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FSL.5.0.9-5.neurodebian-xenial.Dockerfile
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# Copyright (C) 2021-2023 C-PAC Developers
# This file is part of C-PAC.
# C-PAC is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or (at your
# option) any later version.
# C-PAC is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
# License for more details.
# You should have received a copy of the GNU Lesser General Public
# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
FROM ghcr.io/fcp-indi/c-pac/fsl:data as data
FROM ghcr.io/fcp-indi/c-pac/ubuntu:xenial-20200114 as FSL
USER root
ARG DEBIAN_FRONTEND=noninteractive
COPY .github/scripts/make_real.sh /
# install FSL
RUN apt-get update && \
apt-get install -y --no-install-recommends \
fsl-core=5.0.9-5~nd16.04+1 \
fsl-atlases \
fsl-mni152-templates=5.0.7-2 && \
/make_real.sh "/usr/share/fsl/5.0/data"
# setup FSL environment
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:$LD_LIBRARY_PATH \
FSLTCLSH=/usr/bin/tclsh \
FSLWISH=/usr/bin/wish \
AFNI_MODELPATH="/usr/lib/afni/models" \
AFNI_IMSAVE_WARNINGS="NO" \
AFNI_TTATLAS_DATASET="/usr/share/afni/atlases" \
AFNI_PLUGINPATH="/usr/lib/afni/plugins" \
PATH=/usr/lib/fsl/5.0:$PATH
ENTRYPOINT ["/bin/bash"]
# Link libraries for Singularity images
RUN ldconfig && \
apt-get clean && \
apt-get autoremove -y && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
FROM scratch
LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \
FSL 5.0.9-5 stage"
LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC
COPY --from=FSL /etc/fsl /etc/fsl
COPY --from=FSL /usr/lib/fsl /usr/lib/fsl
COPY --from=FSL /usr/lib/libnewmat.so.10 /usr/lib/libnewmat.so.10
COPY --from=FSL /lib/x86_64-linux-gnu/lib*so* /lib/x86_64-linux-gnu/
COPY --from=FSL /usr/lib/libniftiio.so.2 /usr/lib/libniftiio.so.2
COPY --from=FSL /usr/lib/libznz.so.2 /usr/lib/libznz.so.2
COPY --from=FSL /usr/share/doc/fsl-core /usr/share/doc/fsl-core
COPY --from=FSL /usr/share/man/man1/fsl-5.0-core.1.gz /usr/share/man/man1/
COPY --from=FSL /usr/share/man/man1/fsl.1.gz /usr/share/man/man1/
COPY --from=FSL /usr/share/fsl /usr/share/fsl
# install C-PAC resources into FSL
COPY --from=data /fsl_data/standard /usr/share/fsl/5.0/data/standard
COPY --from=data /fsl_data/atlases /usr/share/fsl/5.0/data/atlases