Update Maaslin2 version to use latest from BioC (#46915) #89
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| name: Update build failure list | |
| on: | |
| schedule: | |
| - cron: 5 5 * * * | |
| push: | |
| branches: | |
| - master | |
| paths: | |
| - "**build_failure.*.yaml" | |
| jobs: | |
| update-build-failure-page: | |
| name: Update build failure page | |
| if: github.repository == 'bioconda/bioconda-recipes' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - 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/{common,install-and-set-up-conda,configure-conda}.sh | |
| - name: Restore cache | |
| id: cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: /opt/mambaforge | |
| key: ${{ runner.os }}--master--${{ hashFiles('install-and-set-up-conda.sh', 'common.sh', 'configure-conda.sh') }} | |
| - name: Set up bioconda-utils | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: bash install-and-set-up-conda.sh | |
| # This script can be used to reconfigure conda to use the right channel setup. | |
| # This has to be done after the cache is restored, because | |
| # the channel setup is not cached as it resides in the home directory. | |
| # We could use a system-wide (and therefore cached) channel setup, | |
| # but mamba does not support that at the time of implementation | |
| # (it ignores settings made with --system). | |
| - name: Configure conda | |
| run: bash configure-conda.sh | |
| - name: Generate build failure table | |
| run: | | |
| set -e | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| mkdir build-failures | |
| md=build-failures/build-failures.md | |
| echo "# Build failures" > $md | |
| echo "Automatically updated (nightly) list of build failures that currently block builds from the listed recipes. Please help with fixing them!" >> $md | |
| bioconda-utils list-build-failures recipes --output-format markdown --link-prefix https://github.com/bioconda/bioconda-recipes/blob/master >> $md | |
| - name: Upload build failure to wiki | |
| uses: docker://decathlon/wiki-page-creator-action:latest | |
| env: | |
| GH_PAT: ${{secrets.BIOCONDA_BOT_REPO_TOKEN}} | |
| ACTION_MAIL: [email protected] | |
| ACTION_NAME: BiocondaBot | |
| OWNER: bioconda | |
| REPO_NAME: bioconda-recipes | |
| MD_FOLDER: build-failures | |