Execute AUGUSTUS longrunning test cases #1408
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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/ |