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L2P Galaxy Tool - Repository Summary

📁 Repository Contents

l2p-galaxy-tool/
├── .github/
│   └── workflows/
│       └── docker-publish.yml      # CI/CD for Docker builds
├── test_data/
│   └── deg_results.csv            # Sample test data
├── .gitignore                     # Git ignore patterns
├── CHANGELOG.md                   # Version history
├── Dockerfile                     # Container definition
├── L2P_Single.R                   # Core analysis (802 lines, iteration 19)
├── LICENSE                        # MIT License
├── l2p_single.xml                # Galaxy tool wrapper
├── QUICKSTART.md                  # Setup instructions
├── README.md                      # Full documentation
└── run_L2P_Single.R              # CLI wrapper script

🎯 What's Included

Core Files

  • L2P_Single.R: Main analysis functions with all plot fixes (50pt margins, wrapped labels, corrected x-axis)
  • run_L2P_Single.R: Command-line wrapper that parses arguments and executes analysis
  • l2p_single.xml: Galaxy tool definition (configure for ghcr.io)

Docker

  • Dockerfile: Complete container definition based on rocker/r-ver:4.1.3
  • Includes all R dependencies and L2P packages from CCBR

CI/CD

  • docker-publish.yml: Automated workflow that:
    • Builds on push to main
    • Publishes to GitHub Container Registry
    • Tags with version numbers, SHA, and 'latest'
    • Uses GitHub Actions cache for faster builds

Documentation

  • README.md: Complete user and developer guide
  • QUICKSTART.md: Step-by-step setup instructions
  • CHANGELOG.md: Version history and fixes
  • LICENSE: MIT license

Test Data

  • deg_results.csv: Sample differential expression data for testing

🚀 Ready to Deploy

Before You Start

Replace NIDAP-Community in these files:

  1. README.md (multiple locations)
  2. l2p_single.xml (container reference)
  3. Dockerfile (LABEL org.opencontainers.image.source)
  4. QUICKSTART.md (example commands)

Setup Checklist

  • Create GitHub repository named l2p-galaxy-tool
  • Replace NIDAP-Community with your GitHub username in files above
  • Update LICENSE copyright with your name/organization
  • Initialize git and push to GitHub
  • Wait for first GitHub Action to complete
  • Make container package public (optional)
  • Test by pulling image: docker pull ghcr.io/NIDAP-Community/l2p-galaxy-tool:latest
  • Update your Galaxy tool XML to reference the new container
  • Create v1.1.0 release tag

📊 Key Features

Plot Improvements (Iteration 19)

✅ Bar plots: 50pt top margin (lines 237, 266 in L2P_Single.R) ✅ Bubble plots: 50pt top margin + wrapped labels + fixed x-axis (line 352) ✅ All plots: 10×8 inches @ 150 DPI (1500×1200 pixels)

Technical Stack

  • Base: rocker/r-ver:4.1.3
  • R Version: 4.1.3
  • Key Packages: ggplot2, dplyr, magrittr, stringr, RCurl
  • L2P: v0.0-13 (from CCBR)
  • Input Format: Tab-delimited (Galaxy tabular)
  • Output Formats: PNG (plots), CSV (pathways)

🔄 CI/CD Workflow

Automatic Triggers

  • Push to main → builds latest tag
  • Push tag v* → builds versioned tags (e.g., v1.1.0, v1.1, v1)
  • Pull request → builds but doesn't publish (for testing)

Published Tags

Every successful build creates:

  • ghcr.io/NIDAP-Community/l2p-galaxy-tool:latest
  • ghcr.io/NIDAP-Community/l2p-galaxy-tool:main-<sha>
  • ghcr.io/NIDAP-Community/l2p-galaxy-tool:v1.1.0 (on version tags)

Build Cache

GitHub Actions caches Docker layers for faster subsequent builds.

🔧 Local Development

Build Locally

cd /Users/maggiec/l2p-galaxy-tool
docker build -t l2p-galaxy-tool:dev .

Test Locally

docker run --rm -v $(pwd)/test_data:/data l2p-galaxy-tool:dev \
  Rscript /opt/l2p_single/run_L2P_Single.R \
  /data/deg_results.csv \
  /data/output.csv \
  /data/bar_up.png \
  /data/bar_down.png \
  /data/bubble_up.png \
  /data/bubble_down.png \
  symbol Human TRUE \
  PSA_high-PSA_low_tstat \
  PSA_high-PSA_low_pval \
  PSA_high-PSA_low_FC \
  0.05 1.2

Update and Test Cycle

  1. Edit L2P_Single.R or run_L2P_Single.R
  2. Rebuild: docker build -t l2p-galaxy-tool:dev .
  3. Test with sample data
  4. Commit and push when satisfied
  5. CI/CD automatically publishes

📝 Next Actions

Immediate

  1. Update placeholders: Replace NIDAP-Community throughout
  2. Create repository: Initialize on GitHub
  3. First push: Trigger initial CI/CD build
  4. Verify build: Check GitHub Actions completes successfully
  5. Test pull: Ensure you can pull the published image

After Publishing

  1. Update Galaxy: Modify tool XML to use new container reference
  2. Test in Galaxy: Run with sample data
  3. Create release: Tag v1.1.0 for official release
  4. Document usage: Add examples and screenshots
  5. Share: Announce availability to your team/community

🎉 Benefits of This Setup

✅ Reproducibility: Container ensures consistent environment ✅ Version Control: Git tracks all changes to code ✅ Automated Building: CI/CD handles Docker builds ✅ Easy Updates: Push changes → automatic rebuild ✅ Public Access: Anyone can use ghcr.io/NIDAP-Community/l2p-galaxy-tool:latest ✅ Versioning: Semantic version tags for stable releases ✅ Documentation: Complete guides for users and developers

📚 Documentation Structure

  • README.md: Main documentation (users + developers)
  • QUICKSTART.md: Fast setup guide (step-by-step)
  • CHANGELOG.md: Version history (what changed and when)
  • This file: Repository overview (what's included and why)

🤝 Acknowledgments

Based on L2P package from CCBR/l2p

Plot improvements developed through 19 iterations to achieve publication-quality output with proper margins, label wrapping, and axis calculations.