Update README.md #592
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| name: ResMiCo | |
| on: [push, pull_request] | |
| jobs: | |
| build: | |
| name: build (${{ matrix.python-version }}, ${{ matrix.os }}) | |
| runs-on: ubuntu-latest | |
| env: | |
| DATADIR: data | |
| strategy: | |
| matrix: | |
| python-version: [3.9] | |
| build_type: [Release] | |
| compiler: [g++-9] | |
| include: | |
| - compiler: g++-9 | |
| cxx: g++-9 | |
| cc: gcc-9 | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Checkout submodules | |
| run: git submodule update --init --recursive | |
| - name: bam2feat Create build dir | |
| run: mkdir ${{runner.workspace}}/resmico/ResMiCo-SM/feature_extractor/build | |
| - name: bam2feat Configure CMake | |
| working-directory: ${{runner.workspace}}/resmico/ResMiCo-SM/feature_extractor/build | |
| shell: bash | |
| run: | | |
| export CC=$(which ${{ matrix.cc }}) | |
| export CXX=$(which ${{ matrix.cxx }}) | |
| cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} | |
| - name: bam2feat Build | |
| working-directory: ${{runner.workspace}}/resmico/ResMiCo-SM/feature_extractor/build | |
| shell: bash | |
| run: make -j | |
| - name: bam2feat Test | |
| working-directory: ${{runner.workspace}}/resmico/ResMiCo-SM/feature_extractor/build | |
| shell: bash | |
| run: ./tests | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: 'latest' | |
| auto-update-conda: true | |
| mamba-version: "*" | |
| python-version: ${{ matrix.python-version }} | |
| channels: conda-forge,bioconda | |
| environment-file: environment.yml | |
| activate-environment: resmico | |
| - name: cython contig reader | |
| shell: bash -l {0} | |
| working-directory: ${{runner.workspace}}/resmico/resmico | |
| run: | | |
| python setup.py build_ext --inplace | |
| - name: pip install | |
| shell: bash -l {0} | |
| working-directory: ${{runner.workspace}}/resmico/ | |
| run: | | |
| pip install . | |
| - name: resmico tests | |
| shell: bash -l {0} | |
| working-directory: ${{runner.workspace}}/resmico/resmico/tests | |
| run: | | |
| pytest -s --hide-run-results --script-launch-mode=subprocess | |
| - name: resmico readme example1 | |
| shell: bash -l {0} | |
| working-directory: ${{runner.workspace}}/resmico/ | |
| run: | | |
| mkdir example1 && cd example1 | |
| wget http://ftp.tue.mpg.de/ebio/projects/ResMiCo/UHGG-n9_bam2feat.tar.gz | |
| wget http://ftp.tue.mpg.de/ebio/projects/ResMiCo/UHGG-n9_bam2feat.md5 | |
| md5sum --check UHGG-n9_bam2feat.md5 | |
| tar -pzxvf UHGG-n9_bam2feat.tar.gz && rm -f UHGG-n9_bam2feat.* | |
| resmico bam2feat --outdir features UHGG-n9_bam2feat/map.tsv | |
| resmico evaluate --min-avg-coverage 0.01 --save-path predictions --save-name default-model --feature-files-path features | |
| - name: resmico readme example2 | |
| shell: bash -l {0} | |
| working-directory: ${{runner.workspace}}/resmico/ | |
| run: | | |
| mkdir example2 && cd example2 | |
| wget http://ftp.tue.mpg.de/ebio/projects/ResMiCo/UHGG-n9_features.tar.gz | |
| wget http://ftp.tue.mpg.de/ebio/projects/ResMiCo/UHGG-n9_features.md5 | |
| md5sum --check UHGG-n9_features.md5 | |
| tar -pzxvf UHGG-n9_features.tar.gz && rm -f UHGG-n9_features.* | |
| resmico evaluate --save-path predictions --save-name default-model --feature-files-path UHGG-n9_features/ | |
| resmico filter --outdir filtered-contigs predictions/default-model.csv UHGG-n9_features/fasta/*fna.gz | |
| - name: resmico-sm tests | |
| working-directory: ${{runner.workspace}}/resmico/ResMiCo-SM | |
| shell: bash -l {0} | |
| run: | | |
| wget http://ftp.tue.mpg.de/ebio/projects/ResMiCo/genomes_n10.tar.gz | |
| wget http://ftp.tue.mpg.de/ebio/projects/ResMiCo/genomes_n10.md5 | |
| md5sum --check genomes_n10.md5 | |
| tar -pzxvf genomes_n10.tar.gz && rm -f genomes_n10.tar.gz | |
| snakemake --use-conda -j 1 --force --quiet --dry-run |