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🔒 Replace md5 with sha384 for Dockerfile checksums
Ref #1922 (comment) ‒ #1922 (comment) [rebuild AFNI.23.0.07-bionic] [rebuild ANTs.2.4.3.Python3.10-bionic] [rebuild c3d.1.0.0-bionic] [rebuild connectome-workbench.1.5.0.neurodebian-bionic] [rebuild FSL.6.0.6.4-Python3.10-bionic] [rebuild FSL.data] [rebuild ICA-AROMA.0.4.4-beta-bionic] [rebuild msm.2.0-bionic] [rebuild Ubuntu.Python3.10-bionic-non-free]
1 parent cf7cbe1 commit 4b8c780

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‎.github/Dockerfiles/AFNI.23.0.07-bionic.Dockerfile‎

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@@ -3,7 +3,7 @@ USER root
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# install AFNI
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COPY dev/docker_data/required_afni_pkgs.txt /opt/required_afni_pkgs.txt
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COPY dev/docker_data/checksum/AFNI.23.0.07.md5 /tmp/AFNI.23.0.07.md5
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COPY dev/docker_data/checksum/AFNI.23.0.07.sha384 /tmp/AFNI.23.0.07.sha384
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RUN if [ -f /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0 ]; then \
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ln -svf /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0 /usr/lib/x86_64-linux-gnu/libGL.so.1; \
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fi \
@@ -22,7 +22,7 @@ RUN if [ -f /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0 ]; then \
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&& apt-get update && apt-get install -y libglw1-mesa-dev \
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&& AFNI_VERSION="23.0.07" \
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&& curl -LOJ https://github.com/afni/afni/archive/AFNI_${AFNI_VERSION}.tar.gz \
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&& md5sum --check /tmp/AFNI.23.0.07.md5 \
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&& sha384sum --check /tmp/AFNI.23.0.07.sha384 \
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&& mkdir /opt/afni \
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&& tar -xvf afni-AFNI_${AFNI_VERSION}.tar.gz -C /opt/afni --strip-components 1 \
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&& rm -rf afni-AFNI_${AFNI_VERSION}.tar.gz \

‎.github/Dockerfiles/ANTs.2.4.3.Python3.10-bionic.Dockerfile‎

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FROM ghcr.io/fcp-indi/c-pac/ubuntu:python3.10-bionic-non-free as ANTs
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USER root
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COPY dev/docker_data/checksum/ANTs.2.4.3.md5 /tmp/checksum.md5
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COPY dev/docker_data/checksum/ANTs.2.4.3.sha384 /tmp/checksum.sha384
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RUN curl -sL https://github.com/ANTsX/ANTs/releases/download/v2.4.3/ants-2.4.3-ubuntu-18.04-X64-gcc.zip -o /tmp/ANTs.zip \
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&& curl -sL https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/3133832/Oasis.zip -o /tmp/Oasis.zip \
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&& md5sum --check /tmp/checksum.md5 \
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&& sha384sum --check /tmp/checksum.sha384 \
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&& unzip /tmp/ANTs.zip -d /tmp \
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&& mkdir /usr/lib/ants \
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&& mv /tmp/ants-2.4.3/* /usr/lib/ants \

‎.github/Dockerfiles/FSL.6.0.6.4-Python3.10-bionic.Dockerfile‎

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@@ -31,15 +31,15 @@ ENV FSLDIR=/usr/share/fsl/6.0 \
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TZ=America/New_York
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# Installing and setting up FSL
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COPY dev/docker_data/checksum/FSL.6.0.6.4.md5 /tmp/checksum.md5
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COPY dev/docker_data/checksum/FSL.6.0.6.4.sha384 /tmp/checksum.sha384
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RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime \
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&& echo $TZ > /etc/timezone \
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&& apt-get update \
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&& apt-get install -y tclsh wish \
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&& echo "Downloading FSL ..." \
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&& mkdir -p /usr/share/fsl/6.0 \
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&& curl -sSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.4-centos6_64.tar.gz -o /tmp/fsl.tar.gz \
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&& md5sum --check /tmp/checksum.md5 \
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&& sha384sum --check /tmp/checksum.sha384 \
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&& tar zx -C /usr/share/fsl/6.0 --strip-components=1 \
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--exclude=fsl/bin/mist \
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--exclude=fsl/bin/possum \

‎.github/Dockerfiles/FSL.data.Dockerfile‎

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@@ -3,10 +3,10 @@ FROM ghcr.io/fcp-indi/c-pac/ubuntu:bionic-non-free AS FSL
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USER root
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# install CPAC resources into FSL
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COPY dev/docker_data/checksum/FSL.data.md5 /tmp/checksum.md5
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COPY dev/docker_data/checksum/FSL.data.sha384 /tmp/checksum.sha384
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RUN mkdir -p /fsl_data/atlases/HarvordOxford fsl_data/standard/tissuepriors \
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&& curl -sL http://fcon_1000.projects.nitrc.org/indi/cpac_resources.tar.gz -o /tmp/cpac_resources.tar.gz \
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&& md5sum --check /tmp/checksum.md5 \
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&& sha384sum --check /tmp/checksum.sha384 \
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&& tar xfz /tmp/cpac_resources.tar.gz -C /tmp \
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&& cp -n /tmp/cpac_image_resources/MNI_3mm/* /fsl_data/standard \
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&& cp -n /tmp/cpac_image_resources/MNI_4mm/* /fsl_data/standard \

