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# Copyright (C) 2023 C-PAC Developers | ||
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# This file is part of C-PAC. | ||
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# 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. | ||
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# 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. | ||
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# 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:6.0.6.5-jammy as FSL | ||
FROM ghcr.io/fcp-indi/c-pac/ubuntu:jammy-non-free as AFNI | ||
USER root | ||
ENV AFNI_VERSION="23.1.10" | ||
# To use the same Python environment to share common libraries | ||
COPY --from=FSL /usr/share/fsl/6.0 /usr/share/fsl/6.0 | ||
ENV FSLDIR=/usr/share/fsl/6.0 \ | ||
PATH=/usr/share/fsl/6.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin \ | ||
LD_LIBRARY_PATH=/usr/share/fsl/6.0/lib:$LD_LIBRARY_PATH | ||
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# install AFNI | ||
COPY dev/docker_data/required_afni_pkgs.txt /opt/required_afni_pkgs.txt | ||
COPY dev/docker_data/checksum/AFNI.23.1.10.sha384 /tmp/AFNI.23.1.10.sha384 | ||
RUN apt-get update \ | ||
&& apt-get install -y --no-install-recommends \ | ||
apt-transport-https \ | ||
bc \ | ||
bzip2 \ | ||
cmake \ | ||
curl \ | ||
dh-autoreconf \ | ||
eog \ | ||
evince \ | ||
firefox \ | ||
gedit \ | ||
git \ | ||
gnome-terminal \ | ||
gnome-tweaks \ | ||
gnupg \ | ||
gsl-bin \ | ||
libcanberra-gtk-module \ | ||
libcurl4-openssl-dev \ | ||
libexpat1-dev \ | ||
libgdal-dev \ | ||
libgfortran-11-dev \ | ||
libgiftiio-dev \ | ||
libgl1-mesa-dri \ | ||
libglu1-mesa \ | ||
libglu1-mesa-dev \ | ||
libglw1-mesa \ | ||
libglw1-mesa-dev \ | ||
libgomp1 \ | ||
libgsl-dev \ | ||
libjpeg-progs \ | ||
libjpeg62 \ | ||
libmotif-dev \ | ||
libnode-dev \ | ||
libopenblas-dev \ | ||
libssl-dev \ | ||
libtool \ | ||
libudunits2-dev \ | ||
libx11-dev \ | ||
libxext-dev \ | ||
libxft-dev \ | ||
libxft2 \ | ||
libxi-dev \ | ||
libxm4 \ | ||
libxml2 \ | ||
libxml2-dev \ | ||
libxmu-dev \ | ||
libxmu-headers \ | ||
libxpm-dev \ | ||
libxslt1-dev \ | ||
m4 \ | ||
mesa-common-dev \ | ||
mesa-utils \ | ||
nautilus \ | ||
netpbm \ | ||
ninja-build \ | ||
openssh-client \ | ||
pkg-config \ | ||
r-base-dev \ | ||
rsync \ | ||
software-properties-common \ | ||
tcsh \ | ||
unzip \ | ||
vim \ | ||
wget \ | ||
x11proto-xext-dev \ | ||
xauth \ | ||
xfonts-100dpi \ | ||
xfonts-base \ | ||
xterm \ | ||
xutils-dev \ | ||
xvfb \ | ||
zlib1g-dev \ | ||
&& curl -LOJ https://github.com/afni/afni/archive/AFNI_${AFNI_VERSION}.tar.gz \ | ||
&& sha384sum --check /tmp/AFNI.23.1.10.sha384 \ | ||
&& ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.27 /usr/lib/x86_64-linux-gnu/libgsl.so.19 \ | ||
&& mkdir /opt/afni \ | ||
&& tar -xvf afni-AFNI_${AFNI_VERSION}.tar.gz -C /opt/afni --strip-components 1 \ | ||
&& rm -rf afni-AFNI_${AFNI_VERSION}.tar.gz \ | ||
# Fix GLwDrawA per https://github.com/afni/afni/blob/AFNI_23.1.10/src/other_builds/OS_notes.linux_fedora_25_64.txt | ||
&& cd /usr/include/GL \ | ||
&& mv GLwDrawA.h GLwDrawA.h.orig \ | ||
&& sed 's/GLAPI WidgetClass/extern GLAPI WidgetClass/' GLwDrawA.h.orig > GLwDrawA.h \ | ||
&& cd /opt/afni/src \ | ||
&& sed '/^INSTALLDIR =/c INSTALLDIR = /opt/afni' other_builds/Makefile.linux_ubuntu_22_64 > Makefile \ | ||
&& make vastness && make cleanest \ | ||
&& cd /opt/afni \ | ||
# filter down to required packages | ||
ls > full_ls \ | ||
&& sed 's/linux_openmp_64\///g' /opt/required_afni_pkgs.txt | sort > required_ls \ | ||
&& comm -2 -3 full_ls required_ls | xargs rm -rf full_ls required_ls \ | ||
