Require pysam>=0.21.0; fix mpileup call (#335) #8
Workflow file for this run
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| name: Build ariba images | |
| on: | |
| push: | |
| tags: | |
| - 'v*.*.*' | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| env: | |
| REGISTRY: ghcr.io | |
| IMAGE_NAME: ${{ github.repository }} | |
| jobs: | |
| build: | |
| name: Build | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Set up Go 1.16 | |
| uses: actions/setup-go@v1 | |
| with: | |
| go-version: 1.16 | |
| id: go | |
| - name: Install Dependencies | |
| run: | | |
| sudo apt-get update && sudo apt-get install -y \ | |
| build-essential \ | |
| libssl-dev \ | |
| uuid-dev \ | |
| libgpgme11-dev \ | |
| squashfs-tools \ | |
| libseccomp-dev \ | |
| pkg-config \ | |
| debootstrap \ | |
| debian-keyring \ | |
| debian-archive-keyring \ | |
| rsync | |
| - name: Install Singularity | |
| env: | |
| SINGULARITY_VERSION: 3.5.3 | |
| GOPATH: /tmp/go | |
| run: | | |
| mkdir -p $GOPATH | |
| sudo mkdir -p /usr/local/var/singularity/mnt | |
| mkdir -p $GOPATH/src/github.com/sylabs | |
| cd $GOPATH/src/github.com/sylabs | |
| wget https://github.com/hpcng/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-${SINGULARITY_VERSION}.tar.gz | |
| tar -xzf singularity-${SINGULARITY_VERSION}.tar.gz | |
| cd singularity | |
| ./mconfig -v -p /usr/local | |
| make -j `nproc 2>/dev/null || echo 1` -C ./builddir all | |
| sudo make -C ./builddir install | |
| - name: Check out code for the container build | |
| uses: actions/checkout@v2 | |
| - name: Set release version if is a release | |
| if: startsWith(github.event.ref, 'refs/tags/v') | |
| run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV | |
| - name: Set release version if not a release | |
| if: false == startsWith(github.event.ref, 'refs/tags/v') | |
| run: echo "RELEASE_VERSION=test" >> $GITHUB_ENV | |
| - name: Build Singularity container | |
| env: | |
| SINGULARITY_RECIPE: Singularity.def | |
| OUTPUT_CONTAINER: ariba_${{env.RELEASE_VERSION}}.img | |
| run: | | |
| ls | |
| if [ -f "${SINGULARITY_RECIPE}" ]; then | |
| sudo -E singularity build ${OUTPUT_CONTAINER} ${SINGULARITY_RECIPE} | |
| else | |
| echo "${SINGULARITY_RECIPE} is not found." | |
| echo "Present working directory: $PWD" | |
| ls | |
| fi | |
| - name: Release | |
| if: startsWith(github.event.ref, 'refs/tags/v') | |
| uses: softprops/action-gh-release@v1 | |
| with: | |
| files: ariba*.img | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Log in to github container registry | |
| if: startsWith(github.event.ref, 'refs/tags/v') | |
| uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9 | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Extract metadata (tags, labels) for Docker | |
| if: startsWith(github.event.ref, 'refs/tags/v') | |
| id: meta | |
| uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 | |
| with: | |
| images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} | |
| - name: Build and push Docker image | |
| if: startsWith(github.event.ref, 'refs/tags/v') | |
| uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc | |
| with: | |
| context: . | |
| push: true | |
| tags: ${{ steps.meta.outputs.tags }} | |
| labels: ${{ steps.meta.outputs.labels }} |