Build index binaries #15
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| name: Build index binaries | |
| on: | |
| schedule: | |
| # Run on the first day of every month at midnight UTC | |
| - cron: '0 0 1 * *' | |
| push: | |
| branches: | |
| - feature/build_index_action | |
| workflow_dispatch: | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| # Check out the most recent version of the repository with submodules | |
| - name: Check out repository | |
| uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| # Set up Rust toolchain | |
| - name: Set up Rust | |
| uses: dtolnay/rust-toolchain@stable | |
| # Compile Rust code | |
| - name: Compile Rust code | |
| run: cargo build --release | |
| # Create a directory "build" | |
| - name: Create build directory | |
| run: mkdir -p build/input | |
| # Download the file "suffix-array.zip" from the most recent release of "unipept-database" | |
| - name: Download suffix-array.zip | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| latest_release_url=$(curl -s https://api.github.com/repos/unipept/unipept-database/releases/latest | grep "browser_download_url.*suffix-array.zip" | cut -d '"' -f 4) | |
| release_date=$(curl -s https://api.github.com/repos/unipept/unipept-database/releases/latest | grep '"published_at":' | cut -d '"' -f 4 | cut -d'T' -f1) | |
| release_date_formatted=$(date -d $release_date "+%Y-%m-%d") | |
| SP_VERSION="SP_$release_date_formatted" | |
| echo "SP_VERSION=$SP_VERSION" >> $GITHUB_ENV | |
| curl -L -o build/suffix-array.zip $latest_release_url | |
| # Extract the contents of the output folder from the zip into a folder "build/input" | |
| - name: Extract zip contents | |
| run: | | |
| unzip build/suffix-array.zip '*' -d build/input | |
| # Make a directory with the SP_VERSION and process files | |
| - name: Process files | |
| run: | | |
| mkdir -p build/$SP_VERSION | |
| lz4 -d build/input/uniprot_entries.tsv.lz4 | cut -f2,4,7,8 > build/$SP_VERSION/proteins.tsv | |
| lz4 -d build/input/taxons.tsv.lz4 > build/$SP_VERSION/taxons.tsv | |
| # Step 8: Run the sa-builder command | |
| - name: Run sa-builder | |
| run: | | |
| prefix="build/$SP_VERSION" | |
| ./target/release/sa-builder -d "$prefix/proteins.tsv" -o "$prefix/sa_sparse3_compressed.bin" -s 3 -a lib-div-suf-sort -c | |
| # Zip the contents of the build/$SP_VERSION directory | |
| - name: Zip build contents | |
| run: | | |
| cd "build/$SP_VERSION" && zip "index_$SP_VERSION.zip" "proteins.tsv" "taxons.tsv" "sa_sparse3_compressed.bin" | |
| # Create a GitHub release and upload the zip file | |
| - name: Upload or Update Release | |
| id: upload_or_update_release | |
| uses: softprops/action-gh-release@v1 | |
| with: | |
| files: build/${{ env.SP_VERSION }}/index_${{ env.SP_VERSION }}.zip | |
| tag_name: index-${{ env.SP_VERSION }} | |
| name: Index ${{ env.SP_VERSION }} | |
| commitish: ${{ github.sha }} | |
| draft: false | |
| prerelease: false | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} |