Galaxy-Godocker

A REST based runner for executing Galaxy jobs using GoDocker.

GoDocker is a batch computing/cluster management tool using Docker as execution/isolation system. Galaxy is designed to run jobs on your local system by default, but it can be configured to run jobs on a cluster. The front-end Galaxy application runs on a single server as usual, but tools are run on cluster nodes instead. Here, we use GoDocker system to manage authentication, scheduling and execution of jobs.

REST API of GoDocker is defined here

Project

The project is completed under Google Summer of Code 2016 program for the parent org: Open Genome Informatics.
http://gmod.org/wiki/GSoC

Open Genome Informatics represents the efforts of many bioinformatics projects.

The Open Genome Informatics group is organizing the joint efforts of Dockstore, Galaxy, GBrowse, GMOD, Informatics and Bio-computing (OICR), JBrowse, and Reactome. This is a great opportunity for students to contribute to the work of these established bioinformatics projects.

Galaxy: An open, web-based platform for accessible, reproducible, and transparent computational biomedical research. Link: https://galaxyproject.org/.

#Project structure

.
├── bin
|   ├──  godocker.py        #GoDocker runner code
|   ├──  job_conf.xml       #Job configuration for using GoDocker runner.
|
├── test                    #Contains test results and scripts.
|  
├── tools                   #Contains a Galaxy test tool.
└── ...

Documentation

Runner documentation is available here

Interested in creating a runner? Tutorial is available here

Deliverables

• 1: Title: GoDocker runner for Galaxy
  Pull Request: galaxyproject/galaxy#2653
  Status: Merge pending/ In Review.
  

• 2: Title: A tutorial on Build runner for galaxy
  Pull Request: galaxyproject/galaxy#2700
  Status: Merged.
  

• 3: Title: A GoDocker tool for Galaxy
  Link: https://github.com/varunshankar/galaxy-godocker_tool
  Status: A functional tool is available and needs certain enhancements.
  

Galaxy Quickstart

• Galaxy requires Python 2.7 To check your python version, run:

    $ python -V
    Python 2.7.3

• Runner should be configured for the requirements and user information of GoDocker and is available at job_conf.xml. A template of job_conf.xml is available here

• Galaxy currently requires a shared filesystem between the Galaxy server and the cluster nodes.

• Start Galaxy:

    $ sh run.sh

• Once Galaxy completes startup, you should be able to view Galaxy in your browser at:

http://localhost:8080

• You may wish to make changes from the default configuration. This can be done in the config/galaxy.ini file. Tools can be either installed from the Tool Shed or added manually. For details please see the Galaxy wiki:

https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial

• Not all dependencies are included for the tools provided in the sample tool_conf.xml. A full list of external dependencies is available at:

https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies

• The latest information about Galaxy is available via https://galaxyproject.org/

GoDocker Architecture

Contributors

• Olivier Sallou (Mentor)
• Yvan Le Bras (Mentor)
• S Varun Shankar (Student contributor)