‎.github/Dockerfiles/ICA-AROMA.0.4.4-beta-bionic.Dockerfile‎

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@@ -2,10 +2,10 @@ FROM ghcr.io/fcp-indi/c-pac/ubuntu:bionic-non-free AS ICA-AROMA
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USER root
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# install ICA-AROMA
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COPY dev/docker_data/checksum/ICA-AROMA.0.4.4.md5 /tmp/checksum.md5
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COPY dev/docker_data/checksum/ICA-AROMA.0.4.4.sha384 /tmp/checksum.sha384
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RUN mkdir -p /opt/ICA-AROMA \
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&& curl -sL https://github.com/rhr-pruim/ICA-AROMA/archive/v0.4.4-beta.tar.gz -o /tmp/ICA-AROMA.tar.gz \
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&& md5sum --check /tmp/checksum.md5 \
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&& sha384sum --check /tmp/checksum.sha384 \
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&& tar -xzC /opt/ICA-AROMA --strip-components 1 -f /tmp/ICA-AROMA.tar.gz \
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&& chmod +x /opt/ICA-AROMA/ICA_AROMA.py
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ENV PATH=/opt/ICA-AROMA:$PATH

‎.github/Dockerfiles/Ubuntu.Python3.10-bionic-non-free.Dockerfile‎

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@@ -126,17 +126,17 @@ RUN apt-get update \
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COPY requirements.txt /opt/requirements.txt
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COPY dev/docker_data/get-pip_23.0.1.py /tmp/get-pip.py
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COPY dev/docker_data/github_git-lfs.list /etc/apt/sources.list.d/github_git-lfs.list
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COPY dev/docker_data/checksum/Python3.10-bionic.md5 /tmp/checksum.md5
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COPY dev/docker_data/checksum/Python3.10-bionic.sha384 /tmp/checksum.sha384
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RUN python3.10 /tmp/get-pip.py \
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&& pip install --upgrade pip setuptools \
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&& pip install -r /opt/requirements.txt \
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# install git-lfs
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&& curl -fsSL https://packagecloud.io/github/git-lfs/gpgkey | gpg --dearmor > /etc/apt/trusted.gpg.d/github_git-lfs-archive-keyring.gpg \
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&& md5sum --check /tmp/checksum.md5 \
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&& sha384sum --check /tmp/checksum.sha384 \
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&& apt-get update \
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&& apt-get install -y --no-install-recommends git-lfs \
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&& git lfs install \
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&& rm /tmp/get-pip.py /tmp/checksum.md5
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&& rm /tmp/get-pip.py /tmp/checksum.sha384
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COPY --from=c-pac_templates /cpac_templates /cpac_templates
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COPY --from=dcan-hcp /opt/dcan-tools/pipeline/global /opt/dcan-tools/pipeline/global

‎.github/Dockerfiles/c3d.1.0.0-bionic.Dockerfile‎

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@@ -2,10 +2,10 @@ FROM ghcr.io/fcp-indi/c-pac/ubuntu:bionic-non-free as c3d
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USER root
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# Installing and setting up c3d
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COPY dev/docker_data/checksum/c3d.1.0.0.md5 /tmp/checksum.md5
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COPY dev/docker_data/checksum/c3d.1.0.0.sha384 /tmp/checksum.sha384
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RUN mkdir -p /opt/c3d && \
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curl -sSL "http://downloads.sourceforge.net/project/c3d/c3d/1.0.0/c3d-1.0.0-Linux-x86_64.tar.gz" -o /tmp/c3d.tar.gz \
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&& md5sum --check /tmp/checksum.md5 \
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&& sha384sum --check /tmp/checksum.sha384 \
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&& tar -xzC /opt/c3d --strip-components 1 -f /tmp/c3d.tar.gz
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ENV C3DPATH /opt/c3d/
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ENV PATH $C3DPATH/bin:$PATH

‎.github/Dockerfiles/connectome-workbench.1.5.0.neurodebian-bionic.Dockerfile‎

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@@ -2,9 +2,9 @@ FROM ghcr.io/fcp-indi/c-pac/ubuntu:python3.10-bionic-non-free as base
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USER root
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COPY dev/docker_data/checksum/connectome-workbench.1.5.0.md5 /tmp/checksum.md5
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COPY dev/docker_data/checksum/connectome-workbench.1.5.0.sha384 /tmp/checksum.sha384
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RUN curl -sSL "https://www.humanconnectome.org/storage/app/media/workbench/workbench-linux64-v1.5.0.zip" -o /opt/workbench.zip \
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&& md5sum --check /tmp/checksum.md5 \
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&& sha384sum --check /tmp/checksum.sha384 \
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&& unzip /opt/workbench.zip -d /opt \
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&& rm -rf /opt/workbench.zip
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ENV PATH $PATH:/opt/workbench/bin_linux64

‎.github/Dockerfiles/msm.2.0-bionic.Dockerfile‎

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@@ -13,10 +13,10 @@ RUN apt-get update \
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#---------------------
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# Install MSM Binaries
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#---------------------
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COPY dev/docker_data/checksum/msm.2.0.md5 /tmp/checksum.md5
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COPY dev/docker_data/checksum/msm.2.0.sha384 /tmp/checksum.sha384
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RUN mkdir /opt/msm \
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&& curl -ksSL --retry 5 https://www.doc.ic.ac.uk/~ecr05/MSM_HOCR_v2/MSM_HOCR_v2-download.tgz -o msm.tgz \
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&& md5sum --check /tmp/checksum.md5 \
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&& sha384sum --check /tmp/checksum.sha384 \
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&& tar zx -C /opt -f msm.tgz \
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&& mv /opt/homes/ecr05/MSM_HOCR_v2/* /opt/msm/ \
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&& rm -rf /opt/homes /opt/msm/MacOSX /opt/msm/Centos \

‎dev/docker_data/checksum/AFNI.23.0.07.md5‎

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