Update README.md #71
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| name: build | |
| on: | |
| push: | |
| branches: [ "main", "dev" ] | |
| pull_request: | |
| branches: [ "main" ] | |
| jobs: | |
| build: | |
| runs-on: ${{matrix.config.os}} | |
| name: amplisim on ${{ matrix.config.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - os: macos-12 | |
| - os: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Build amplisim on Linux | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update -y | |
| sudo apt-get install -y lzma libbz2-dev libcurl4-openssl-dev | |
| git submodule init | |
| git submodule update --init --recursive | |
| mkdir build | |
| make -C lib/htslib | |
| make | |
| - name: Build amplisim on macOS | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install xz curl glib-openssl argp-standalone | |
| git submodule init | |
| git submodule update --init --recursive | |
| mkdir build | |
| make -C lib/htslib | |
| make | |
| - name: Run amplisim | |
| run: | | |
| mkdir testdata && cd testdata | |
| wget https://raw.githubusercontent.com/artic-network/primer-schemes/master/nCoV-2019/V5.3.2/SARS-CoV-2.primer.bed | |
| wget https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3 | |
| sed 's/>ENA|MN908947|MN908947.3 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome./>MN908947.3/g' MN908947.3 > MN908947.3.fasta | |
| cd .. | |
| ./amplisim -s 479 -o testdata/amplicons.1.fasta testdata/MN908947.3.fasta testdata/SARS-CoV-2.primer.bed | |
| ./amplisim -s 479 -m 20 -n 2 -o testdata/amplicons.2.fasta testdata/MN908947.3.fasta testdata/SARS-CoV-2.primer.bed | |
| cmp testdata/amplicons.1.fasta testdata/amplicons.2.fasta || echo "Comparison failed. File with default parameters is different." | |
| ./amplisim -s 400 -o testdata/amplicons.3.fasta testdata/MN908947.3.fasta testdata/SARS-CoV-2.primer.bed | |
| ./amplisim -s 479 -x 0.00001 -o testdata/amplicons.4.fasta testdata/MN908947.3.fasta testdata/SARS-CoV-2.primer.bed | |
| - name: Verify md5sum on macOS | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install coreutils | |
| md5sum testdata/amplicons.1.fasta | |
| md5sum testdata/amplicons.2.fasta | |
| md5sum testdata/amplicons.3.fasta | |
| md5sum testdata/amplicons.4.fasta | |
| md5sum -c test/sarscov2.macos.md5 | |
| - name: Verify md5sum on Ubuntu | |
| if: runner.os == 'Linux' | |
| run: | | |
| md5sum testdata/amplicons.1.fasta | |
| md5sum testdata/amplicons.2.fasta | |
| md5sum testdata/amplicons.3.fasta | |
| md5sum testdata/amplicons.4.fasta | |
| md5sum -c test/sarscov2.ubuntu.md5 |