binary tarball #1207
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| name: binary tarball | |
| on: | |
| workflow_dispatch: | |
| release: | |
| branches: [ master ] | |
| repository_dispatch: | |
| types: [linux-binary-test, install-test] | |
| schedule: | |
| - cron: '15 15 * * *' # 3:15pm every day | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: prerequisites | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y hmmer ncbi-blast+ curl build-essential | |
| - name: download | |
| run: bash -x .github/workflows/get_binary_release.sh | |
| - name: Software and db version | |
| run: ./amrfinder --database_version | |
| - name: run tests included with distribution | |
| run: | | |
| ./amrfinder --plus -p test_prot.fa -g test_prot.gff -O Escherichia --print_node > test_prot.got | |
| diff test_prot.expected test_prot.got | |
| ./amrfinder --plus -n test_dna.fa -O Escherichia --mutation_all test_dna_mut_all.got --print_node > test_dna.got | |
| diff test_dna.expected test_dna.got | |
| ./amrfinder --plus -n test_dna.fa -p test_prot.fa -g test_prot.gff -O Escherichia --print_node > test_both.got | |
| diff test_both.expected test_both.got | |
| - name: Run tests | |
| run: | | |
| # temporarily we need to download the test script. Can remove | |
| # once we have a new software release and it's included in the | |
| # distribution | |
| BASE_URL="https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/master" | |
| echo "BASE_URL=${BASE_URL}" | |
| 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 | |
| bash -x ./test_amrfinder.sh |