Merge branch 'master' into connect-minimap-hits #2441
Workflow file for this run
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| name: Build and Test MiCall | |
| on: push | |
| jobs: | |
| main: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - run: mkdir -p ~/bin | |
| - run: echo ~/bin >> $GITHUB_PATH | |
| - name: Run apt update | |
| run: sudo apt-get update | |
| - name: Install IVA assembler dependencies | |
| run: | | |
| sudo apt-get install -qq zlib1g-dev libncurses5-dev libncursesw5-dev mummer ncbi-blast+ | |
| cd ~/bin | |
| wget -q http://sun.aei.polsl.pl/kmc/download-2.1.1/linux/kmc | |
| wget -q http://sun.aei.polsl.pl/kmc/download-2.1.1/linux/kmc_dump | |
| # Server doesn't support HTTPS, so check for changed files. | |
| echo "\ | |
| db1935884aec2d23d4d623ff85eb4eae8d7a946c9ee0c33ea1818215c40d3099 kmc | |
| 34a97db2dab5fdae0276d2589c940142813e9cd87ae10e5e2dd37ed3545b4436 kmc_dump" | sha256sum --check | |
| chmod +x kmc kmc_dump | |
| wget -q https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 | |
| tar -xf samtools-1.3.1.tar.bz2 --no-same-owner --bzip2 | |
| cd samtools-1.3.1 | |
| ./configure --prefix=$HOME | |
| make | |
| make install | |
| cd ~ | |
| wget -q https://downloads.sourceforge.net/project/smalt/smalt-0.7.6-bin.tar.gz | |
| tar -xzf smalt-0.7.6-bin.tar.gz | |
| ln -s ~/smalt-0.7.6-bin/smalt_x86_64 ~/bin/smalt | |
| - name: Install Rust and merge-mates | |
| run: | | |
| sudo curl https://sh.rustup.rs -sSf | sh -s -- -y | |
| source ~/.cargo/env | |
| cargo install --root ~/ --git https://github.com/jeff-k/merge-mates.git --rev 2fec61363f645e2008a4adff553d098beae21469 | |
| - name: Install Bowtie2 | |
| run: | | |
| wget -q -O bowtie2.zip https://github.com/BenLangmead/bowtie2/releases/download/v2.2.8/bowtie2-2.2.8-linux-x86_64.zip | |
| sudo unzip -qq bowtie2.zip -d /opt/ | |
| sudo ln -s /opt/bowtie2-2.2.8/ /opt/bowtie2 | |
| rm bowtie2.zip | |
| # Add to system path | |
| echo "/opt/bowtie2" >> $GITHUB_PATH | |
| - name: Install MiCall's Python dependencies | |
| # Have to clean up alignment build files. Otherwise, they'll get reused | |
| # in Singularity build with the wrong GLIBC libraries. | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install .[dev,test] | |
| - name: Run type checker | |
| run: | | |
| mypy | |
| - name: Run linter | |
| run: | | |
| ruff check | |
| - name: Test with pytest | |
| run: coverage run --source=micall/core,micall/g2p,micall/resistance,micall/monitor -m pytest | |
| - name: Report code coverage | |
| run: | | |
| rm -rf micall/tests/microtest/scratch | |
| python -m pip install codecov | |
| codecov | |
| docker-test: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Build docker image | |
| run: docker build --tag micall --file Dockerfile . | |
| - name: Run docker image entrypoint | |
| run: docker run micall --help | |
| - name: Check docker image entrypoint | |
| run: docker run micall --help | grep -i -e 'docker' | |
| singularity-test: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - uses: actions/setup-go@v2 | |
| with: | |
| go-version: '^1.15.6' | |
| - name: Run apt update | |
| run: sudo apt-get update | |
| - name: Install Singularity | |
| run: | | |
| sudo apt-get install -qq \ | |
| build-essential \ | |
| uuid-dev \ | |
| libgpgme-dev \ | |
| squashfs-tools \ | |
| libseccomp-dev \ | |
| wget \ | |
| pkg-config \ | |
| git \ | |
| cryptsetup-bin | |
| git clone https://github.com/singularityware/singularity.git | |
| cd singularity | |
| git checkout -q tags/v3.7.1 | |
| ./mconfig && \ | |
| make -C ./builddir && \ | |
| sudo make -C ./builddir install | |
| cd .. | |
| rm -rf singularity | |
| singularity --version | |
| - name: Singularity build | |
| run: sudo singularity build micall.simg Singularity | |
| - name: Singularity test | |
| run: python micall/main.py release_test_microtest micall.simg | |
| - name: Upload Singularity Image | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: micall.simg | |
| path: micall.simg |