Add diskcache and update pybedtools #226
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # Thid workflow will build and push the import pipeline container. | |
| # the plan later will be to include unit tests as well | |
| name: Building Pipeline Containers | |
| on: | |
| push: | |
| branches: ['dev','python-update'] | |
| paths: ['pyproject.toml', 'poetry.lock', 'Cargo.toml', 'Cargo.lock', 'Dockerfile', 'utils/**'] | |
| jobs: | |
| starting-notification: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Intital notification | |
| uses: rtCamp/action-slack-notify@v2 | |
| env: | |
| SLACK_MESSAGE: 'Creating new pipeline image in docker hub' | |
| SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }} | |
| MSG_MINIMAL: true | |
| create-docker-image: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: docker login | |
| env: | |
| DOCKER_USER: ${{ secrets.DOCKER_USER }} | |
| DOCKER_PASSWORD: ${{ secrets.DOCKER_PASSWORD }} | |
| run: docker login -u $DOCKER_USER -p $DOCKER_PASSWORD | |
| - name: docker build | |
| run: docker build -f Dockerfile -t rnacentral/rnacentral-import-pipeline:latest . | |
| - name: docker push | |
| run: docker push rnacentral/rnacentral-import-pipeline:latest | |
| finished-notification: | |
| needs: | |
| - create-docker-image | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Finished notification | |
| uses: rtCamp/action-slack-notify@v2 | |
| env: | |
| SLACK_MESSAGE: 'New pipeline image pushed to docker hub' | |
| SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }} | |
| MSG_MINIMAL: true | |
| singularity-conversion: | |
| needs: | |
| - create-docker-image | |
| uses: rnacentral/rnacentral-import-pipeline/.github/workflows/singularity.yaml@dev | |
| secrets: inherit | |
| finished-singularity: | |
| needs: | |
| - singularity-conversion | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Finished notification | |
| uses: rtCamp/action-slack-notify@v2 | |
| env: | |
| SLACK_MESSAGE: 'New singularity image pushed to ghcr' | |
| SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }} | |
| MSG_MINIMAL: true |