Add CHISEL preprocess and combocall commands #69
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| name: CI | |
| on: | |
| push: | |
| branches: [ master, develop, py3, ci ] | |
| pull_request: | |
| branches: [ master, develop, py3, ci ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python: [2.7.18] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| lfs: false | |
| - name: Cache Testing Data | |
| id: cache-test-data | |
| uses: actions/cache@v2 | |
| with: | |
| path: testdata | |
| key: testdata | |
| - name: Download Testing Data | |
| if: steps.cache-test-data.outputs.cache-hit != 'true' | |
| run: | | |
| pip3 install wheel | |
| pip3 install setuptools | |
| pip3 install zenodo-get | |
| python3 -m zenodo_get 10.5281/zenodo.3950299 --output-dir=testdata | |
| - name: Set Testing Data Envvar | |
| run: | | |
| echo "TEST_DIRECTORY=$(realpath testdata)" >> $GITHUB_ENV | |
| - name: Install SAMtools | |
| run: | | |
| wget https://sourceforge.net/projects/samtools/files/samtools/1.7/samtools-1.7.tar.bz2/download -O samtools-1.7.tar.bz2 | |
| tar xvjf samtools-1.7.tar.bz2 | |
| (cd samtools-1.7 && ./configure && make) | |
| echo $(realpath samtools-1.7) >> $GITHUB_PATH | |
| - name: Install BCFTools | |
| run: | | |
| wget https://sourceforge.net/projects/samtools/files/samtools/1.7/bcftools-1.7.tar.bz2/download -O bcftools-1.7.tar.bz2 | |
| tar xvjf bcftools-1.7.tar.bz2 | |
| (cd bcftools-1.7 && ./configure && make) | |
| echo $(realpath bcftools-1.7) >> $GITHUB_PATH | |
| - name: Download and index hg19.fa | |
| run: | | |
| wget https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz --directory-prefix=${TEST_DIRECTORY} | |
| (cd ${TEST_DIRECTORY} && gunzip -df hg19.fa.gz && samtools faidx hg19.fa && samtools dict hg19.fa > hg19.dict) | |
| - name: Setup Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: Install Tox and any other packages | |
| run: | | |
| python -m pip install coverage tox tox-gh-actions | |
| - name: Test with tox | |
| run: | | |
| tox | |
| env: | |
| PLATFORM: ${{ matrix.python }} |