Create create_blast_db.yml #1
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| name: Create BLAST Databases | |
| on: | |
| pull_request: | |
| types: [closed] | |
| branches: [main] | |
| jobs: | |
| create-blast-db: | |
| if: github.event.pull_request.merged == true | |
| runs-on: blast | |
| steps: | |
| - name: Checkout configuration repository | |
| uses: actions/checkout@v3 | |
| with: | |
| path: config | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| - name: Get changed files | |
| id: changed | |
| run: | | |
| CHANGED_FILE=$(git -C config diff --name-only ${{ github.event.pull_request.base.sha }} ${{ github.event.pull_request.head.sha }} | grep -E '\.json$' || true) | |
| echo "file=$CHANGED_FILE" >> $GITHUB_OUTPUT | |
| - name: Run BLAST DB creation | |
| run: | | |
| # Change to the blast manager directory | |
| cd /home/ec2-user/gitroot/agr_blastdb_manager | |
| # Pull latest changes from manager repo | |
| git pull origin main | |
| # Run the script with poetry | |
| 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) |