-components 1
ENV PATH="$ANTSPATH:$PATH"
# FSL 6.0.5.1
RUN curl -sSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.5.1-centos7_64.tar.gz | tar zxv --no-same-owner -C /opt \
--exclude='fsl/doc' \
--exclude='fsl/refdoc' \
--exclude='fsl/python/oxford_asl' \
--exclude='fsl/data/possum' \
--exclude='fsl/data/first' \
--exclude='fsl/data/mist' \
--exclude='fsl/data/atlases' \
--exclude='fsl/data/xtract_data' \
--exclude='fsl/extras/doc' \
--exclude='fsl/extras/man' \
--exclude='fsl/extras/src' \
--exclude='fsl/src' \
--exclude='fsl/tcl'
ENV FSLDIR="/opt/fsl" \
PATH="/opt/fsl/bin:$PATH" \
FSLOUTPUTTYPE="NIFTI_GZ" \
FSLMULTIFILEQUIT="TRUE" \
FSLTCLSH="/opt/fsl/bin/fsltclsh" \
FSLWISH="/opt/fsl/bin/fslwish" \
FSLLOCKDIR="" \
FSLMACHINELIST="" \
FSLREMOTECALL="" \
FSLGECUDAQ="cuda.q" \
POSSUMDIR="/opt/fsl" \
LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/opt/fsl"
# Unless otherwise specified each process should only use one thread - nipype
# will handle parallelization
ENV MKL_NUM_THREADS=1 \
OMP_NUM_THREADS=1
# Convert3D (neurodocker build)
RUN echo "Downloading Convert3D ..." \
&& mkdir -p /opt/convert3d-1.0.0 \
&& curl -fsSL --retry 5 https://sourceforge.net/projects/c3d/files/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz/download \
| tar -xz -C /opt/convert3d-1.0.0 --strip-components 1 \
--exclude "c3d-1.0.0-Linux-x86_64/lib" \
--exclude "c3d-1.0.0-Linux-x86_64/share" \
--exclude "c3d-1.0.0-Linux-x86_64/bin/c3d_gui"
ENV C3DPATH="/opt/convert3d-1.0.0" \
PATH="/opt/convert3d-1.0.0/bin:$PATH"
# Create a shared $HOME directory
RUN useradd -m -s /bin/bash -G users niworkflows
WORKDIR /home/niworkflows
ENV HOME="/home/niworkflows" \
LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH"
# Unless otherwise specified each process should only use one thread - nipype
# will handle parallelization
ENV MKL_NUM_THREADS=1 \
OMP_NUM_THREADS=1
WORKDIR /src/niworkflows/
COPY . /src/niworkflows/
ARG VERSION
RUN echo "${VERSION}" > /src/niworkflows/niworkflows/VERSION && \
echo "include niworkflows/VERSION" >> /src/niworkflows/MANIFEST.in && \
pip install --no-cache-dir -e .[all] && \
rm -rf $HOME/.cache/pip
COPY docker/files/nipype.cfg /home/niworkflows/.nipype/nipype.cfg
# Cleanup and ensure perms.
RUN rm -rf $HOME/.npm $HOME/.conda $HOME/.empty && \
find $HOME -type d -exec chmod go=u {} + && \
find $HOME -type f -exec chmod go=u {} +
# Final settings
WORKDIR /tmp
ARG BUILD_DATE
ARG VCS_REF
LABEL org.label-schema.build-date=$BUILD_DATE \
org.label-schema.name="niworkflows" \
org.label-schema.description="niworkflows - NeuroImaging workflows" \
org.label-schema.url="https://github.com/nipreps/niworkflows" \
org.label-schema.vcs-ref=$VCS_REF \
org.label-schema.vcs-url="https://github.com/nipreps/niworkflows" \
org.label-schema.version=$VERSION \
org.label-schema.schema-version="1.0"