refactor initial commit
This commit is contained in:
bpinsard
commit
59e04d6e90
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image: docker:20.10.16
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variables:
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# When you use the dind service, you must instruct Docker to talk with
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# the daemon started inside of the service. The daemon is available
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# with a network connection instead of the default
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# /var/run/docker.sock socket. Docker 19.03 does this automatically
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# by setting the DOCKER_HOST in
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# https://github.com/docker-library/docker/blob/d45051476babc297257df490d22cbd806f1b11e4/19.03/docker-entrypoint.sh#L23-L29
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#
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# The 'docker' hostname is the alias of the service container as described at
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# https://docs.gitlab.com/ee/ci/services/#accessing-the-services.
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#
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# Specify to Docker where to create the certificates. Docker
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# creates them automatically on boot, and creates
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# `/certs/client` to share between the service and job
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# container, thanks to volume mount from config.toml
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DOCKER_TLS_CERTDIR: "/certs"
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services:
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- name: docker:20.10.16-dind
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# command: ["--registry-mirror", "http://maple.criugm.qc.ca:5000" ] # Specify the registry mirror to use
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stages:
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- build
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.build_tpl:
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stage: build
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script:
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- export IMAGE_TAG=$IMAGE:$CI_COMMIT_REF_SLUG
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- echo $CI_REGISTRY_USER $CI_REGISTRY $IMAGE_TAG
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- docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
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- docker pull $IMAGE:latest || true
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- docker build --cache-from $IMAGE:latest -t $IMAGE:$CI_COMMIT_SHA -t $IMAGE:$CI_COMMIT_SHORT_SHA -t $IMAGE_TAG -t $IMAGE:latest ./docker/datalad-docker
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- docker push --all-tags $IMAGE
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build_docker-datalad:
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extends: .build_tpl
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variables:
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IMAGE: $CI_REGISTRY_IMAGE/docker-datalad
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rules:
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- changes:
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- docker/datalad-docker/**/*
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- .gitlab-ci.yml
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build_datalad-apptainer:
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extends: .build_tpl
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variables:
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IMAGE: $CI_REGISTRY_IMAGE/datalad-apptainer
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rules:
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- changes:
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- docker/datalad-apptainer/**/*
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- .gitlab-ci.yml
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build_heudiconv:
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extends: .build_tpl
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variables:
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IMAGE: $CI_REGISTRY_IMAGE/heudiconv
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rules:
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- changes:
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- docker/heudiconv/**/*
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- .gitlab-ci.yml
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build_deface:
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extends: .build_tpl
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variables:
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IMAGE: $CI_REGISTRY_IMAGE/deface
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rules:
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- changes:
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- docker/deface/**/*
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- .gitlab-ci.yml
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build_pydeface:
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extends: .build_tpl
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variables:
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IMAGE: $CI_REGISTRY_IMAGE/pydeface
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rules:
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- changes:
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- docker/pydeface/**/*
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- .gitlab-ci.yml
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# ni-dataops containers
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This repo contains builds of containers used in the ci-pipelines
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To build these, it requires a docker-in-docker runner.
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Any changes to Dockerfile or folder of a container should trigger a rebuild and push to gitlab registry.
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## datalad-apptainer
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A simple lightweight container (alpine-based) that contains datalad, datalad-containers and apptainer.
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It's an apptainer-in-docker setup, which avoids caveats of using docker-in-docker (DinD), and allow to use community or custom containers made for rootless HPC usage.
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That simple env allows notably to run ReproNim bids-app on bids repos but could also run other apptainer images.
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## datalad-docker
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Not currently used, replaced by datalad-apptainer.
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## heudiconv
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Container used for the dicom to BIDS conversion.
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## deface
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Custom defacing
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## pydeface
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Not currently used.
