Merge pull request #218 from uclahs-cds/tyamaguchi-ucla-convertString… #380
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| name: CI | |
| on: | |
| push: | |
| branches: [ master, develop ] | |
| pull_request: | |
| branches: [ master, develop ] | |
| jobs: | |
| run_tests: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python: [3.7, 3.8, 3.9] | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| lfs: true | |
| - name: Upgrade setuptools | |
| run: | | |
| pip3 install wheel --upgrade | |
| pip3 install setuptools --upgrade | |
| - name: Install Gurobi | |
| run: | | |
| wget https://packages.gurobi.com/9.0/gurobi9.0.2_linux64.tar.gz -O gurobi9.0.2_linux64.tar.gz | |
| tar xvzf gurobi9.0.2_linux64.tar.gz | |
| (cd gurobi902/linux64/src/build && make) | |
| (cd gurobi902/linux64/lib && ln -f -s ../src/build/libgurobi_c++.a libgurobi_c++.a) | |
| echo "GUROBI_HOME=$(realpath gurobi902)" >> $GITHUB_ENV | |
| - name: Activate Gurobi License | |
| run: | | |
| (cd gurobi902/linux64/bin && ./grbgetkey -q ${{ secrets.GUROBI_KEYCODE }} --path ${GUROBI_HOME}) | |
| echo "GRB_LICENSE_FILE=${GUROBI_HOME}/gurobi.lic" >> $GITHUB_ENV | |
| continue-on-error: true | |
| - name: Setup Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: Install HATCHet with dev dependencies | |
| run: | | |
| python -m pip install .[dev] | |
| env: | |
| CXXFLAGS: -pthread | |
| - name: Pre-commit checks | |
| run: | | |
| pre-commit run --all-files | |
| - name: Download Testing Data | |
| run: | | |
| pip3 install zenodo-get | |
| python3 -m zenodo_get 10.5281/zenodo.4046906 --output-dir=testdata | |
| echo "HATCHET_TESTS_BAM_DIRECTORY=$(realpath testdata)" >> $GITHUB_ENV | |
| - name: Install coinor-cbc | |
| run: | | |
| sudo apt install coinor-cbc | |
| echo "HATCHET_COMPUTE_CN_SOLVER=cbc" >> $GITHUB_ENV | |
| - name: Install SAMtools | |
| run: | | |
| wget https://sourceforge.net/projects/samtools/files/samtools/1.7/samtools-1.7.tar.bz2/download -O samtools-1.7.tar.bz2 | |
| tar xvjf samtools-1.7.tar.bz2 | |
| (cd samtools-1.7 && ./configure && make) | |
| echo "HATCHET_PATHS_SAMTOOLS=$(realpath samtools-1.7)" >> $GITHUB_ENV | |
| - name: Install BCFTools | |
| run: | | |
| wget https://sourceforge.net/projects/samtools/files/samtools/1.7/bcftools-1.7.tar.bz2/download -O bcftools-1.7.tar.bz2 | |
| tar xvjf bcftools-1.7.tar.bz2 | |
| (cd bcftools-1.7 && ./configure && make) | |
| echo "HATCHET_PATHS_BCFTOOLS=$(realpath bcftools-1.7)" >> $GITHUB_ENV | |
| - name: Install tabix | |
| run: | | |
| wget https://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.6.tar.bz2/download -O tabix-0.2.6.tar.bz2 | |
| bzip2 -d tabix-0.2.6.tar.bz2 | |
| tar -xvf tabix-0.2.6.tar | |
| (cd tabix-0.2.6 && make) | |
| echo "HATCHET_PATHS_TABIX=$(realpath tabix-0.2.6)" >> $GITHUB_ENV | |
| echo "HATCHET_PATHS_BGZIP=$(realpath tabix-0.2.6)" >> $GITHUB_ENV | |
| - name: Install mosdepth | |
| run: | | |
| wget https://github.com/brentp/mosdepth/releases/download/v0.3.2/mosdepth -O mosdepth | |
| chmod 775 mosdepth | |
| echo "HATCHET_PATHS_MOSDEPTH=$(pwd)" >> $GITHUB_ENV | |
| - name: Install picard | |
| run: | | |
| wget https://github.com/broadinstitute/picard/releases/download/2.26.2/picard.jar -O picard.jar | |
| echo "HATCHET_PATHS_PICARD=$(pwd)" >> $GITHUB_ENV | |
| - name: Install shapeit2 | |
