Database #16
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| name: Database | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| # * is a special character in YAML so you have to quote this string | |
| - cron: '0 0 1 * *' | |
| jobs: | |
| generate_tsv_files: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| type: ['database', 'suffix-array'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: dtolnay/rust-toolchain@stable | |
| - uses: Swatinem/rust-cache@v2 | |
| id: cache | |
| with: | |
| shared-key: ${{ env.CACHE_KEY }} | |
| - run: cd scripts/helper_scripts/unipept-database-rs && cargo fetch | |
| if: ${{ !steps.cache.outputs.cache-hit }} | |
| - run: ./scripts/build_binaries.sh | |
| - name: Get current date | |
| id: date | |
| run: echo "date=$(date +'%Y-%m-%d')" >> $GITHUB_ENV | |
| - name: Install required utilities | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get -y install git curl unzip gawk sqlite3 libsqlite3-dev pv nodejs wget uuid-runtime pigz lz4 parallel libxml2-utils | |
| - name: Prepare temporary directories | |
| run: sudo mkdir -p "index" "unipept-temp" | |
| - name: Generate tsv.gz files | |
| shell: bash | |
| run: sudo ./scripts/build_database.sh -i "index" -d "unipept-temp" -m "256M" "${{ matrix.type }}" "swissprot" "https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz" "output" | |
| - name: Zip all tsv.gz files | |
| shell: bash | |
| run: cd output && zip -r "../${{ matrix.type }}.zip" * && zip -u "../${{ matrix.type }}.zip" ".version"ß | |
| - name: Upload or Update Release | |
| id: upload_or_update_release | |
| uses: softprops/action-gh-release@v1 | |
| with: | |
| files: ${{ matrix.type }}.zip | |
| tag_name: database-${{ env.date }} | |
| name: Database ${{ env.date }} | |
| commitish: ${{ github.sha }} | |
| draft: false | |
| prerelease: false | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} |