fixed install pfam from local dir #187
Workflow file for this run
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: build | |
| on: | |
| push: | |
| branches: [ master ] | |
| tags: | |
| - '*' | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.8] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 pytest wheel | |
| sudo apt-get -y install hmmer | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test | |
| run: | | |
| pwd | |
| echo "*** INSTALL FAS..." | |
| pip install . | |
| echo "*** DOWNLOAD DEPENDENCIES AND SETUP FAS..." | |
| wget https://github.com/BIONF/data4travis/raw/main/dtu/signalp-4.1g.Linux.tar.gz &> /dev/null | |
| wget https://github.com/BIONF/data4travis/raw/main/dtu/tmhmm-2.0c.Linux.tar.gz &> /dev/null | |
| fas.setup -t /home/runner/work/FAS/FAS -d /home/runner/work/FAS/FAS | |
| less annoTools.txt | grep -v "COILS2" > annoTools.txt.mod | |
| mv annoTools.txt.mod annoTools.txt | |
| echo "*** TEST FAS.DOANNO..." | |
| fas.doAnno -i test_annofas.fa -o anno_output | |
| echo "*** TEST FAS.RUN..." | |
| fas.run -s greedyFAS/annoFAS/test_annofas.fa -q greedyFAS/annoFAS/test_annofas.fa -a anno_output -o fas_output | |
| echo "*** TEST FAS.DOANNO REDO..." | |
| fas.doAnno -i test_annofas.fa -o anno_output --redo pfam | |
| echo "*** TEST FAS.CHECKANNO..." | |
| fas.checkAnno -s greedyFAS/annoFAS/test_annofas.fa -a anno_output/test_annofas.json -o tmp | |
| echo "*** TEST FAS.GETPROTBYANNO..." | |
| fas.getProtByAnno -a anno_output/test_annofas.json -f G-alpha | |
| echo "*** TEST FAS.CALCCOMPLEXITY..." | |
| fas.calcComplexity -i anno_output/test_annofas.json | |
| echo "*** TEST FAS.GETDOMAINS..." | |
| fas.getDomains -j anno_output/test_annofas.json -p A0A1S4GN31 -o A0A1S4GN31.domains | |
| echo "*** TEST FAS.SPLITANNO..." | |
| echo "A0A1W5C929" > id.txt | |
| fas.splitAnno -x id.txt -i anno_output/test_annofas.json -o anno_output/out.json | |
| echo "*** TEST FAS.RUNMULTITAXA..." | |
| cp anno_output/test_annofas.json anno_output/spec_a.json | |
| cp anno_output/test_annofas.json anno_output/spec_b.json | |
| echo -e "A0A1U7F4Y7\tspec_a\tA0A1S4GN82\tspec_b\nA0A1U7F5Z4\tspec_a\tA0A1S4GN82\tspec_b" > test_multi.txt | |
| fas.runMultiTaxa --input test_multi.txt -a anno_output -o fas_output | |
| ls fas_output | |
| echo "*** TEST FAS.MERGEJSON..." | |
| fas.mergeJson -i fas_output -n merged_json -o fas_output | |
| echo "*** TEST FAS.RUNFDOGFAS..." | |
| wget https://github.com/BIONF/data4travis/raw/main/fas_test.tar.gz &> /dev/null | |
| tar -xf fas_test.tar.gz | |
| fas.runFdogFas -i test.extended.fa -w annotation_dir | |
| ls | |
| - name: Deploy | |
| if: startsWith(github.event.ref, 'refs/tags') | |
| uses: casperdcl/deploy-pypi@v2 | |
| with: | |
| password: ${{ secrets.pypi }} | |
| build: true | |
| upload: ${{ github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') }} |