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author galaxyp
date Fri, 10 May 2013 17:58:22 -0400
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Tool wrapper for SearchGUI + PeptideShaker. This tool takes any number
of mgf files and performs X! Tandem and OMSSA searches on these via
SearchGUI and merges the results using PeptideShaker.

For Galaxy-P we are installing this tool via CloudBioLinux
(https://github.com/jmchilton/cloudbiolinux/blob/proteomics/cloudbio/custom/bio_proteomics.py). While
this fabric script may not be exactly appropriate for your environment
it may serve as a template for how to install this software. In
particular these tools require CLI wrappers to be placed for
PeptideShaker and SearchGUI that can be installed as demostrated in
these fabric functions.

Note: Also SearchGUI requires a version greater than 1.12.2 which
contained several bugs preventing this from working on the
command-line and via Linux.

Also, PeptideShaker may require xvfb to simulate an X environment if
this is installed on a headless server.