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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.
+# Obtaining Tools
+
+Repositories for all Galaxy-P tools can be found at
+https:/bitbucket.org/galaxyp/.
+
+# Contact
+
+Please send suggestions for improvements and bug reports to
+jmchilton@gmail.com.
+
+# License
+
+All Galaxy-P tools are licensed under the Apache License Version 2.0
+unless otherwise documented.
+
+# Tool Versioning
+
+Galaxy-P tools will have versions of the form X.Y.Z. Versions
+differing only after the second decimal should be completely
+compatible with each other. Breaking changes should result in an
+increment of the number before and/or after the first decimal. All
+tools of version less than 1.0.0 should be considered beta.