Galaxy tutorial

Erasmus Mundus MSc Marine Environment and Resources 2014

Genomics of Marine Resources

Mikel Egaña Aranguren
http://mikeleganaaranguren.com / mikel.egana.aranguren@gmail.com

Functional Genomics Group (http://www.genomic-resources.eu/)
University of Basque Country (UPV-EHU)

Galaxy tutorial

GitHub repo (slides and papers): http://github.com/mikel-egana-aranguren/Galaxy_MSc_Marine_Environment

GitHub page (to view this slides): http://mikel-egana-aranguren.github.io/Galaxy_MSc_Marine_Environment/galaxy.html

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

http://usegalaxy.org/u/aun1/p/heteroplasmy

More information

Galaxy project: http://galaxyproject.org/

Galaxy documentation: http://wiki.galaxyproject.org

Galaxy main server (Limitations on data size, computational resources): http://usegalaxy.org/

Using Galaxy

Main interface

Hands-on exercise

Jennifer Hillman-Jackson and Galaxy Team. Using galaxy to perform Large-Scale interactive data analyses. Current protocols in bioinformatics

Basic Protocol 1: finding human coding exons with highest SNP density

http://usegalaxy.org/u/galaxyproject/p/using-galaxy-2012

Hands-on exercise Step 12

12. Import coordinates ...

• group: Variation and Repeats Variation
• track: Common SNPs(132) Common SNPs (138)

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*)

Python

Mercurial (hg)

Install with Mercurial

hg clone https://bitbucket.org/galaxy/galaxy-dist/

cd galaxy-dist

hg update stable

Use

Run:

• ./run.sh
• nohup ./run.sh &
• ./run.sh --daemon

Open http://127.0.0.1:8080/ and do your thing

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

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

Update

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)