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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.

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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.

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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.

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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.

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+ Recent activity + RSS feed fo galaxyp-toolshed-peptideshaker +

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Owner
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galaxyp
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Access level
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Public
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Type
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Mercurial
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Last updated
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Created
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Size
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+ 1.4 MB + (download) +
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Tip: Filter by directory path e.g. /media app.js to search for public/media/app.js.
+
Tip: Use camelCasing e.g. ProjME to search for ProjectModifiedEvent.java.
+
Tip: Filter by extension type e.g. /repo .js to search for all .js files in the /repo directory.
+
Tip: Separate your search with spaces e.g. /ssh pom.xml to search for src/ssh/pom.xml.
+
Tip: Use ↑ and ↓ arrow keys to navigate and return to view the file.
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Tip: You can also navigate files with Ctrl+j (next) and Ctrl+k (previous) and view the file with Ctrl+o.
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Tip: You can also navigate files with Alt+j (next) and Alt+k (previous) and view the file with Alt+o.
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