Update bbmap to 39.13 #2873
Workflow file for this run
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| name: PR Check | |
| on: | |
| pull_request: | |
| types: [opened, synchronize, reopened] | |
| concurrency: | |
| group: build-${{ github.event.pull_request.number || github.head_ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| lint: | |
| name: Lint | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: true | |
| max-parallel: 13 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: set path | |
| run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| - name: Fetch conda install script | |
| run: | | |
| wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh | |
| - name: Set up bioconda-utils | |
| run: bash install-and-set-up-conda.sh | |
| - name: Configure conda | |
| run: bash configure-conda.sh | |
| - name: Perform lint | |
| env: | |
| # Mimic circleci | |
| OSTYPE: "linux-gnu" | |
| CI: "true" | |
| run: | | |
| set -e | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| source common.sh | |
| echo '============' | |
| conda info --all | |
| conda config --show-sources | |
| python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")' | |
| echo '============' | |
| if [ -z "$GITHUB_BASE_REF" ] ; then | |
| export GITHUB_BASE_REF="master" | |
| fi | |
| git fetch origin "$GITHUB_BASE_REF" | |
| bioconda-utils lint --loglevel debug --full-report --git-range origin/"$GITHUB_BASE_REF" HEAD | |
| conda clean -y --all | |
| build-linux: | |
| name: Linux Tests | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: true | |
| max-parallel: 13 | |
| needs: lint | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: set path | |
| run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| - name: Fetch conda install script | |
| run: | | |
| wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh | |
| - name: Set up bioconda-utils | |
| run: bash install-and-set-up-conda.sh | |
| # This script can be used to reconfigure conda to use the right channel setup. | |
| - name: Configure conda | |
| run: bash configure-conda.sh | |
| - name: Build and test | |
| env: | |
| # Mimic circleci | |
| OSTYPE: "linux-gnu" | |
| CI: "true" | |
| run: | | |
| set -e | |
| # Clean up lingering build artifacts | |
| for n in linux-64 osx-64 noarch; do | |
| rm -f /opt/mambaforge/envs/bioconda/conda-bld/$n/*.tar.bz2 | |
| rm -f /opt/mambaforge/envs/bioconda/conda-bld/$n/*.conda | |
| done | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| source common.sh | |
| if [ -z "$GITHUB_BASE_REF" ] ; then | |
| export GITHUB_BASE_REF="master" | |
| fi | |
| git fetch origin "$GITHUB_BASE_REF" | |
| bioconda-utils build recipes config.yml \ | |
| --docker --mulled-test \ | |
| --git-range origin/"$GITHUB_BASE_REF" HEAD | |
| - name: Prepare artifacts | |
| run: | | |
| ( | |
| rm -rf /tmp/artifacts | |
| mkdir -p /tmp/artifacts/packages | |
| cd /opt/mambaforge/envs/bioconda/conda-bld || exit 0 | |
| find -name .cache | xargs rm -rf || true | |
| for n in index.html channeldata.json linux-64 osx-64 noarch; do | |
| cp -rv $n /tmp/artifacts/packages || true | |
| done | |
| if command -V docker >/dev/null; then | |
| mkdir -p /tmp/artifacts/images | |
| cd /tmp/artifacts/images | |
| docker image ls --format='{{.Repository}}:{{.Tag}}' | \ | |
| { grep biocontainers || true ; } | \ | |
| xargs -n1 -P4 bash -c ' | |
| test -n "${1+x}" || exit 0 | |
| echo "Start compressing docker image ${1} ..." | |
| docker save "${1}" | gzip -c > "${1##*/}.tar.gz" | |
| echo "Finished compressing docker image ${1} ." | |
| ' -- | |
| # There's no : allowed in artifact names, replace it with --- | |
| for f in /tmp/artifacts/images/*:* ; do mv -- "$f" "${f//:/---}"; done | |
| fi | |
| ) || true | |
| - name: Archive packages | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: linux-packages | |
| path: | | |
| /tmp/artifacts | |
| build-osx-64: | |
| name: OSX-64 Tests | |
| runs-on: macos-13 | |
| strategy: | |
| fail-fast: true | |
| max-parallel: 4 | |
| # Limited concurrency for osx, so first make sure linux can pass | |
| needs: build-linux | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: set path | |
