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| # ref https://github.com/marketplace/actions/setup-miniconda | ||
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| # This workflow uses actions that are not certified by GitHub. | ||
| # They are provided by a third-party and are governed by | ||
| # separate terms of service, privacy policy, and support | ||
| # documentation. | ||
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| # GitHub recommends pinning actions to a commit SHA. | ||
| # To get a newer version, you will need to update the SHA. | ||
| # You can also reference a tag or branch, but the action may change without warning. | ||
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| # By default, GitHub Actions uses different shells based on the runner operating system: | ||
| # Ubuntu (Linux) and macOS: bash | ||
| # Windows: cmd | ||
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| # We can test tRFtarget-pipeline on multiple OS by setting os: ["ubuntu-latest", "macos-13", "windows-latest"] | ||
| # Note: We use macOS 13 Ventura instead of the latest macOS because ARM64 processors (M1, M2, M3 series) may have issues running the Docker image. | ||
| # The Docker image supports the linux/amd64 architecture, so it will not work on macOS with an ARM64 CPU or on Windows | ||
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| name: Test tRFtarget-pipeline across different OS | ||
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| on: | ||
| push: | ||
| branches: | ||
| - main | ||
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| jobs: | ||
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| test-docker: | ||
| name: test-docker (${{ matrix.os }}) | ||
| runs-on: ${{ matrix.os }} | ||
| defaults: | ||
| run: | ||
| # bash login mode is needed for activate environment in Ubuntu and macOS (ref https://github.com/marketplace/actions/setup-miniconda#important) | ||
| # cmd in Windows is fine | ||
| shell: bash -el {0} # `-e` means the shell will stop executing if any command returns a non-zero status (error). `-l` makes Bash act as if it had been invoked as a login shell | ||
| strategy: | ||
| fail-fast: false # all job combinations will run to completion even if one of them fails | ||
| matrix: # uses a matrix strategy to run multiple test configurations across different operating systems and Python versions | ||
| os: ["ubuntu-latest", "macos-13"] | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
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| - name: Download test files for Ubuntu and macOS # note to use URL for the raw file | ||
| if: runner.os != 'Windows' | ||
| run: | | ||
| mkdir testfolder | ||
| wget -P "$(pwd)/testfolder" https://raw.githubusercontent.com/ZWang-Lab/tRFtarget-pipeline/main/sample_data/test_tRF.fasta | ||
| wget -P "$(pwd)/testfolder" https://raw.githubusercontent.com/ZWang-Lab/tRFtarget-pipeline/main/sample_data/test_transcript.fasta | ||
| #- name: Download test files for Windows | ||
| # if: runner.os == 'Windows' | ||
| # shell: powershell | ||
| # run: | | ||
| # mkdir testfolder | ||
| # Invoke-WebRequest -Uri 'https://raw.githubusercontent.com/ZWang-Lab/tRFtarget-pipeline/main/sample_data/test_tRF.fasta' -OutFile 'testfolder/test_tRF.fasta' | ||
| # Invoke-WebRequest -Uri 'https://raw.githubusercontent.com/ZWang-Lab/tRFtarget-pipeline/main/sample_data/test_transcript.fasta' -OutFile 'testfolder/test_transcript.fasta' | ||
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| - name: Extract version number from tag on Ubuntu and macOS # note to create an environment variable for later reference; note the workflow is not trigged by release event; note only works for public repo | ||
| if: runner.os != 'Windows' | ||
| run: | | ||
| LATEST_TAG=$(curl --silent "https://api.github.com/repos/ZWang-Lab/tRFtarget-pipeline/releases/latest" | awk -F '"' '/"tag_name":/ {print $4}') | ||
| echo "LATEST_TAG: $LATEST_TAG" | ||
| if [ -z "$LATEST_TAG" ]; then | ||
| echo "Error: Failed to retrieve the latest tag" | ||
| exit 1 | ||
| fi | ||
| VERSION_NUMBER=${LATEST_TAG#v} | ||
| echo "VERSION_NUMBER: $VERSION_NUMBER" | ||
| echo "VERSION_NUMBER=$VERSION_NUMBER" >> $GITHUB_ENV | ||
| #- name: Extract version number from tag on windows # note to create an environment variable for later reference; note the workflow is not trigged by release event; note only works for public repo | ||
| # if: runner.os == 'Windows' # https://github.com/actions/runner/issues/1636 | ||
| # shell: powershell | ||
| # run: | | ||
| # $latestTag = (Invoke-WebRequest -Uri "https://api.github.com/repos/ZWang-Lab/tRFtarget-pipeline/releases/latest" | ConvertFrom-Json).tag_name | ||
| # $versionNumber = $latestTag -replace '^v' | ||
| # echo "VERSION_NUMBER=$versionNumber" | Out-File -FilePath $env:GITHUB_ENV -Append # no need for -Encoding utf8 | ||
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| - name: Check if Homebrew is installed on macOS | ||
| if: runner.os == 'macOS' | ||
| run: | | ||
| if ! command -v brew &> /dev/null; then | ||
| echo "Homebrew not found. Installing Homebrew..." | ||
| /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" | ||
| else | ||
| echo "Homebrew is already installed." | ||
| fi | ||
| - name: Install Docker using Homebrew on macOS | ||
| if: runner.os == 'macOS' | ||
| run: | | ||
| brew install tree colima docker | ||
| - name: Start Docker on macOS # https://stackoverflow.com/a/76490257 | ||
| if: runner.os == 'macOS' | ||
| run: | | ||
| colima start | ||
| while ! docker info &>/dev/null; do | ||
| echo "Waiting for Docker to start...It can take over 2 minutes..." | ||
| sleep 20 | ||
| done | ||
| - name: Download docker image with specific version | ||
| run: | | ||
| docker pull az7jh2/trftarget:${{ env.VERSION_NUMBER }} | ||
| - name: Test version | ||
| run: | | ||
| PACKAGE_VERSION=$(docker run --rm az7jh2/trftarget:${{ env.VERSION_NUMBER }} tRFtarget -v | tail -n 1 | grep -o '[0-9]\+\.[0-9]\+\.[0-9]\+') | ||
| if [ "$PACKAGE_VERSION" == "${{ env.VERSION_NUMBER }}" ]; then | ||
| echo "Version matches: $PACKAGE_VERSION" | ||
| else | ||
| echo "Version mismatch. Expected ${{ env.VERSION_NUMBER }}, but got $PACKAGE_VERSION" | ||
| exit 1 | ||
| fi | ||
| - name: Test pipeline | ||
| run: | | ||
| docker run --rm -v $(pwd)/testfolder:/data az7jh2/trftarget:${{ env.VERSION_NUMBER }} tRFtarget -q test_tRF.fasta \ | ||
| -t test_transcript.fasta \ | ||
| -n 4 \ | ||
| --e_rnahybrid -15 \ | ||
| --e_intarna 0 \ | ||
| -b 1 \ | ||
| -s 6 | ||
| - name: Print result | ||
| run: | | ||
| docker run --rm az7jh2/trftarget:${{ env.VERSION_NUMBER }} python --version | ||
| docker run --rm az7jh2/trftarget:${{ env.VERSION_NUMBER }} tRFtarget -v | ||
| tree $(pwd)/testfolder |
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