This is a how-to guide for implementing the NEXT-RNAi program into your local Galaxy environment.
Galaxy is a framework, delevoped by Galaxy Team, for integrating computational tools. It allows nearly any tool that can be run from the command line to be wrapped in a structured, well defined interface.
On top of these tools, Galaxy provides an accessible environment for interactive analysis that transparently tracks the details of analyses, a workflow system for convenient reuse, data management, sharing, publishing, and more.
You can find more information about Galaxy here. Wiki documentation is also available.
NEXT-RNAi is a software for the design and evaluation of genome-wide RNAi libraries and performs all steps from the prediction of specific and efficient RNAi target sites to the visualization of designed reagents in their genomic context. The software enables the design and evaluation of siRNAs and long dsRNAs and was implemented in an organism-independent manner allowing designs for all sequenced and annotated genomes. It requires minimal input such as the desired target sequences and an off-target database.
Full documentation can be found here.
1. Galaxy environment. Installation guide from the Galaxy wiki site is available here.
2. NEXT-RNAi program. You can download the software here. Installation of NEXT-RNAi into your local environment is described at this wiki page.
3. Galaxy configuration files for NEXT-RNAi. Download the Galaxy configuration bundle for NEXT-RNAi which includes:
You can find a short introduction to location files in Galaxy here.
Before you start, please read this short tutorial on how to add a tool into Galaxy in general.
For adding NEXT-RNAi into Galaxy take the following steps:
<section name="NextRNAi" id="nextrnai"> <tool file="b110_tools/nextrnai.xml" /> </section>
Note: There are three location files:
If you successfully installed Galaxy, you should be able to see an interface similar to the following:
Please contact b110-it if you have any suggestion or find a bug.
Thomas Horn, Thomas Sandmann and Michael Boutros. Design and evaluation of genome-wide libraries for RNAi screens. Genome Biol. 2010 Jun 15;11(6):R61. Link to manuscript
Goecks, J, Nekrutenko, A, Taylor, J and The Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010 Aug 25;11(8):R86.
Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. "Galaxy: a web-based genome analysis tool for experimentalists". Current Protocols in Molecular Biology. 2010 Jan; Chapter 19:Unit 19.10.1-21.