{2023.06}[foss/2023a] GATK v4.5.0.0 #92
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| # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions | |
| name: Check for missing software installations in software.eessi.io | |
| on: [push, pull_request, workflow_dispatch] | |
| permissions: | |
| contents: read # to fetch code (actions/checkout) | |
| jobs: | |
| check_missing: | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| EESSI_VERSION: | |
| - 2023.06 | |
| EESSI_SOFTWARE_SUBDIR_OVERRIDE: | |
| - aarch64/generic | |
| - aarch64/neoverse_n1 | |
| - aarch64/neoverse_v1 | |
| - x86_64/amd/zen2 | |
| - x86_64/amd/zen3 | |
| - x86_64/intel/haswell | |
| - x86_64/intel/skylake_avx512 | |
| - x86_64/generic | |
| steps: | |
| - name: Check out software-layer repository | |
| uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1 | |
| - name: Mount EESSI CernVM-FS pilot repository | |
| uses: cvmfs-contrib/github-action-cvmfs@55899ca74cf78ab874bdf47f5a804e47c198743c # v4.0 | |
| with: | |
| cvmfs_config_package: https://github.com/EESSI/filesystem-layer/releases/download/latest/cvmfs-config-eessi_latest_all.deb | |
| cvmfs_http_proxy: DIRECT | |
| cvmfs_repositories: software.eessi.io | |
| - name: Test check_missing_installations.sh script | |
| run: | | |
| export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}} | |
| source /cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}/init/bash | |
| # set $EESSI_CPU_FAMILY to the CPU architecture that corresponds to $EESSI_SOFTWARE_SUBDIR_OVERRIDE (part before the first slash), | |
| # to prevent issues with checks in the Easybuild configuration that use this variable | |
| export EESSI_CPU_FAMILY=${EESSI_SOFTWARE_SUBDIR_OVERRIDE%%/*} | |
| module load EasyBuild | |
| which eb | |
| eb --version | |
| export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}} | |
| export EESSI_OS_TYPE=linux | |
| env | grep ^EESSI | sort | |
| echo "just run check_missing_installations.sh (should use easystacks/software.eessi.io/${{matrix.EESSI_VERSION}}/eessi-${{matrix.EESSI_VERSION}}-*.yml)" | |
| for easystack_file in $(ls easystacks/software.eessi.io/${{matrix.EESSI_VERSION}}/eessi-${{matrix.EESSI_VERSION}}-eb-*.yml); do | |
| echo "check missing installations for ${easystack_file}..." | |
| ./check_missing_installations.sh ${easystack_file} | |
| ec=$? | |
| if [[ ${ec} -ne 0 ]]; then echo "missing installations found for ${easystack_file}!" >&2; exit ${ec}; fi | |
| done | |
| - name: Test check_missing_installations.sh with missing package (GCC/8.3.0) | |
| run: | | |
| export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}} | |
| source /cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}/init/bash | |
| # set $EESSI_CPU_FAMILY to the CPU architecture that corresponds to $EESSI_SOFTWARE_SUBDIR_OVERRIDE (part before the first slash), | |
| # to prevent issues with checks in the Easybuild configuration that use this variable | |
| export EESSI_CPU_FAMILY=${EESSI_SOFTWARE_SUBDIR_OVERRIDE%%/*} | |
| module load EasyBuild | |
| which eb | |
| eb --version | |
| export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}} | |
| export EESSI_OS_TYPE=linux | |
| env | grep ^EESSI | sort | |
| # create dummy easystack file with a single entry (something that is not installed in EESSI) | |
| easystack_file="test.yml" | |
| echo "easyconfigs:" > ${easystack_file} | |
| echo " - GCC-8.3.0:" >> ${easystack_file} | |
| echo "created easystack file '${easystack_file}' with a missing installation (GCC/8.3.0):" | |
| cat ${easystack_file} | |
| # note, check_missing_installations.sh exits 1 if a package was | |
| # missing, which is intepreted as false (exit code based, not | |
| # boolean logic), hence when the script exits 0 if no package was | |
| # missing it is interpreted as true, thus the test did not capture | |
| # the missing package | |
| if ./check_missing_installations.sh ${easystack_file}; then | |
| echo "did NOT capture missing package; test FAILED" | |
| exit 1 | |
| else | |
| echo "captured missing package; test PASSED" | |
| exit 0 | |
| fi |