Update species probes #56
Workflow file for this run
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| name: Mykrobe builds | |
| on: | |
| push: | |
| tags: | |
| - 'v*.*.*' | |
| branches: | |
| - master | |
| pull_request: | |
| branches: | |
| - master | |
| env: | |
| REGISTRY: ghcr.io | |
| IMAGE_NAME: ${{ github.repository }} | |
| jobs: | |
| build_containers: | |
| name: Build linux/singularity container | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Set up Go 1.16 | |
| uses: actions/setup-go@v1 | |
| with: | |
| go-version: 1.16 | |
| id: go | |
| - name: Install Dependencies | |
| run: | | |
| sudo apt-get update && sudo apt-get install -y \ | |
| build-essential \ | |
| libssl-dev \ | |
| uuid-dev \ | |
| libgpgme11-dev \ | |
| squashfs-tools \ | |
| libseccomp-dev \ | |
| pkg-config \ | |
| debootstrap \ | |
| debian-keyring \ | |
| debian-archive-keyring \ | |
| rsync | |
| - name: Install Singularity | |
| env: | |
| SINGULARITY_VERSION: 3.5.3 | |
| GOPATH: /tmp/go | |
| run: | | |
| mkdir -p $GOPATH | |
| sudo mkdir -p /usr/local/var/singularity/mnt | |
| mkdir -p $GOPATH/src/github.com/sylabs | |
| cd $GOPATH/src/github.com/sylabs | |
| wget https://github.com/hpcng/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-${SINGULARITY_VERSION}.tar.gz | |
| tar -xzf singularity-${SINGULARITY_VERSION}.tar.gz | |
| cd singularity | |
| ./mconfig -v -p /usr/local | |
| make -j `nproc 2>/dev/null || echo 1` -C ./builddir all | |
| sudo make -C ./builddir install | |
| - name: Check out code for the container build | |
| uses: actions/checkout@v3 | |
| - name: Set release version if is a release | |
| if: startsWith(github.event.ref, 'refs/tags/v') | |
| run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV | |
| - name: Set release version if not a release | |
| if: false == startsWith(github.event.ref, 'refs/tags/v') | |
| run: echo "RELEASE_VERSION=test" >> $GITHUB_ENV | |
| - name: Build Singularity container | |
| env: | |
| SINGULARITY_RECIPE: Singularity.def | |
| OUTPUT_CONTAINER: mykrobe_${{env.RELEASE_VERSION}}.img | |
| run: | | |
| ls | |
| if [ -f "${SINGULARITY_RECIPE}" ]; then | |
| sudo -E singularity build ${OUTPUT_CONTAINER} ${SINGULARITY_RECIPE} | |
| else | |
| echo "${SINGULARITY_RECIPE} is not found." | |
| echo "Present working directory: $PWD" | |
| ls | |
| fi | |
| - name: Release | |
| if: startsWith(github.event.ref, 'refs/tags/v') | |
| uses: softprops/action-gh-release@v1 | |
| with: | |
| files: mykrobe*.img | |
| draft: true | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| mac_build: | |
| name: Build mac os command line | |
| runs-on: macos-11 | |
| steps: | |
| - name: Check out code for the build | |
| uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.8' | |
| - name: Install dependencies | |
| run: | | |
| git clone --recursive -b geno_kmer_count https://github.com/phelimb/mccortex mccortex | |
| cd mccortex | |
| make MAXK=31 | |
| cd .. | |
| cp mccortex/bin/mccortex31 src/mykrobe/cortex/ | |
| python -m pip install -r requirements.txt wheel pyinstaller | |
| sudo python -m pip install . | |
| - name: Set release version if is a release | |
| if: startsWith(github.event.ref, 'refs/tags/v') | |
| run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV | |
| - name: Set release version if not a release | |
| if: false == startsWith(github.event.ref, 'refs/tags/v') | |
| run: echo "RELEASE_VERSION=test" >> $GITHUB_ENV | |
| - name: Test and build command line tarball | |
| env: | |
| OUTPUT_TARBALL: mykrobe.command_line.osx.${{env.RELEASE_VERSION}}.tar.gz | |
| run: | | |
| # mongod default data directory is /data/db, which is not writeable. | |
| mkdir $HOME/mongodb_data | |
| chown -R `id -un` $HOME/mongodb_data | |
| sudo mongod --dbpath=$HOME/mongodb_data --quiet &> /dev/null & | |
| sleep 3s | |
| pytest --cov-report term-missing --cov=mykrobe | |
| mykrobe panels update_metadata --panels_dir src/mykrobe/data | |
