EurOPDX-Galaxy

This repository contains recipe for docker version of Galaxy platform, expanded with tools and workflows for PDX(Patient Derived Xenograft) model molecular data analysis.

To use this docker image, you need to have Docker and Docker Compose installed.

Quick start

This is a tutorial for UNIX-like environment (Lunix, MacOS)

Setup a work-dir

mkdir ~/docker-galaxy
cd ~/docker-galaxy
mkdir reference-data

Download the docker-compose.yml

In the ~/docker-galaxy directory

wget https://raw.githubusercontent.com/BorisYourich/EurOPDX-Galaxy/main/docker-compose.yml

Configure

Set the import volume as the path to the directory where you store the data you want to process, to avoid copying the files into the container.

Set the reference-data volume to match the new, empty directory that you created in the first step. This directory is where the container will store all the reference data for mapping software. (To avoid re-creating the data ech time the container is run)

version: '3.5'

services:
  galaxy:
    container_name: galaxy
    restart: always
    image: registry.gitlab.ics.muni.cz:443/europdx/pdx-pipelines/galaxy-docker
    ports:
      - 8080:8080

    volumes:
      - /your/import/dir:/import
      - ~/docker-galaxy/reference-data:/galaxy/reference-data/

Run the container

In the ~/docker-galaxy directory

docker-compose up

After execution, a log from the container will show up in the terminal. If you run this for the first time, it will take a few minutes (depending on you internet connection) to pull the image.

Use Galaxy (Quickstart)

When the download is finished, the container will start and you can see the EurOPDX Galaxy instance on localhost:8080 on your machine.

Log into the admin profile with the name admin and password password

In the Toolbox select section Prepare reference Data, select the reference data for pipelines you are planning to use, and if needed, the testing data.

Once All the jobs have finished, select from the top menu workflows and run one of the workflows as described in Documentation