biocontainers import #195
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| 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 |