performance: run profiler on *all* tests and update performance document #1193
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| on: | |
| push: | |
| branches: [ main ] | |
| paths-ignore: | |
| - '**/*.md' | |
| pull_request: | |
| branches: [ main ] | |
| paths-ignore: | |
| - '**/*.md' | |
| name: build and test | |
| jobs: | |
| build_and_test: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install required packages | |
| run: sudo apt-get update && sudo apt-get install -y | |
| git | |
| bash | |
| cmake | |
| make | |
| g++ | |
| python3-dev | |
| libatomic-ops-dev | |
| autoconf | |
| libgsl-dev | |
| zlib1g-dev | |
| libdeflate-dev | |
| libhts-dev | |
| samtools | |
| libjemalloc-dev | |
| bedtools | |
| - name: Init and update submodules | |
| run: git submodule update --init --recursive | |
| - name: Build wfmash | |
| run: cmake -H. -Bbuild -D CMAKE_BUILD_TYPE=Debug -DWFA_PNG_AND_TSV=ON && cmake --build build -- -j 2 | |
| - name: Run cmake tests (exclude lengthy ones) | |
| run: | | |
| cd build | |
| ctest -E all2all | |
| - name: Install Rust and Cargo | |
| uses: actions-rs/toolchain@v1 | |
| with: | |
| toolchain: stable | |
| override: true | |
| - name: Install wgatools | |
| run: cargo install --git https://github.com/wjwei-handsome/wgatools.git | |
| - name: Install wgatools | |
| run: cargo install --git https://github.com/ekg/pafcheck.git | |
| - name: Run wfmash and generate PAF | |
| run: build/bin/wfmash -t 8 -T SGDref -Q S288C -Y '#' data/scerevisiae8.fa.gz > test.paf | |
| - name: check PAF coordinates and extended CIGAR validity | |
| run: pafcheck --query-fasta data/scerevisiae8.fa.gz --paf test.paf | |
| - name: Convert PAF to MAF using wgatools | |
| run: wgatools paf2maf --target data/scerevisiae8.fa.gz --query data/scerevisiae8.fa.gz test.paf > test.maf | |
| - name: Check if MAF file is not empty | |
| run: | | |
| if [ -s test.maf ]; then | |
| echo "MAF file is not empty. Test passed." | |
| else | |
| echo "MAF file is empty. Test failed." | |
| exit 1 | |
| fi |