Update pbmm2 to 1.16.99 (#52790) #1078
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| name: Upload | |
| on: | |
| push: | |
| branches: | |
| - master | |
| jobs: | |
| build-linux: | |
| name: Linux Upload | |
| if: github.repository == 'bioconda/bioconda-recipes' | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| fail-fast: false | |
| 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 | |
| # 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 upload | |
| env: | |
| QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }} | |
| QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }} | |
| ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} | |
| INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # Mimic circleci | |
| OSTYPE: "linux-gnu" | |
| CI: "true" | |
| run: | | |
| set -ex | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| bioconda-utils handle-merged-pr recipes config.yml \ | |
| --repo bioconda/bioconda-recipes \ | |
| --git-range ${GITHUB_SHA}~1 ${GITHUB_SHA} \ | |
| --quay-upload-target biocontainers \ | |
| --fallback build \ | |
| --artifact-source github-actions | |
| build-osx-64: | |
| name: OSX-64 Upload | |
| if: github.repository == 'bioconda/bioconda-recipes' | |
| runs-on: macos-13 | |
| strategy: | |
| fail-fast: false | |
| max-parallel: 4 | |
| 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: | |
| QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }} | |
| QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }} | |
| ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} | |
| INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }} | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # Mimic circleci | |
| OSTYPE: "darwin" | |
| CI: "true" | |
| run: | | |
| set -e | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| # Sets up OSX SDK | |
| run_conda_forge_build_setup | |
| bioconda-utils handle-merged-pr recipes config.yml \ | |
| --repo bioconda/bioconda-recipes \ | |
| --git-range ${GITHUB_SHA}~1 ${GITHUB_SHA} \ | |
| --fallback build \ | |
| --artifact-source github-actions | |
| # Disabled due to concurrency limits on GHA for OSX. osx-arm64 builds are on CircleCI. | |
| # build_and_upload-osx-arm64: | |
| # name: OSX-ARM64 Upload | |
| # if: github.repository == 'bioconda/bioconda-recipes' | |
| # runs-on: macOS-14 # M1 | |
| # strategy: | |
| # fail-fast: false | |
| # max-parallel: 4 | |
| # steps: | |
| # - uses: actions/checkout@v4 | |
| # with: | |
| # fetch-depth: 0 | |
| # # bail if there's no osx-arm64 recipes | |
| # - name: Check for Additional Platforms | |
| # id: additional_platforms | |
| # run: | | |
| # result=$(./scripts/check-for-additional-platforms.sh "${GITHUB_SHA}~1 ${GITHUB_SHA}" "build_and_upload" "${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 Upload | |
| # if: steps.additional_platforms.outputs.skip_build != 'true' | |
| # env: | |
| # QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }} | |
| # QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }} | |
| # ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} | |
| # INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }} | |
| # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| # # Mimic circleci | |
| # OSTYPE: "darwin" | |
| # CI: "true" | |
| # run: | | |
| # set -xe | |
| # eval "$(conda shell.bash hook)" | |
| # conda activate bioconda | |
| # source common.sh | |
| # # Sets up OSX SDK | |
| # run_conda_forge_build_setup | |
| # bioconda-utils handle-merged-pr recipes config.yml \ | |
| # --repo bioconda/bioconda-recipes \ | |
| # --git-range ${GITHUB_SHA}~1 ${GITHUB_SHA} \ | |
| # --fallback build \ | |
| # --artifact-source github-actions |