| run: | | |
| wget https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.v2.r904.glibcv2.17.linux.tar.gz -O shapeit.v2.r904.glibcv2.17.linux.tar.gz | |
| tar -xf shapeit.v2.r904.glibcv2.17.linux.tar.gz | |
| echo "HATCHET_PATHS_SHAPEIT=$(realpath shapeit.v2.904.3.10.0-693.11.6.el7.x86_64/bin)" >> $GITHUB_ENV | |
| - name: Install bedtools | |
| run: | | |
| wget https://github.com/arq5x/bedtools2/releases/download/v2.30.0/bedtools.static.binary -O bedtools | |
| chmod 775 bedtools | |
| echo "$(pwd)" >> $GITHUB_PATH | |
| - name: Download and index hg19.fa | |
| working-directory: testdata | |
| run: | | |
| wget https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz | |
| gunzip hg19.fa.gz | |
| $HATCHET_PATHS_SAMTOOLS/samtools faidx hg19.fa | |
| $HATCHET_PATHS_SAMTOOLS/samtools dict hg19.fa > hg19.dict | |
| echo "HATCHET_PATHS_REFERENCE=$(realpath hg19.fa)" >> $GITHUB_ENV | |
| # Instead of downloading the entire 1000GP_Phase3 panel (huge) using | |
| # wget https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.tgz | |
| # we download equivalent data only for chr22, from zenodo | |
| - name: Download 1000GP reference panel | |
| working-directory: testdata | |
| run: | | |
| python3 -m zenodo_get 10.5281/zenodo.6709541 | |
| tar zxvf 1000GP_Phase3.tgz --wildcards *chr22* *sample | |
| echo "HATCHET_DOWNLOAD_PANEL_REFPANELDIR=$(pwd)" >> $GITHUB_ENV | |
| - name: HATCHet Check | |
| run: | | |
| hatchet check | |
| - name: Pytest | |
| run: | | |
| pytest tests --cov=hatchet | |
| # We may end up with files that have a ':' in their filenames, | |
| # due to the <chr>:start:end notation of chromosomes we process through SAMtools/BCFtools. | |
| # upload-artifact is unable to handle these, so we replace colons with dashes | |
| - name: Clean up artifact filenames | |
| run: | | |
| sudo apt install rename | |
| find tests/out -name "*:*" -exec rename 's|:|-|g' {} \; | |
| - name: Save Pytest Output Data | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: test-results | |
| path: tests/out | |
| - name: Convert coverage | |
| run: | | |
| python -m coverage xml | |
| continue-on-error: true | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v1 | |
| with: | |
| fail_ci_if_error: false | |
| build_docs: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python: [3.8] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| lfs: true | |
| - name: Upgrade setuptools | |
| run: | | |
| pip3 install wheel --upgrade | |
| pip3 install setuptools --upgrade | |
| - name: Install Gurobi | |
| run: | | |
| wget https://packages.gurobi.com/9.0/gurobi9.0.2_linux64.tar.gz -O gurobi9.0.2_linux64.tar.gz | |
| tar xvzf gurobi9.0.2_linux64.tar.gz | |
| (cd gurobi902/linux64/src/build && make) | |
| (cd gurobi902/linux64/lib && ln -f -s ../src/build/libgurobi_c++.a libgurobi_c++.a) | |
| echo "GUROBI_HOME=$(realpath gurobi902)" >> $GITHUB_ENV | |
| - name: Setup Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: Install package | |
| run: | | |
| CXXFLAGS=-pthread pip install .[dev] | |
| - name: Build docs | |
| run: | | |
| cd docs && sphinx-apidoc -f -o ./source/src ../src/hatchet -H Modules && make html && touch build/html/.nojekyll | |
| - name: Update gh-pages | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: "docs/buildDocs.sh" | |
| shell: bash |