fixed search taxa list when using --coreTaxa #170
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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 | |
| - 0.1.0 | |
| 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: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 pytest wheel | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test | |
| run: | | |
| pwd | |
| pip install . | |
| path=$(fdog.setup -d ./ --getSourcepath); for i in $(less $path/data/dependencies.txt); do sudo apt-get install -y -qq $i; done | |
| echo "TEST fdog.setup" | |
| fdog.setup -d /home/runner/work/fDOG/fDOG/dt --woFAS | |
| echo "TEST fdog.checkData" | |
| fdog.checkData -s /home/runner/work/fDOG/fDOG/dt/searchTaxa_dir -c /home/runner/work/fDOG/fDOG/dt/coreTaxa_dir -a /home/runner/work/fDOG/fDOG/dt/annotation_dir --reblast | |
| echo "TEST fdog.showTaxa" | |
| fdog.showTaxa | |
| echo "TEST fdog.run" | |
| fdog.run --seqFile infile.fa --jobName test --refspec HUMAN@9606@3 --fasOff --group mammalia | |
| mkdir seeds | |
| path=$(fdog.setup -d ./ --getSourcepath); a="1 2 3"; for i in ${a[@]}; do cp $path/data/infile.fa seeds/$i.fa; done | |
| echo "TEST fdogs.run" | |
| fdogs.run --seqFolder seeds --jobName test_multi --refspec HUMAN@9606@3 --fasOff --searchTaxa PARTE@5888@3,THAPS@35128@3 --hmmScoreType sequence | |
| echo "TEST fdog.addTaxon" | |
| head /home/runner/work/fDOG/fDOG/dt/searchTaxa_dir/HUMAN@9606@3/HUMAN@[email protected] > hm.fa | |
| fdog.addTaxon -f hm.fa -i 9606 -o ./ -c -a | |
| 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') }} |