force added samtools #141
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| name: testing_and_building_repo | |
| on: [push, pull_request, workflow_dispatch] | |
| jobs: | |
| build: | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| runs-on: ${{matrix.os}} | |
| name: Workflow on ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: '0' | |
| - name: install libgd-dev and liblzma-dev | |
| run: | | |
| # https://github.com/actions/runner-images/issues/2139 | |
| sudo apt-get remove -y nginx libgd3 | |
| sudo apt-get install -y libgd-dev liblzma-dev libcurl4-openssl-dev | |
| sudo apt-get install -y samtools | |
| - name: clone samtools branch | |
| run: | | |
| export HTSLIB=${{ github.workspace }}/htslib | |
| git clone --branch $HTSLIB_BRANCH https://github.com/samtools/htslib.git $HTSLIB | |
| env: | |
| HTSLIB_BRANCH: develop | |
| - name: make HTSLIB | |
| run: | | |
| export HTSLIB=${{ github.workspace }}/htslib | |
| export HTSDIR=${{ github.workspace }}/htslib/b | |
| cd $HTSLIB | |
| git submodule update --init --recursive | |
| (autoreconf -i && mkdir b && ./configure --prefix=$HTSDIR && make && make install) | |
| - name: make and configure | |
| run: | | |
| export HTSDIR=${{ github.workspace }}/htslib/b | |
| autoreconf -i | |
| ./configure --with-htslib=$HTSDIR | |
| make | |
| make check | |
| #make distcheck #TODO | |
| - name: Archive test logs | |
| uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: test-logs | |
| path: test-suite.log | |
| retention-days: 1 | |
| # running ./Build dist and exporting files | |
| - name: run ./Build dist | |
| run: | | |
| make dist | |
| export DIST_FILE=$(ls bambi-*.tar.gz) | |
| export SHA256_FILE=$DIST_FILE.sha256 | |
| shasum -a 256 $DIST_FILE > $SHA256_FILE |