Bystro Annotator Install Script (RPM) #197
Workflow file for this run
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| name: Bystro Annotator Install Script (RPM) | |
| on: | |
| release: | |
| types: [published] | |
| pull_request: | |
| paths: | |
| - "install-rpm.sh" | |
| - "install/**" | |
| workflow_dispatch: # Optional: allows manual triggering of the workflow | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: amazonlinux:2023 | |
| steps: | |
| - name: Install dependencies | |
| run: | | |
| dnf install -y sudo tar | |
| # Checkout the repository | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| # Run the install script | |
| - name: Install Bystro using RPM script | |
| run: | | |
| touch ~/.profile | |
| ./install-rpm.sh --profile-file ~/.profile | |
| # Test that bystro-annotate.pl works | |
| # When it runs with --help it exits with 255 | |
| - name: Verify installation by running bystro-annotate.pl --help | |
| continue-on-error: true | |
| run: | | |
| source ~/.profile | |
| output=$(bystro-annotate.pl --help 2>&1) | |
| exit_code=$? | |
| first_line=$(echo "$output" | head -n 1) | |
| if [ "$exit_code" -eq 255 ]; then | |
| echo "Exit code 255 confirmed." | |
| else | |
| echo "Unexpected exit code: $exit_code" >&2 | |
| exit 1 | |
| fi | |
| if [[ "$first_line" == "usage: bystro-annotate.pl"* ]]; then | |
| echo "First line matches the expected 'usage: bystro-annotate.pl'." | |
| else | |
| echo "First line does not match the expected 'usage: bystro-annotate.pl'." >&2 | |
| echo "Actual first line: $first_line" >&2 | |
| exit 1 | |
| fi | |
| # Test that bystro-build.pl works | |
| # when it runs with --help it exits with 1 | |
| - name: Verify installation by running bystro-build.pl --help | |
| continue-on-error: true | |
| run: | | |
| source ~/.profile | |
| output=$(bystro-build.pl --help 2>&1) | |
| first_line=$(echo "$output" | head -n 1) | |
| if [[ "$first_line" == "Usage:"* ]]; then | |
| echo "First line matches the expected 'Usage:'" | |
| else | |
| echo "First line does not match the expected 'Usage:'" >&2 | |
| echo "Actual first line: $first_line" >&2 | |
| exit 1 | |
| fi | |
| - name: Run tests | |
| run: | | |
| cd perl | |
| source ~/.profile | |
| prove -r -j$(nproc) t | |
| - name: Check that expected programs are in the PATH | |
| run: | | |
| source ~/.profile | |
| if command -v bystro-annotate.pl > /dev/null; then | |
| echo "bystro-annotate.pl is in the PATH" | |
| else | |
| echo "bystro-annotate.pl is not in the PATH" >&2 | |
| exit 1 | |
| fi | |
| if command -v bystro-build.pl > /dev/null; then | |
| echo "bystro-build.pl is in the PATH" | |
| else | |
| echo "bystro-build.pl is not in the PATH" >&2 | |
| exit 1 | |
| fi | |
| if command -v bystro-vcf > /dev/null; then | |
| echo "bystro-vcf is in the PATH" | |
| else | |
| echo "bystro-vcf is not in the PATH" >&2 | |
| exit 1 | |
| fi | |
| if command -v bystro-snp > /dev/null; then | |
| echo "bystro-snp is in the PATH" | |
| else | |
| echo "bystro-snp is not in the PATH" >&2 | |
| exit 1 | |
| fi | |
| if command -v bystro-stats > /dev/null; then | |
| echo "bystro-stats is in the PATH" | |
| else | |
| echo "bystro-stats is not in the PATH" >&2 | |
| exit 1 | |
| fi | |
| if command -v bgzip > /dev/null; then | |
| echo "bgzip is in the PATH" | |
| else | |
| echo "bgzip is not in the PATH" >&2 | |
| exit 1 | |
| fi | |
| if command -v yq > /dev/null; then | |
| echo "yq is in the PATH" | |
| else | |
| echo "yq is not in the PATH" >&2 | |
| exit 1 | |
| fi |