Create BLAST Databases #4
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| name: Create BLAST Databases | |
| on: | |
| pull_request: | |
| types: [closed] | |
| branches: [main] | |
| workflow_dispatch: | |
| inputs: | |
| json_file: | |
| description: 'Full path to JSON file (e.g., conf/WB/databases.WB.WS295.json)' | |
| required: true | |
| type: string | |
| jobs: | |
| create-blast-db: | |
| if: github.event.pull_request.merged == true || github.event_name == 'workflow_dispatch' | |
| runs-on: blast | |
| timeout-minutes: 180 | |
| concurrency: | |
| group: blast-${{ github.ref }} | |
| cancel-in-progress: true | |
| steps: | |
| - name: Checkout configuration repository | |
| uses: actions/checkout@v3 | |
| with: | |
| path: config | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| fetch-depth: 2 | |
| - name: Get file to process | |
| id: changed | |
| run: | | |
| if [ "${{ github.event_name }}" = "workflow_dispatch" ]; then | |
| echo "file=${{ github.event.inputs.json_file }}" >> $GITHUB_OUTPUT | |
| else | |
| CHANGED_FILE=$(git -C config diff --name-only ${{ github.event.pull_request.base.sha }} ${{ github.event.pull_request.head.sha }} | grep -E '\.json$' || true) | |
| if [ -z "$CHANGED_FILE" ]; then | |
| echo "No JSON files changed" | |
| exit 0 | |
| fi | |
| echo "file=$CHANGED_FILE" >> $GITHUB_OUTPUT | |
| fi | |
| - name: Run BLAST DB creation | |
| run: | | |
| cd /home/ec2-user/gitroot/agr_blastdb_manager | |
| git pull origin main || { | |
| echo "Failed to pull latest changes" | |
| exit 1 | |
| } | |
| poetry run python src/create_blast_db.py \ | |
| -j $GITHUB_WORKSPACE/config/${{ steps.changed.outputs.file }} \ | |
| -u \ | |
| -e $(basename ${{ steps.changed.outputs.file }} .json | cut -d'.' -f3) |