remove TOC #66
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| # This workflow will install RGI dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | |
| name: Build RGI and test | |
| on: | |
| push: | |
| branches: [ 'master' ] | |
| pull_request: | |
| branches: [ 'master' ] | |
| workflow_dispatch: | |
| env: | |
| BLAST_VERSION: 2.14.1 | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.7","3.8","3.9","3.10","3.11"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| architecture: 'x64' | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get -qq update | |
| sudo apt-get -qq install -y prodigal tree | |
| sudo apt-get -qq install -y libtbb-dev | |
| sudo apt-get -qq install -y cmake g++ make | |
| echo "install blast ..." | |
| wget --quiet http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLAST_VERSION}/ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz | |
| tar xzf ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz | |
| sudo mv ncbi-blast-${BLAST_VERSION}+/bin/* /usr/bin | |
| wget --quiet https://github.com/BenLangmead/bowtie2/releases/download/v2.4.5/bowtie2-2.4.5-linux-x86_64.zip | |
| unzip -q bowtie2-2.4.5-linux-x86_64.zip | |
| sudo mv bowtie2-2.4.5-linux-x86_64/bowtie2* /usr/bin | |
| wget --quiet http://github.com/bbuchfink/diamond/releases/download/v0.8.36/diamond-linux64.tar.gz | |
| tar xzf diamond-linux64.tar.gz | |
| sudo mv diamond /usr/bin | |
| git clone --quiet https://github.com/lh3/bwa.git | |
| pushd bwa && make --quiet && sudo mv bwa /usr/bin && popd | |
| wget --quiet https://github.com/gmarcais/Jellyfish/releases/download/v2.2.10/jellyfish-linux | |
| mv jellyfish-linux jellyfish && chmod +x jellyfish && sudo mv jellyfish /usr/bin | |
| wget --quiet https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 | |
| tar jxf samtools-1.9.tar.bz2 | |
| pushd samtools-1.9 && ./configure --enable-silent-rules && make --quiet && sudo mv samtools /usr/bin && popd | |
| wget --quiet https://github.com/pezmaster31/bamtools/archive/v2.5.2.tar.gz | |
| tar xzf v2.5.2.tar.gz | |
| pushd bamtools-2.5.2/ && mkdir build && cd build && cmake .. && make --quiet && sudo make install --quiet && popd | |
| bamtools --version | |
| wget --quiet https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools | |
| chmod +x bedtools && sudo mv bedtools /usr/bin | |
| git clone --quiet https://bitbucket.org/genomicepidemiology/kma.git | |
| pushd kma && make --quiet && sudo mv kma /usr/bin && popd | |
| python -m pip install --upgrade --quiet pip | |
| #python -m pip install --quiet flake8 pytest | |
| python -m pip install --quiet pytest | |
| python -m pip install --quiet setuptools | |
| - name: Install rgi | |
| run: | | |
| echo "=====> install rgi ..." | |
| echo `pwd` | |
| pip3 install -r requirements.txt | |
| pip3 install setuptools | |
| pip3 install . | |
| - name: Check versions | |
| run: | | |
| echo "=====> check versions installed ..." | |
| echo `pwd` | |
| blastp -version | |
| bowtie2 --version | |
| diamond --version | |
| jellyfish --version | |
| samtools --version | |
| bedtools --version | |
| kma -v | |
| rgi -h | |
| # - name: Lint with flake8 | |
| # run: | | |
| # # stop the build if there are Python syntax errors or undefined names | |
| # flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test with pytest | |
| run: | | |
| bash test.sh |