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FROM golang:1.20.1-alpine3.17 as builder
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RUN apk add --no-cache \
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# Required for apptainer to find min go version
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bash \
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cryptsetup \
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gawk \
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gcc \
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git \
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libc-dev \
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linux-headers \
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libressl-dev \
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libuuid \
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libseccomp-dev \
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make \
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util-linux-dev
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ARG APPTAINER_COMMITISH="main"
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ARG MCONFIG_OPTIONS="--with-suid"
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WORKDIR $GOPATH/src/github.com/apptainer
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RUN git clone https://github.com/apptainer/apptainer.git \
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&& cd apptainer \
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&& git checkout "$APPTAINER_COMMITISH" \
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&& ./mconfig $MCONFIG_OPTIONS -p /usr/local/apptainer \
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&& cd builddir \
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&& make \
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&& make install
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FROM alpine:3.17.2
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COPY --from=builder /usr/local/apptainer /usr/local/apptainer
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ENV PATH="/usr/local/apptainer/bin:$PATH" \
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APPTAINER_TMPDIR="/tmp-apptainer"
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RUN apk add --no-cache ca-certificates libseccomp squashfs-tools tzdata fuse2fs fuse-overlayfs \
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python3 py3-pip git openssh-client git-annex curl bzip2 bash glab\
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&& mkdir -p $APPTAINER_TMPDIR \
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&& cp /usr/share/zoneinfo/UTC /etc/localtime \
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&& apk del tzdata \
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&& rm -rf /tmp/* /var/cache/apk/*
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RUN apk add --no-cache squashfuse --repository=https://dl-cdn.alpinelinux.org/alpine/edge/testing
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RUN pip install --no-cache-dir datalad datalad-container pytest ssh_agent_setup python-gitlab
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WORKDIR /work
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@ -0,0 +1,4 @@
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FROM docker:20.10.16
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RUN apk add git git-annex python3 py3-pip p7zip glab
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RUN pip install --no-cache-dir datalad datalad-container python-gitlab
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@ -0,0 +1,13 @@
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FROM python:3.8-slim
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RUN apt-get update \
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&& apt-get -y install git git-annex build-essential\
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&& apt-get autoremove && apt-get clean && rm -rf /var/lib/apt/lists/*
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RUN git clone https://github.com/courtois-neuromod/ds_prep.git && \
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cd ds_prep && git checkout gitlab && \
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pip install --no-cache-dir packaging datalad && \
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pip install --no-cache-dir -r requirements.txt
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RUN git config --global user.name docker_bot && \
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git config --global user.email docket_bot@dummy.net
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RUN cd /ds_prep && \
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datalad get global/templates/*.nii.gz
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@ -0,0 +1,14 @@
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FROM python:3.10-slim
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RUN apt-get update \
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&& apt-get -y install 7zip curl git git-annex dcm2niix \
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&& apt-get autoremove && apt-get clean && rm -rf /var/lib/apt/lists/*
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ARG GLAB_VERSION=1.25.3
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RUN curl -O -L https://gitlab.com/gitlab-org/cli/-/releases/v${GLAB_VERSION}/downloads/glab_${GLAB_VERSION}_Linux_x86_64.deb \
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&& dpkg -i glab_${GLAB_VERSION}_Linux_x86_64.deb \
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&& rm -f glab_${GLAB_VERSION}_Linux_x86_64.deb
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RUN ln -s /usr/bin/7zz /usr/bin/7z
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RUN pip install --no-cache-dir frozendict bids datalad
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RUN pip install --no-cache-dir git+https://github.com/UNFmontreal/heudiconv@enh-custom-seqinfo
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@ -0,0 +1,32 @@
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FROM nipreps/fmriprep:unstable as fsl_source
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FROM python:3.10-slim
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COPY --from=fsl_source /opt/conda/envs/fmriprep/bin/flirt /opt/fsl/bin/
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COPY --from=fsl_source /opt/conda/envs/fmriprep/lib/libquadmath.so.0.0.0 /opt/fsl/lib/
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COPY --from=fsl_source /opt/conda/envs/fmriprep/lib/libgfortran.so.5.0.0 /opt/fsl/lib/
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COPY --from=fsl_source /opt/conda/envs/fmriprep/lib/libfsl-NewNifti.so /opt/fsl/lib/
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COPY --from=fsl_source /opt/conda/envs/fmriprep/lib/libfsl-cprob.so /opt/fsl/lib/
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COPY --from=fsl_source /opt/conda/envs/fmriprep/lib/libfsl-miscmaths.so /opt/fsl/lib/
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COPY --from=fsl_source /opt/conda/envs/fmriprep/lib/libfsl-newimage.so /opt/fsl/lib/
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COPY --from=fsl_source /opt/conda/envs/fmriprep/lib/libfsl-utils.so /opt/fsl/lib/
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COPY --from=fsl_source /opt/conda/envs/fmriprep/lib/libfsl-znz.so /opt/fsl/lib/
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COPY --from=fsl_source /opt/conda/envs/fmriprep/lib/libgcc_s.so.1 /opt/fsl/lib/
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COPY --from=fsl_source /opt/conda/envs/fmriprep/lib/libopenblasp-r0.3.23.so /opt/fsl/lib/
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COPY --from=fsl_source /opt/conda/envs/fmriprep/lib/libstdc++.so.6.0.31 /opt/fsl/lib/
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COPY --from=fsl_source /opt/conda/envs/fmriprep/lib/libz.so.1.2.13 /opt/fsl/lib/
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RUN ln -s libopenblasp-r0.3.23.so /opt/fsl/lib/liblapack.so.3
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RUN ln -s libopenblasp-r0.3.23.so /opt/fsl/lib/libblas.so.3
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RUN ln -s libquadmath.so.0.0.0 /opt/fsl/lib/libquadmath.so.0
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RUN ln -s libgfortran.so.5.0.0 /opt/fsl/lib/libgfortran.so.5
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RUN ln -s libstdc++.so.6.0.31 /opt/fsl/lib/libstdc++.so.6
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RUN ln -s libz.so.1.2.13 /opt/fsl/lib/libz.so.1
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ENV LD_LIBRARY_PATH=/opt/fsl/lib
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RUN pip --no-cache-dir install pydeface
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ENV PATH=$PATH:/opt/fsl/bin
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ENV FSLDIR=/opt/fsl/bin
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RUN sed -i "s/shutil.which('fsl')/shutil.which('flirt')/g" /usr/local/lib/python3.10/site-packages/pydeface/utils.py
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