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docker-galaxy-pyclone

Overview

docker-galaxy-pyclone is a project that integrates the PyClone-VI tool with Galaxy Docker.

Features

  • Clonal Evolution Analysis: Analyze clonal evolution in cancer samples.
  • Cluster Prevalence Plotting: Visualize cluster prevalence over samples.
  • Docker Integration: Easily deploy and run the tool in a Docker container.

Requirements

  • Docker

Installation

  1. Clone the repository:

    git clone https://github.com/yourusername/docker-galaxy-pyclone.git
cd docker-galaxy-pyclone

  2. Build the Docker image:

    docker build -t galaxy-pyclone .

Configuration

Set the following environment variables to configure the Galaxy instance and PyClone-VI tool:

export GALAXY_URL='http://your-galaxy-instance-url'
export PYLONE_API_KEY='your-pyclone-api-key'
export PYLONE_DATA_PATH='/path/to/your/data'

Usage

  1. Run the Docker container:

    docker run -p 8081:8081 -e GALAXY_URL -e PYLONE_API_KEY -e PYLONE_DATA_PATH galaxy-pyclone

  2. Access the Galaxy instance at http://localhost:8081.

Adding a tool

Two files need to be modified to add a tool.

  1. config/tool_conf.xml Follow the official documentation to add your tool: https://docs.galaxyproject.org/en/master/admin/tool_panel.html
  2. Dockerfile If your tool is not part of Galaxy toolshed you need to add the wrapper and code to the Docker images. For example, with Pyclone-VI:
# Clone Pyclone-VI tools from GitHUb
RUN git clone https://github.com/jCHENEBY/galaxy-tool-pyclone-vi.git /galaxy/server/tools/pyclone_vi
RUN chown -R galaxy:galaxy /galaxy/server/tools/pyclone_vi

This Docker image uses conda to install requirements from the tool XML file, so you don't need to modify the Dockerfile further.