Added --test-run parameter #74
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| name: CI | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v1 | |
| - name: Build and push | |
| uses: docker/build-push-action@v2 | |
| with: | |
| context: . | |
| file: ./ci/Dockerfile | |
| tags: recognizer:latest | |
| outputs: type=docker,dest=/tmp/recognizer.tar | |
| - name: Upload artifact | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: recognizer | |
| path: /tmp/recognizer.tar | |
| vanilla-annotation: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: recognizer | |
| path: /tmp | |
| - name: Load Docker image | |
| run: | | |
| docker load --input /tmp/recognizer.tar | |
| docker image ls -a | |
| - name: Default annotation | |
| run: docker run recognizer /bin/bash -c "mkdir resources_directory; mv reCOGnizer/ci/cdd.tar.gz resources_directory; recognizer -f reCOGnizer/ci/proteomes.fasta -rd resources_directory --quiet -dbs COG,TIGRFAM --test-run" | |
| taxonomy-based-annotation: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: recognizer | |
| path: /tmp | |
| - name: Load Docker image | |
| run: | | |
| docker load --input /tmp/recognizer.tar | |
| docker image ls -a | |
| - name: Taxonomy-based annotation | |
| run: docker run recognizer /bin/bash -c "mkdir resources_directory; mv reCOGnizer/ci/cdd.tar.gz resources_directory; recognizer -f reCOGnizer/ci/proteomes.fasta -rd resources_directory --tax-file reCOGnizer/ci/UPIMAPI_results.tsv --tax-col 'Taxonomic lineage IDs (SPECIES)' --protein-id-col qseqid --species-taxids --quiet --test-run" | |
| custom-database-annotation: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: recognizer | |
| path: /tmp | |
| - name: Load Docker image | |
| run: | | |
| docker load --input /tmp/recognizer.tar | |
| docker image ls -a | |
| - name: Custom database annotation | |
| run: docker run recognizer /bin/bash -c "mkdir resources_directory; mv reCOGnizer/ci/cdd.tar.gz resources_directory; tar -xzf resources_directory/cdd.tar.gz -C resources_directory; makeprofiledb -in reCOGnizer/ci/ci.pn -out resources_directory/db; recognizer -f reCOGnizer/ci/proteomes.fasta -rd resources_directory --quiet -dbs resources_directory/db --custom-databases --test-run" |