| run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| - name: Fetch conda install script | |
| run: | | |
| wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh | |
| - name: Set up bioconda-utils | |
| run: bash install-and-set-up-conda.sh | |
| # This script can be used to reconfigure conda to use the right channel setup. | |
| - name: Configure conda | |
| run: bash configure-conda.sh | |
| - name: Build and Test | |
| env: | |
| # Mimic circleci | |
| OSTYPE: "darwin" | |
| CI: "true" | |
| run: | | |
| set -e | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| source common.sh | |
| # Sets up OSX SDK | |
| run_conda_forge_build_setup | |
| # Clean up lingering build artifacts | |
| for n in linux-64 osx-64 noarch; do | |
| rm -f /opt/mambaforge/envs/bioconda/conda-bld/$n/*.tar.bz2 | |
| done | |
| if [ -z "$GITHUB_BASE_REF" ] ; then | |
| export GITHUB_BASE_REF="master" | |
| fi | |
| git fetch origin "$GITHUB_BASE_REF" | |
| bioconda-utils build recipes config.yml \ | |
| --git-range origin/"$GITHUB_BASE_REF" HEAD | |
| - name: Prepare artifacts | |
| run: | | |
| ( | |
| rm -rf /tmp/artifacts | |
| mkdir -p /tmp/artifacts/packages | |
| cd /opt/mambaforge/envs/bioconda/conda-bld || exit 0 | |
| find -name .cache | xargs rm -rf || true | |
| for n in index.html channeldata.json linux-64 osx-64 noarch; do | |
| cp -rv $n /tmp/artifacts/packages || true | |
| done | |
| ) || true | |
| - name: Archive packages | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: osx-packages | |
| path: | | |
| /tmp/artifacts | |
| # Disabled due to concurrency limits on GHA for OSX. osx-arm64 builds are on CircleCI. | |
| # build_and_test-osx-arm64: | |
| # name: OSX-ARM64 Tests | |
| # runs-on: macOS-14 # M1 | |
| # strategy: | |
| # fail-fast: true | |
| # max-parallel: 4 | |
| # needs: build-linux | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # # bail if there's no osx-arm64 recipes | |
| # - name: Check for Additional Platforms | |
| # id: additional_platforms | |
| # run: | | |
| # result=$(./scripts/check-for-additional-platforms.sh "origin/master...HEAD" "build_and_test" "${GITHUB_JOB}") | |
| # if [[ ${result} != "build" ]] | |
| # then | |
| # echo "No recipes using this platform, skipping rest of job." | |
| # echo "skip_build=true" >> $GITHUB_OUTPUT | |
| # fi | |
| # - name: set path | |
| # run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| # - name: Fetch conda install script | |
| # if: steps.additional_platforms.outputs.skip_build != 'true' | |
| # run: | | |
| # wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh | |
| # - name: Set up bioconda-utils | |
| # if: steps.additional_platforms.outputs.skip_build != 'true' | |
| # run: bash install-and-set-up-conda.sh | |
| # - name: Configure conda | |
| # if: steps.additional_platforms.outputs.skip_build != 'true' | |
| # run: bash configure-conda.sh | |
| # - name: Build and Test | |
| # if: steps.additional_platforms.outputs.skip_build != 'true' | |
| # env: | |
| # # Mimic circleci | |
| # OSTYPE: "darwin" | |
| # CI: "true" | |
| # run: | | |
| # set -xe | |
| # eval "$(conda shell.bash hook)" | |
| # conda activate bioconda | |
| # source common.sh | |
| # # Sets up OSX SDK | |
| # run_conda_forge_build_setup | |
| # if [ -z "$GITHUB_BASE_REF" ] ; then | |
| # export GITHUB_BASE_REF="master" | |
| # fi | |
| # git fetch origin "$GITHUB_BASE_REF" | |
| # bioconda-utils build recipes config.yml \ | |
| # --lint --git-range origin/"$GITHUB_BASE_REF" HEAD | |
| # - name: Prepare artifacts | |
| # if: steps.additional_platforms.outputs.skip_build != 'true' | |
| # run: | | |
| # ( | |
| # rm -rf /tmp/artifacts | |
| # mkdir -p /tmp/artifacts/packages | |
| # cd /opt/mambaforge/envs/bioconda/conda-bld || exit 0 | |
| # find -name .cache | xargs rm -rf || true | |
| # for n in index.html channeldata.json osx-arm64 noarch; do | |
| # cp -rv $n /tmp/artifacts/packages || true | |
| # done | |
| # ) || true | |
| # - name: Archive packages | |
| # if: steps.additional_platforms.outputs.skip_build != 'true' | |
| # uses: actions/upload-artifact@v4 | |
| # with: | |
| # name: osx-arm64-packages | |
| # path: | | |
| # /tmp/artifacts |