pandagma pan #10
Workflow file for this run
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| name: pandagma pan | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| pandagma-conf: | |
| # Glycine5_21_29_6 times out | |
| default: '["Arachis3_5_2_0", "Cicer3_4_2_0", "Glycine_7_3_2", "Medicago3_8_0_15", "Vigna4_7_1_4"]' | |
| description: Run pandagma pan for each config/NAME.conf file in the (JSON) array | |
| required: true | |
| ssh_enabled: | |
| type: boolean | |
| description: 'Stop after cloning repository and enable SSH access for debugging' | |
| required: false | |
| default: false | |
| jobs: | |
| pandagma: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| PANDAGMA_CONF: ${{ fromJSON(github.event.inputs.pandagma-conf) }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Setup SSH session for debugging | |
| uses: mxschmitt/action-tmate@v3 | |
| if: ${{ inputs.ssh_enabled }} | |
| with: | |
| limit-access-to-actor: false | |
| - name: Fetch data | |
| run: | | |
| mkdir data | |
| PATH=$PWD/bin:$PATH make -C data -f "${PWD}/get_data/${{ matrix.PANDAGMA_CONF }}.mk" | |
| - name: Create conda environment | |
| run: conda env create && conda clean --all -y | |
| # Need transparent filesystem compression for larger datasets | |
| - name: Create work filesystem | |
| run: | | |
| sudo apt update | |
| sudo apt install -y --no-install-recommends zfsutils-linux | |
| sudo truncate -s $((55*2**30)) /mnt/zpool | |
| sudo zpool create work -O atime=off -O compression=lz4 /mnt/zpool | |
| sudo chmod 777 /work | |
| - name: Run pandagma | |
| env: | |
| PANDAGMA_CONF: ${{ matrix.PANDAGMA_CONF }} | |
| # explicitly use bash to enforce pipefail | |
| # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#exit-codes-and-error-action-preference | |
| shell: bash | |
| run: | | |
| mkdir -p ${PANDAGMA_OUT:=upload-artifact/pandagma-pan-${PANDAGMA_CONF}} | |
| printf 'GITHUB_REPOSITORY: %s\n\n' "${GITHUB_REPOSITORY}" > ${PANDAGMA_OUT}/VERSION | |
| git show --quiet >> ${PANDAGMA_OUT}/VERSION | |
| cp config/${PANDAGMA_CONF}.conf ${PANDAGMA_OUT} | |
| env PATH=$PWD/bin:$PATH time -v conda run -n pandagma --no-capture-output pandagma TEfilter -d data -c "config/${PANDAGMA_CONF}.conf" -w /work 2>&1 | tee ${PANDAGMA_OUT}/pandagma.log | |
| env PATH=$PWD/bin:$PATH time -v conda run -n pandagma --no-capture-output pandagma pan -d data_TEfilter -c "config/${PANDAGMA_CONF}.conf" -w /work -r -o ${PANDAGMA_OUT} 2>&1 | tee ${PANDAGMA_OUT}/pandagma.log | |
| - name: Upload output artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: pandagma-pan-${{ matrix.PANDAGMA_CONF }} | |
| # Need to create subdirectory to unzip as directory | |
| # https://github.com/actions/upload-artifact/issues/248 | |
| path: upload-artifact | |
| if-no-files-found: error | |
| retention-days: 90 | |
| compression-level: 9 |