Fragpipe Peptide Ranking

This repository provides scripts to summarize FragPipe peptide results and generate peptide ranking outputs and heatmaps.

Prerequisites

1. Docker installed and running.
2. Access to image: pgc-images.sbgenomics.com/rokita-lab/peptide-rank:v1.0.0.

Quick Start

1. Clone the repository:

git clone git@github.com:rokitalab/fragpipe-peptide-ranking.git
cd fragpipe-peptide-ranking

2. Pull the Docker image:

docker pull pgc-images.sbgenomics.com/rokita-lab/peptide-rank:v1.0.0

3. Start the container from the repository root:

docker run --platform linux/amd64 \
  --name peptide-rank \
  -d \
  -e PASSWORD=pass \
  -p 8787:8787 \
  -v "$PWD":/home/rstudio/fragpipe-peptide-ranking \
  pgc-images.sbgenomics.com/rokita-lab/peptide-rank:v1.0.0

4. Open RStudio in a browser:

• Local machine: http://localhost:8787
• Remote VM/EC2: http://<INSTANCE_IP>:8787

Login credentials:

• username: rstudio
• password: value of PASSWORD above (default shown: pass)

5. Open a shell in the running container:

docker exec -ti peptide-rank bash

Detailed Workflow

For CAVATICA mount/copy steps and running both ranking scripts, see:

• analyses/impact-peptide-ranking/README.md