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author galaxyp
date Fri, 10 May 2013 17:58:22 -0400
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1 Tool wrapper for SearchGUI + PeptideShaker. This tool takes any number
2 of mgf files and performs X! Tandem and OMSSA searches on these via
3 SearchGUI and merges the results using PeptideShaker.
4
5 For Galaxy-P we are installing this tool via CloudBioLinux
6 (https://github.com/jmchilton/cloudbiolinux/blob/proteomics/cloudbio/custom/bio_proteomics.py). While
7 this fabric script may not be exactly appropriate for your environment
8 it may serve as a template for how to install this software. In
9 particular these tools require CLI wrappers to be placed for
10 PeptideShaker and SearchGUI that can be installed as demostrated in
11 these fabric functions.
12
13 Note: Also SearchGUI requires a version greater than 1.12.2 which
14 contained several bugs preventing this from working on the
15 command-line and via Linux.
16
17 Also, PeptideShaker may require xvfb to simulate an X environment if
18 this is installed on a headless server.
19 # Obtaining Tools
20
21 Repositories for all Galaxy-P tools can be found at
22 https:/bitbucket.org/galaxyp/.
23
24 # Contact
25
26 Please send suggestions for improvements and bug reports to
27 jmchilton@gmail.com.
28
29 # License
30
31 All Galaxy-P tools are licensed under the Apache License Version 2.0
32 unless otherwise documented.
33
34 # Tool Versioning
35
36 Galaxy-P tools will have versions of the form X.Y.Z. Versions
37 differing only after the second decimal should be completely
38 compatible with each other. Breaking changes should result in an
39 increment of the number before and/or after the first decimal. All
40 tools of version less than 1.0.0 should be considered beta.