binary tarball #1024
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |