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comparison README.rst @ 21:dfaea053e32f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
author iracooke
date Tue, 16 Jun 2015 23:43:39 -0400
parents 2cafc729b2ae
children 815f93bb3e1b
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20:2cafc729b2ae 21:dfaea053e32f
12 Perform protein identification combining numerous search engines (using SearchGUI) followed by peptide and protein inference with PeptideShaker. 12 Perform protein identification combining numerous search engines (using SearchGUI) followed by peptide and protein inference with PeptideShaker.
13 13
14 Includes tool wrappers for SearchGUI and PeptideShaker. The SearchGUI tool takes any number of mgf files and performs searches on these. It creates a large zip archive with all search results, the original database and spectra. This can then be fed to the PeptideShaker tool which merges the results and performs peptide and protein inference. 14 Includes tool wrappers for SearchGUI and PeptideShaker. The SearchGUI tool takes any number of mgf files and performs searches on these. It creates a large zip archive with all search results, the original database and spectra. This can then be fed to the PeptideShaker tool which merges the results and performs peptide and protein inference.
15 15
16 16
17 Configuration 17 General Requirements
18 ------------- 18 --------------------
19 19
20 This tool requires a Java runtime 1.6 or greater to work. To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell: 20 This tool requires a Java runtime 1.6 or greater to work. To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell:
21 21
22 export _JAVA_OPTIONS='-Xmx1500M' 22 export _JAVA_OPTIONS='-Xmx1500M'
23 23
25 25
26 export _JAVA_OPTIONS='-Xmx1500M -XX:MaxPermSize=256M' 26 export _JAVA_OPTIONS='-Xmx1500M -XX:MaxPermSize=256M'
27 27
28 It is also possible to set this on a per tool basis using advanced features of the galaxy job config system. 28 It is also possible to set this on a per tool basis using advanced features of the galaxy job config system.
29 29
30 Note: 30 MSAmanda on linux
31 -----------------
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33 Running MS Amanda on Linux requires that you have Mono installed. Mono 3.2.1 or newer is required. If you install via the toolshed Mono should be installed automatically, however if this does not work you can install it manually.
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35 On ubuntu Mono can be installed as follows
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37 sudo apt-get install mono-runtime
38 sudo apt-get install libmono-system-core4.0-cil
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40 For more help on installing Mono please see http://www.mono-project.com/download.
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42 Note
43 ----
31 44
32 - PeptideShaker may require xvfb to simulate an X environment if this is installed on a headless server. 45 - PeptideShaker may require xvfb to simulate an X environment if this is installed on a headless server.
33 46
34 See: 47 See:
35 48
73 * Bjoern Gruening <bjoern.gruening@gmail.com> 86 * Bjoern Gruening <bjoern.gruening@gmail.com>
74 * Ira Cooke 87 * Ira Cooke
75 * Cody Wang 88 * Cody Wang
76 * Fred Sadler 89 * Fred Sadler
77 * John Chilton <jmchilton@gmail.com> 90 * John Chilton <jmchilton@gmail.com>
91 * Gerben Menschaert
92 * Elvis Ndah
78 * Minnesota Supercomputing Institute, Univeristy of Minnesota 93 * Minnesota Supercomputing Institute, Univeristy of Minnesota