Mercurial > repos > galaxyp > peptideshaker

annotate README_REPO.md @ 0:0578e296cab4 draft

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Initial commit.
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
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2 of mgf files and performs X! Tandem and OMSSA searches on these via
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3 SearchGUI and merges the results using PeptideShaker.
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5 For Galaxy-P we are installing this tool via CloudBioLinux
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6 (https://github.com/jmchilton/cloudbiolinux/blob/proteomics/cloudbio/custom/bio_proteomics.py). While
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7 this fabric script may not be exactly appropriate for your environment
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8 it may serve as a template for how to install this software. In
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9 particular these tools require CLI wrappers to be placed for
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10 PeptideShaker and SearchGUI that can be installed as demostrated in
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11 these fabric functions.
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13 Note: Also SearchGUI requires a version greater than 1.12.2 which
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14 contained several bugs preventing this from working on the
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15 command-line and via Linux.
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17 Also, PeptideShaker may require xvfb to simulate an X environment if
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18 this is installed on a headless server.