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Carrie edited this page Nov 21, 2018 · 7 revisions

Welcome to CTAT Galaxy Docker!

This intro goes over the features and functionality of running CTAT Galaxy from a docker image.

What it is

CTAT Galaxy Docker is a a collection of Docker images, scripts, and support files that contain everything you need to launch your own Galaxy for running the CTAT tools; such as Trinity, STAR- or GMAP-fusion, Fusion Inspector, the Mutation Pipeline, Metagenomics and lncRNA tools.

Requirements

The docker image is a full-fledged Galaxy; you will need enough computational power to run any of the CTAT tools. Star-fusion and Trinity will both require large amounts of memory; at least 40GB of RAM for STAR and more for Trinity, depending on the complexity of the inputs you intend to use. All resource files, inputs, and outputs will need to fit on a disk or volume of sufficient size. The resources libraries require ~70GB of disk when all is built. Additional space may be needed if you need to rebuild the Docker image, or if you need to re-download resources and keep a redundant compressed .gzip file until it completes.

In addition to hardware, you will need root or sudo access in order to run Docker. Several support files included will also assume you have sudo in order to create new users and modify files.

Implementation

CTAT Galaxy Docker is built from the stable Galaxy docker image put together by Björn Grüning. Additional Documentation/Readme information can be found on the docker-galaxy-stable Github page.

The code for the CTAT Galaxy Docker code can be found in this Github repository.

Getting started

  1. Running the Docker from a fresh VM
  2. Building the Docker instance from source
  3. Development
  4. Troubleshooting
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