Update ADMIXTOOLS compilation #54
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| # Workflow derived from https://github.com/r-lib/actions/tree/master/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| name: test-coverage | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test-coverage: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install ADMIXTOOLS/admixr dependencies | |
| run: sudo apt-get install libopenblas-dev libgsl-dev liblapack-dev bedtools | |
| - name: Compile and install ADMIXTOOLS | |
| run: | | |
| # create a single directory for all external software | |
| mkdir -p ~/deps | |
| cd ~/deps | |
| # download and unpack the ADMIXTOOLS source code | |
| curl -LO https://github.com/DReichLab/AdmixTools/archive/v7.0.2.tar.gz | |
| tar xf v7.0.2.tar.gz | |
| cd AdmixTools-7.0.2 | |
| # set compiler flags (compilation on macOS was failing unable to find | |
| # openblas library files) | |
| export LDFLAGS="-L/usr/local/opt/openblas/lib" | |
| export CPPFLAGS="-I/usr/local/opt/openblas/include" | |
| # compile ADMIXTOOLS and move binaries under bin/ | |
| cd src | |
| make clobber | |
| make LDLIBS="-llapack" all | |
| make install | |
| # for some reason, mergeit isn't built in 6.x and 5.x? | |
| # compile it and copy it | |
| make mergeit | |
| cp mergeit ../bin | |
| # download testing data for unit tests | |
| cd ../ | |
| curl -LO https://reich.hms.harvard.edu/sites/reich.hms.harvard.edu/files/inline-files/AdmixTools_Example_Data.tar_.gz | |
| tar xf AdmixTools_Example_Data.tar_.gz | |
| # run the Perl script with tests for the compiled binaries | |
| cd examples | |
| # fix unportable Perl shebang | |
| if [[ "$OSTYPE" == "darwin"* ]]; then | |
| sed -i '' "1s/.*/\#\!\/usr\/bin\/env perl -w/" mklog | |
| else | |
| sed -i "1s/.*/\#\!\/usr\/bin\/env perl/" mklog | |
| fi | |
| ./mklog | |
| cd ../ | |
| # we need to do this in bash because of $OSTYPE above | |
| shell: bash | |
| - name: Populate PATH with compiled binaries | |
| run: | | |
| export PATH="$HOME/deps/AdmixTools-7.0.2/bin:$PATH" | |
| echo "PATH=$PATH" > ~/.Renviron | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: covr | |
| - name: Test coverage | |
| run: covr::codecov(type = c("tests", "vignettes")) | |
| shell: Rscript {0} |