| mykrobe panels update_species --panels_dir src/mykrobe/data --debug all | |
| cd dist | |
| pyinstaller --workpath='./pyinstaller_build/binary_cache' --distpath='./pyinstaller_build' mykrobe_atlas_pyinstaller.spec | |
| cd pyinstaller_build | |
| tar cvfz ../../${OUTPUT_TARBALL} mykrobe_atlas/ | |
| - name: Release | |
| if: startsWith(github.event.ref, 'refs/tags/v') | |
| uses: softprops/action-gh-release@v1 | |
| with: | |
| files: mykrobe.command_line.osx.*.tar.gz | |
| draft: true | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| windows_build: | |
| name: Build Windows command line | |
| runs-on: windows-2019 | |
| steps: | |
| - uses: msys2/setup-msys2@v2 | |
| with: | |
| update: true | |
| install: >- | |
| autotools gcc git libcurl-devel bzip2 liblzma zip libbz2-devel xz zlib zlib-devel libtool wget liblzma-devel ncurses-devel base-devel openssl-devel mingw64/mingw-w64-x86_64-python3 mingw64/mingw-w64-x86_64-python3-pip mingw-w64-x86_64-python3-numpy mingw-w64-x86_64-python3-setuptools mingw-w64-x86_64-python3-wheel mingw-w64-x86_64-python-biopython | |
| - name: Check out code for the build | |
| uses: actions/checkout@v3 | |
| - name: Set release version if is a release | |
| if: startsWith(github.event.ref, 'refs/tags/v') | |
| run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV | |
| shell: msys2 {0} | |
| - name: Set release version if not a release | |
| if: false == startsWith(github.event.ref, 'refs/tags/v') | |
| run: echo "RELEASE_VERSION=test" >> $GITHUB_ENV | |
| shell: msys2 {0} | |
| - name: Start MongoDB service | |
| run: | | |
| sc.exe config MongoDB start= auto | |
| sc.exe start MongoDB | |
| - name: Test and build command line tarball | |
| env: | |
| OUTPUT_TARBALL: mykrobe.command_line.windows.${{env.RELEASE_VERSION}}.tar.gz | |
| run: | | |
| export PYTHONPATH="/mingw64/lib/python3.11/:/mingw64/lib/python3.11/site-packages:${PYTHONPATH}" | |
| echo "PATH:" | |
| echo "${PATH}" | |
| echo "ls /mingw64/lib/python3.11/" | |
| ls /mingw64/lib/python3.11/ | |
| echo "ls /mingw64/lib/python3.11/site-packages" | |
| ls /mingw64/lib/python3.11/site-packages | |
| C:\\msys64\\mingw64\\bin\\python3.exe -m ensurepip --upgrade | |
| C:\\msys64\\mingw64\\bin\\python3.exe -m pip install pyinstaller requests pytest | |
| echo "clone mccortex" | |
| rm -rf mccortex | |
| git clone --recursive -b geno_kmer_count https://github.com/phelimb/mccortex | |
| cd mccortex/libs/htslib | |
| git checkout bcf9bff178f81c9c1cf3a052aeb6cbe32fe5fdcc | |
| cd ../bcftools | |
| git checkout b406a3906b153faa8bec0a53df07b2adf18a3052 | |
| cd ../samtools | |
| git checkout 2d4907cf9a34ccf7cde60143158b39e1cb40ac0c | |
| cd ../../../ | |
| python ./ci/windows_file_fixes.py | |
| cd mccortex | |
| echo "make mccortex" | |
| make all | |
| echo "make tests mccortex" | |
| make tests | |
| cd .. | |
| echo "pip install requirements" | |
| C:\\msys64\\mingw64\\bin\\python3.exe -m pip install -r requirements.txt | |
| echo "pip install ." | |
| C:\\msys64\\mingw64\\bin\\python3.exe -m pip install . | |
| echo "pytest" | |
| export MYKROBE_MCCORTEX="${PWD}/mccortex/bin/mccortex31" | |
| C:\\msys64\\mingw64\\bin\\python3.exe -m pytest | |
| echo "update panels" | |
| C:\\msys64/mingw64/bin/mykrobe.exe panels update_metadata --panels_dir src/mykrobe/data | |
| C:\\msys64/mingw64/bin/mykrobe.exe panels update_species --panels_dir src/mykrobe/data --debug all | |
| cd dist | |
| C:\\msys64/mingw64/bin/pyinstaller.exe --workpath='./pyinstaller_build/binary_cache' --distpath='./pyinstaller_build' mykrobe_atlas_pyinstaller_windows.spec | |
| cd pyinstaller_build | |
| tar cvfz ../../${OUTPUT_TARBALL} mykrobe_atlas/ | |
| shell: msys2 {0} | |
| - name: Release | |
| if: startsWith(github.event.ref, 'refs/tags/v') | |
| uses: softprops/action-gh-release@v1 | |
| with: | |
| files: mykrobe.command_line.windows.*.tar.gz | |
| draft: true | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} |