# get rid of stuff we just needed for building | ||
&& apt-get remove -y \ | ||
bzip2 \ | ||
cmake \ | ||
curl \ | ||
dh-autoreconf \ | ||
evince \ | ||
firefox \ | ||
gedit \ | ||
git \ | ||
gnome-terminal \ | ||
gnome-tweaks \ | ||
libglw1-mesa-dev \ | ||
m4 \ | ||
ninja-build \ | ||
openssh-client \ | ||
unzip \ | ||
wget \ | ||
xterm \ | ||
&& ldconfig \ | ||
&& rm -rf /opt/afni/src | ||
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# set up AFNI | ||
ENV PATH=/opt/afni:$PATH | ||
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ENTRYPOINT ["/bin/bash"] | ||
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# Link libraries for Singularity images | ||
RUN ldconfig | ||
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RUN apt-get clean \ | ||
&& apt-get autoremove -y \ | ||
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/* | ||
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FROM scratch | ||
LABEL org.opencontainers.image.description "NOT INTENDED FOR USE OTHER THAN AS A STAGE IMAGE IN A MULTI-STAGE BUILD \ | ||
AFNI 23.1.10 (Publius Helvius Pertinax) stage" | ||
LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC | ||
COPY --from=AFNI /lib/x86_64-linux-gnu/ld* /lib/x86_64-linux-gnu/ | ||
COPY --from=AFNI /lib/x86_64-linux-gnu/lib*so* /lib/x86_64-linux-gnu/ | ||
COPY --from=AFNI /lib64/ld* /lib64/ | ||
COPY --from=AFNI /opt/afni/ /opt/afni/ |
18 changes: 17 additions & 1 deletion
18
...s/ANTs.2.4.3.Python3.10-bionic.Dockerfile → ...b/Dockerfiles/ANTs.2.4.3-jammy.Dockerfile
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# Copyright (C) 2022-2023 C-PAC Developers | ||
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# This file is part of C-PAC. | ||
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# 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. | ||
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||
# 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. | ||
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# 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/stage-base:standard-v1.8.6.dev1 | ||
LABEL org.opencontainers.image.description "Full C-PAC image" | ||
LABEL org.opencontainers.image.source https://github.com/FCP-INDI/C-PAC | ||
USER root | ||
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# install C-PAC | ||
COPY dev/circleci_data/pipe-test_ci.yml /cpac_resources/pipe-test_ci.yml | ||
COPY . /code | ||
RUN pip cache purge && pip install -e /code | ||
# set up runscript | ||
COPY dev/docker_data /code/docker_data | ||
RUN rm -Rf /code/docker_data/checksum && \ | ||
mv /code/docker_data/* /code && \ | ||
rm -Rf /code/docker_data && \ | ||
chmod +x /code/run.py && \ | ||
chmod +x /code/run-with-freesurfer.sh | ||
ENTRYPOINT ["/code/run-with-freesurfer.sh"] | ||
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# link libraries & clean up | ||
# link libraries & clean up | ||
RUN rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /root/.cache/* \ | ||
&& find / -type f -print0 | sort -t/ -k2 | xargs -0 rdfind -makehardlinks true \ | ||
&& rm -rf results.txt \ | ||
&& apt-get remove rdfind -y \ | ||
&& apt-get clean \ | ||
&& apt-get autoremove -y \ | ||
&& ldconfig \ | ||
&& chmod 777 / \ | ||
&& chmod 777 $(ls / | grep -v sys | grep -v proc) | ||
ENV PYTHONUSERBASE=/home/c-pac_user/.local | ||
ENV PATH=$PATH:/home/c-pac_user/.local/bin \ | ||
PYTHONPATH=$PYTHONPATH:$PYTHONUSERBASE/lib/python3.10/site-packages | ||
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# set user | ||
# USER c-pac_user |
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