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| name: Singularity Build | ||
| on: | ||
| push: | ||
| tags: | ||
| - sif-* | ||
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| jobs: | ||
| build-and-push-image: | ||
| runs-on: ubuntu-latest | ||
| name: Build Apptainer image | ||
| permissions: | ||
| contents: read | ||
| packages: write | ||
| steps: | ||
| - name: Install Apptainer | ||
| run: deb=$(curl -w "%{filename_effective}" -LO https://github.com/apptainer/apptainer/releases/download/v1.2.4/apptainer_1.2.4_amd64.deb) && sudo apt install -y "./$deb"; rm -f "$deb"; unset deb | ||
| - name: Check out code for the container build | ||
| uses: actions/checkout@v4 | ||
| - name: Build Container | ||
| run: | | ||
| cont_name="${GITHUB_REF_NAME#sif-}" | ||
| echo "Container name is ${cont_name:-}." | ||
| [ -d "${cont_name:-}" ] || exit 1 | ||
| pushd "${cont_name}" && apptainer build --fakeroot --fix-perms --warn-unused-build-args --build-arg ORAS_REPO="${{ github.repository }}" ../${cont_name}.sif Singularity && popd | ||
| tag="${tag:-latest}" | ||
| echo "Tag is $tag." | ||
| echo "tag=$tag" >> $GITHUB_ENV | ||
| echo "cont_name=$cont_name" >> $GITHUB_ENV | ||
| popd | ||
| - name: Login and Deploy Container | ||
| run: | | ||
| [ -r "${cont_name}.sif" ] || exit 1 | ||
| apptainer remote login -u ${{ github.actor }} -p ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io | ||
| apptainer push "${cont_name}.sif" oras://ghcr.io/${{ github.repository }}/${cont_name}:${tag} | ||
| rm -f "${cont_name}.sif" | ||
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| # Building the containers on GitHub Actions | ||
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| The containers are built using GitHub Actions. The workflow is defined in [`.github/workflows/apptainer-image.yml`](.github/workflows/apptainer-image.yml). | ||
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| The workflow is triggered on every push with the tag `sif-<containername>`. It builds the named container and pushes it to the GitHub Container Registry. | ||
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| Before containers that depend on other containers can be built, the dependent containers must be built and pushed to the registry. So, if `ubuntu22.04_turbovnc` depends on `ubuntu22.04_interactive`, you must first push a commit with the tag `sif-ubuntu22.04_interactive` for it to be built. Then, you can push a commit with the tag `sif-ubuntu22.04_turbovnc`. | ||
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| #!/bin/sh | ||
| # Install FreeSurfer: | ||
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| export FREESURFER_VERSION="${FREESURFER_VERSION:-7.4.1}" | ||
| FREESURFER_DOWNLOAD_ROOT="https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/${FREESURFER_VERSION}" | ||
| export FREESURFER_HOME="${FREESURFER_HOME:-/usr/local/freesurfer/${FREESURFER_VERSION}}" | ||
| export FREESURFER_DOWNLOAD_URL="${FREESURFER_DOWNLOAD_URL:-}" | ||
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| if ! command -v curl >/dev/null 2>&1; then | ||
| echo "warning: curl not found!" >&2 | ||
| exit 1 | ||
| fi | ||
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| if [ -z "${FREESURFER_DOWNLOAD_URL:-}" ]; then | ||
| if command -v dpkg >/dev/null 2>&1; then | ||
| # Is Debian/Ubuntu. Package filename looks like turbovnc_3.0.91_arm64.deb | ||
| arch="$(dpkg --print-architecture)" | ||
| if [ -r /etc/os-release ]; then | ||
| . /etc/os-release | ||
| elif [ -r /usr/lib/os-release ]; then | ||
| . /usr/lib/os-release | ||
| else | ||
| echo >&2 "error: cannot determine OS release" | ||
| exit 1 | ||
| fi | ||
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| case "${ID:-} ${ID_LIKE:-}" in | ||
| *ubuntu*) echo "Running on an Ubuntu-like platform, using Ubuntu .deb packages" ;; | ||
| *) | ||
| echo >&2 "Error: Must be Ubuntu-like" | ||
| exit 1 | ||
| ;; | ||
| esac | ||
| ubuntu_major_version="${VERSION_ID%%.*}" | ||
| [ -z "${ubuntu_major_version:-}" ] && { | ||
| echo >&2 "error: cannot determine Ubuntu major version" | ||
| exit 1 | ||
| } | ||
| filename="freesurfer_ubuntu${ubuntu_major_version}-${FREESURFER_VERSION}_${arch}.deb" | ||
| elif command -v yum >/dev/null 2>&1; then | ||
| # Is RHEL/CentOS/Rocky. Package filename looks like turbovnc-3.0.91.x86_64.rpm | ||
| arch="$(uname -m)" | ||
| if [ -r /etc/os-release ]; then | ||
| . /etc/os-release | ||
| elif [ -r /usr/lib/os-release ]; then | ||
| . /usr/lib/os-release | ||
| else | ||
| echo >&2 "error: cannot determine OS release" | ||
| exit 1 | ||
| fi | ||
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| case "${ID:-} ${ID_LIKE:-}" in | ||
| *rhel* | *centos* | *fedora* | *rocky*) echo "Running on an CentOS-like platform, using CentOS .rpm packages" ;; | ||
| *) | ||
| echo >&2 "Error: Must be CentOS-like" | ||
| exit 1 | ||
| ;; | ||
| esac | ||
| centos_major_version="${VERSION_ID%%.*}" | ||
| [ -z "${centos_major_version:-}" ] && { | ||
| echo >&2 "error: cannot determine CentOS major version" | ||
| exit 1 | ||
| } | ||
| filename="freesurfer_CentOS${centos_major_version}-${FREESURFER_VERSION}.${arch}.rpm" | ||
| else | ||
| echo >&2 "error: cannot determine architecture and package extension for this OS" | ||
| exit 1 | ||
| fi | ||
| FREESURFER_DOWNLOAD_URL="${FREESURFER_DOWNLOAD_ROOT}/${filename}" | ||
| fi | ||
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| echo "Downloading ${TURBOVNC_DOWNLOAD_URL}..." | ||
| dlpath=$(curl -w "%{filename_effective}" -fLO "${TURBOVNC_DOWNLOAD_URL}") | ||
| trap 'rm -f "${dlpath:-}"' INT QUIT TERM EXIT | ||
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| if [ -r "${dlpath}" ]; then | ||
| if command -v dpkg >/dev/null 2>&1; then | ||
| # Is Debian/Ubuntu | ||
| dpkg --install --force-depends "${dlpath:-}" && apt-get install --fix-broken --yes --quiet && export success=1 || echo >&2 "warning: failed to install ${dlpath} via yum" | ||
| elif command -v yum >/dev/null 2>&1; then | ||
| # Is RHEL/CentOS/Rocky | ||
| yum install -y -q "${dlpath}" && export success=1 || echo >&2 "warning: failed to install ${dlpath} via yum" | ||
| else | ||
| echo >&2 "Cannot determine package manager for this OS" | ||
| fi | ||
| fi | ||
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| [ -n "${success:-}" ] && exit 0 || exit 1 |
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