Merge branch 'master' of https://github.com/vastgroup/vast-tools #18
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| name: Publish Docker image (latest) | |
| on: | |
| workflow_dispatch: | |
| push: | |
| branches: | |
| # Default branches below | |
| - main | |
| - master | |
| jobs: | |
| push_to_registries: | |
| name: Push Docker image to multiple registries | |
| runs-on: ubuntu-latest | |
| permissions: | |
| packages: write | |
| contents: read | |
| steps: | |
| - | |
| name: Checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| - | |
| name: Set up QEMU | |
| uses: docker/setup-qemu-action@v2 | |
| - | |
| name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Log in to Docker Hub | |
| uses: docker/login-action@v2 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Log in to GitHub Docker Registry | |
| uses: docker/login-action@v2 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - | |
| name: Build Docker | |
| uses: docker/build-push-action@v3 | |
| with: | |
| context: . | |
| platforms: linux/amd64,linux/arm64 | |
| push: true | |
| tags: ghcr.io/${{ github.repository_owner }}/vast-tools:latest | |
| - | |
| name: Sleep for 30 seconds | |
| uses: whatnick/wait-action@master | |
| with: | |
| time: '30s' | |
| - | |
| name: Testing Docker image | |
| uses: addnab/docker-run-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| image: ${{ github.repository_owner }}/vast-tools:latest | |
| options: -v ${{ github.workspace }}/db:/VASTDB -v ${{ github.workspace }}/share:/share -v ${{ github.workspace }}/tests:/tests | |
| run: | | |
| echo "Download DB" | |
| cd /VASTDB | |
| curl --silent --remote-name https://vastdb.crg.eu/libs/vastdb.hsa.16.02.18.tar.gz | |
| tar zxf vastdb.hsa.16.02.18.tar.gz | |
| rm vastdb.hsa.16.02.18.tar.gz | |
| echo "Running test" | |
| mkdir -p /share/reads | |
| mkdir -p /share/out | |
| cp /tests/data/NewFQ_Test_Hsa-51/NewFQ_Test_Hsa-51.fq.gz /share/reads | |
| vast-tools align /share/reads/NewFQ_Test_Hsa-51.fq.gz -sp Hsa --expr -o /share/out/test | |
| bash /tests/tests.sh /tests/data /share/out/test | |
| - | |
| name: Push Docker | |
| uses: docker/build-push-action@v3 | |
| with: | |
| context: . | |
| platforms: linux/amd64,linux/arm64 | |
| push: true | |
| tags: | | |
| ${{ secrets.DOCKERHUB_ACCOUNT }}/vast-tools:latest | |
| ghcr.io/${{ github.repository_owner }}/vast-tools:latest |