biocontainers import #169
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
| name: biocontainers import | |
| on: | |
| schedule: | |
| - cron: "0 0 * * 0" | |
| workflow_dispatch: | |
| jobs: | |
| build: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| repository: bio-tools/content-ecosystem-utils | |
| path: content-ecosystem-utils | |
| ref: 'biocontainers-annotation-import' | |
| - uses: actions/checkout@v2 | |
| with: | |
| path: content | |
| - name: import biocontainers annotations | |
| env: | |
| GITHUB_USER: ${{ secrets.GITHUB_USER }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| BIOCONTAINERS_URL: https://raw.githubusercontent.com/BioContainers/tools-metadata/master/annotations.yaml | |
| run: | | |
| cd ${{ github.workspace }}/content/data | |
| if ${{ github.workspace }}/content-ecosystem-utils/scripts/git-utils/checkout-pr-if-exist.sh biocontainers-import; then | |
| IS_PR_CREATED=true | |
| else | |
| IS_PR_CREATED=false | |
| fi | |
| # Run importing script | |
| sudo pip3 install virtualenv | |
| virtualenv -p python3 venv | |
| . venv/bin/activate | |
| pip3 install setuptools wheel jinja2 pyyaml requests | |
| python3 ${{ github.workspace }}/content-ecosystem-utils/scripts/biocontainers-annotations-import/biocontainers-importer.py ${{ github.workspace }}/content/data/ $BIOCONTAINERS_URL | |
| ${{ github.workspace }}/content-ecosystem-utils/scripts/git-utils/import-changes.sh $IS_PR_CREATED biocontainers-import | |
| - name: Cache multiple paths | |
| uses: actions/cache@v2 | |
| with: | |
| path: | | |
| .venv/ | |
| key: ${{ runner.os }}-biocontainers-import |