Linux bioconda #1656
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| name: Linux bioconda | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: '15 3 * * *' # 3:15am everyday | |
| repository_dispatch: | |
| types: [linux-bioconda-test, install-test] | |
| jobs: | |
| install_and_test: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: When was this run | |
| run: date | |
| - name: configure conda | |
| run: | | |
| . $CONDA/bin/activate | |
| conda config --add channels defaults | |
| conda config --add channels bioconda | |
| conda config --add channels conda-forge | |
| - name: install AMRFinderPlus | |
| run: | | |
| . $CONDA/bin/activate | |
| conda install --update-deps -c conda-forge -c bioconda -y ncbi-amrfinderplus | |
| amrfinder --version | |
| - name: download latest AMRFinderPlus database | |
| run: | | |
| source /usr/share/miniconda/bin/activate | |
| echo CONDA_PREFIX = ${CONDA_PREFIX} | |
| /usr/share/miniconda/bin/amrfinder --force_update | |
| - name: Software and DB version | |
| run: | | |
| source /usr/share/miniconda/bin/activate | |
| amrfinder --database_version | |
| - name: download tests | |
| run: | | |
| BASE_URL=https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/master | |
| curl --silent -L \ | |
| -O ${BASE_URL}/test_dna.fa \ | |
| -O ${BASE_URL}/test_prot.fa \ | |
| -O ${BASE_URL}/test_prot.gff \ | |
| -O ${BASE_URL}/test_both.expected \ | |
| -O ${BASE_URL}/test_dna.expected \ | |
| -O ${BASE_URL}/test_dna_mut_all.expected \ | |
| -O ${BASE_URL}/test_prot.expected \ | |
| -O ${BASE_URL}/test_amrfinder.sh | |
| - name: run tests | |
| run: | | |
| source /usr/share/miniconda/bin/activate | |
| echo CONDA_PREFIX = $CONDA_PREFIX | |
| bash ./test_amrfinder.sh path |