Galaxy tutorial

CBGP 2013

Mikel Egaña Aranguren /
Biological Informatics Group (, CBGP, UPM, Madrid

Galaxy tutorial

GitHub repo (slides, data, documentation, ...):

GitHub page (this slides):


What is Galaxy?

What is Galaxy for?

A web server that offers the usual bioinformatics tools in a central space with ...

... data storage

... history

... workflows

Why is Galaxy so good?

Very complex computational analyses

... easily

... with provenance

Reproducible science!

On reproducible science

On reproducible science

Rule 1: For Every Result, Keep Track of How It Was Produced

Rule 5: Record All Intermediate Results, When Possible in Standardized Formats

Rule 9: Connect Textual Statements to Underlying Results

Rule 10: Provide Public Access to Scripts, Runs, and Results

Reproducible science: Galaxy for executable papers

More information

Galaxy main server (Limitations on data size, computational resources):

Our own server at CBGP:

Galaxy documentation:

Using Galaxy

Main interface

Hands-on 1 (Guided exercise based on Galaxy 101)

Hands-on 2 (On your own)

What genes of Arabidopsis thaliana are annotated against the "cell cycle" (GO:0007049) subtree of the Gene Ontology (GO)?

Hints (General steps)

  1. get data; upload file
    • data/gene_ontology.1_2.obo (GO)
    • data/gene_association.tair (GAF)
  2. Prepare GAF by removing lines starting with "!" (with a regular expression) and converting tab separated content to actual columns
  3. Use OBO ontology manipulation; Get the descendent terms of a given OBO term to obtain the cell cycle subtree from GO
  4. Compare the GO ids list with GAF to extract the rows that match


Use the Workflow (import and run) or the history

Sharing your stuff

You can make workflows and histories public with a URL, share with other users, and import/export them

You can also create a Galaxy page

Local installation

Usually a good idea to install Galaxy locally, even just for yourself:

... provenance when you sit down and write the paper

... sensitive data

... install/develop other Galaxy tools

Local installation requirements

Some UNIX flavour (GNU/Linux, MAC OS X*)


Mercurial (hg)

Install with Mercurial

hg clone

cd galaxy-dist

hg update stable



  • ./
  • nohup ./ &

Open and do your thing

Stop (history, workflows etc. will be stored but execution will interrupt):

  • Close terminal or CTRL-C
  • kill -9 PID


hg incoming

hg pull -u

Installing tools

Add yourself as admin (add admin_users = your_email to universe_wsgi.ini)

Restart, log in and install through admin; tool sheds

or install manually* (Very basic XML and UNIX skills needed)

Finishing remarks

Feel free to use (No security/performance warranty though ;-)

If you need a tool and you don't find it in the tool shed, let us know and perhaps we can develop it (specially if there is a CLI version of the tool and/or the tool is interesting).

This presentation was produced using Reveal.js