Explicitely specify index and temp directories #3
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| name: Database | |
| on: | |
| push: | |
| branches: | |
| - "feature/generate-tsv-action" | |
| 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: | |
| branch: ['database', 'suffix-array'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ matrix.branch }} | |
| - 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: ${{ !steps.cache.outputs.cache-hit }} | |
| - run: ./scripts/build_binaries.sh | |
| - name: Get current date | |
| id: date | |
| run: echo "::set-output name=date::$(date +'%Y-%m-%d')" | |
| - 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 | |
| - name: Generate tsv.gz files | |
| shell: bash | |
| run: ./scripts/build_database.sh -i "/index" -d "/unipept-temp" -m "128M" database "swissprot" "https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.xml.gz" "output" | |
| - name: Rename the tsv.gz files according to the branch used | |
| shell: bash | |
| run: cd output && for file in *.tsv.gz; do mv "$file" "${file%.tsv.gz}.${{ matrix.branch }}.tsv.gz"; done | |
| - name: Zip all tsv.gz files | |
| shell: bash | |
| run: zip -r output/${{ matrix.branch }}.zip output/*.tsv.gz | |
| - name: Create Release | |
| id: create_release | |
| uses: actions/create-release@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| tag_name: database-${{ steps.date.outputs.date }} | |
| release_name: Database ${{ steps.date.outputs.date }} | |
| draft: false | |
| prerelease: false | |
| - name: Upload Static Database Release Asset | |
| id: upload-database-release-asset | |
| uses: actions/upload-release-asset@v1 | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| upload_url: ${{ steps.create_release.outputs.upload_url }} | |
| asset_path: output/${{ matrix.branch }}.zip | |
| asset_name: ${{ matrix.branch }}-${{ steps.date.outputs.date }}.zip | |
| asset_content_type: application/zip |