Tip of the Week: Galaxy Tool Shed

This week I attended and gave a talk at ISMB in Long Beach. While there I had the opportunity to attend a session on Galaxy where Jeremy Goecks spoke on Galaxy Visualizations and Greg Von Kuster spoke about the “first biomedical AppStore,” the Galaxy Toolshed. As always, I learned a few new things.

Today’s tip is a quick introduction to the Galaxy Tool Shed. The Tool shed is a place to share tools you’ve developed or to find tools that other developers have developed for your local instance of Galaxy. This is a quick introduction. I won’t be going into the mechanics and specifics of the toolshed, it’s not specifically for the experimental biologist end user, but rather for developers of tools for use in Galaxy. That said, it can be useful for the end user to know what tools might be available and get them into their local installation. If you or your institution is installing a local instance of Galaxy, you might want to check out the extensive documentation on how to use the toolshed.

There are a lot of tools available in the tool shed, over 1800 at last count. They range through many different categories. Though it’s only been a couple years since the implementation of the toolshed, some published tools such as CodonLogo which is a logo-based viewer for codon patterns in aligned sequences, have been added to the toolshed.

If you want to learn more about Galaxy.

We have a  webinar tomorrow (July 19, 2012 at 11am PDT)  introducing Galaxy (free).

We have an online tutorial (fee)

And we’ve done tips (free of course) on Galaxy visualization, getting flanking sequences and converting genome coordinates using Galaxy,  and Galaxy pages. And we’ve tipped and blogged a lot of Galaxy-related stuff.

Quick Links:
Galaxy Main Instance
Galaxy Tool Box
Galaxy Tool Box How-to
Setting up a local instance

 

Sharma V, Murphy DP, Provan G, & Baranov PV (2012). CodonLogo: a sequence logo-based viewer for codon patterns. Bioinformatics (Oxford, England), 28 (14), 1935-6 PMID: 22595210