Execute AUGUSTUS longrunning test cases #1076
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| # This workflow builds AUGUSTUS and executes the | |
| # longrunning test cases | |
| name: Execute AUGUSTUS longrunning test cases | |
| on: | |
| schedule: | |
| # execute workflow daily at 23:30 | |
| - cron: '30 23 * * *' | |
| env: | |
| TOOLDIR: /data/tools | |
| PERL5LIB: /data/eval | |
| DB_USER: ${{ secrets.TEST_DB_USER }} | |
| DB_PASSWD: ${{ secrets.TEST_DB_PASSWD }} | |
| jobs: | |
| check_latest_commit_in_db: | |
| runs-on: [self-hosted, linux, default] | |
| outputs: | |
| commit: ${{ steps.step3.outputs.hash }} | |
| steps: | |
| - name: Check out repository | |
| id: step1 | |
| uses: actions/checkout@v2 | |
| - name: Get latest commit in DB | |
| id: step2 | |
| run: | | |
| echo 'LATEST_COMMIT_IN_DB<<EOF' >> $GITHUB_ENV | |
| ./check_latest_commit_influx.py --dbname testresults --dbhost localhost --dbport 8086 --dbuser $DB_USER --dbpasswd $DB_PASSWD >> $GITHUB_ENV | |
| echo 'EOF' >> $GITHUB_ENV | |
| working-directory: tests/longrunning/ | |
| - name: Set output | |
| id: step3 | |
| run: echo '::set-output name=hash::${{ env.LATEST_COMMIT_IN_DB }}' | |
| longrunning_test: | |
| runs-on: [self-hosted, linux, default] | |
| needs: check_latest_commit_in_db | |
| # Only execute test cases if the last commit in db is different from the last commit on default branch | |
| if: ${{ needs.check_latest_commit_in_db.outputs.commit != github.sha }} | |
| # Maximum number of minutes to let a job run before GitHub automatically cancels it. Default: 360 | |
| timeout-minutes: 600 | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v2 | |
| # Install required python packages | |
| - name: Install python wget | |
| run: pip3 install wget | |
| - name: Install gitpython | |
| run: pip3 install gitpython | |
| - name: Install profiling tools | |
| run: pip3 install psutil memory_profiler | |
| - name: Build AUGUSTUS | |
| run: make all | |
| - name: Execute single genome test cases | |
| run: ./test_single.py --evalDir /data/eval/ --jobs 8 --pathToGitRepo ../../../.git | |
| working-directory: tests/longrunning/single_genome/ | |
| - name: Extract desired accuracy values (single genome test case) | |
| run: ./extract_accuracy_values.py --path single_genome/output/eval | |
| working-directory: tests/longrunning/ | |
| - name: Write to influxdb (single genome test case) | |
| run: ./write_to_influx.py --dbname testresults --dbhost localhost --dbport 8086 --dbuser $DB_USER --dbpasswd $DB_PASSWD --pathToDataDir single_genome/output/ --mode single | |
| working-directory: tests/longrunning/ | |
| - name: Execute cgp test case | |
| run: ./executeTestCGP.py --chunks 27 30 47 54 57 80 86 101 118 --eval --augustusDir ../../../ --dataDir data --evalDir /data/eval --jobs 8 --pathToGitRepo ../../../.git | |
| working-directory: tests/longrunning/cgp/ | |
| - name: Extract desired accuracy values (cgp test case) | |
| run: ./extract_accuracy_values.py --path cgp/data/cgp12way/ACCURACY | |
| working-directory: tests/longrunning/ | |
| - name: Write to influxdb (cgp test case) | |
| run: ./write_to_influx.py --dbname testresults --dbhost localhost --dbport 8086 --dbuser $DB_USER --dbpasswd $DB_PASSWD --pathToDataDir cgp/data/cgp12way/ --mode cgp | |
| working-directory: tests/longrunning/ |