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comparison README.rst @ 48:b72821cab1d7 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
author galaxyp
date Fri, 15 Jan 2021 14:05:46 +0000
parents c353378140ca
children 560a08e0de13
comparison
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47:5da80a2c0ef9 48:b72821cab1d7
1 GalaxyP - PeptideShaker 1 GalaxyP - PeptideShaker
2 ======================= 2 =======================
3 3
4 - Home: <https://github.com/galaxyproteomics/tools-galaxyp/> 4 - Home: <https://github.com/galaxyproteomics/tools-galaxyp/>
5 - Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/peptideshaker> 5 - Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/peptideshaker>
6 - Tool ID: `peptideshaker`, `search_gui` 6 - Tools ID: `peptide_shaker`, `search_gui`, `ident_params`, `fasta_cli`
7 7
8 8
9 Description 9 Description
10 ----------- 10 -----------
11 11
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 FastaCLI, IdentificationParametersCLI, SearchGUI and PeptideShaker.
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18 FastaCLI adds decoy sequences to any fasta file.
19
20 The Identification Parameters tool allows to create a parameters (par) file which can be (re)used later to parameterize SearchGUI or PeptideShaker.
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22 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.
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24 This can then be fed to the PeptideShaker tool which merges the results and performs peptide and protein inference.
15 25
16 26
17 General Requirements 27 General Requirements
18 -------------------- 28 --------------------
19 29
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: 30 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 31
22 export _JAVA_OPTIONS='-Xmx1500M' 32 export _JAVA_OPTIONS='-Xmx1500M'
23 33
24 On some systems you may also need to adjust the amount of memory available for class definitions in addition to the maximum heapspace. For example: 34 On some systems you may also need to adjust the amount of memory available for class definitions in addition to the maximum heapspace. For example:
25 35
29 39
30 MSAmanda on linux 40 MSAmanda on linux
31 ----------------- 41 -----------------
32 42
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. 43 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.
34 44
35 On ubuntu Mono can be installed as follows 45 On ubuntu Mono can be installed as follows
36 46
37 sudo apt-get install mono-runtime 47 sudo apt-get install mono-runtime
38 sudo apt-get install libmono-system-core4.0-cil 48 sudo apt-get install libmono-system-core4.0-cil
39 49
40 For more help on installing Mono please see http://www.mono-project.com/download. 50 For more help on installing Mono please see http://www.mono-project.com/download.
41 51
42 Note 52 Note
43 ---- 53 ----
44 54
45 - Requires Galaxy release v15.10 or later, which fixes the installation of package_peptideshaker_1_1 and provides a searchgui_archive datatype that includes a version 55 - Requires Galaxy release v16.01 or later.
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47 - PeptideShaker may require xvfb to simulate an X environment if this is installed on a headless server.
48 56
49 See: 57 See:
50 58
51 * <https://code.google.com/p/peptide-shaker/> 59 * <http://compomics.github.io/projects/peptide-shaker.html/>
52 * <https://code.google.com/p/searchgui/> 60 * <http://compomics.github.io/projects/searchgui.html/>
53
54
55 Search GUI - Fixed and Variable Modifications
56 -------------------------------------------
57
58 - Options for modifications are read from local data file: searchgui_mods.loc
59 This is copied from searchgui_mods.loc.sample on the first installation.
60
61 The modifications are from: https://github.com/compomics/compomics-utilities/blob/master/src/main/java/com/compomics/util/experiment/identification/search_parameters_cli/IdentificationParametersInputBean.java
62 61
63 GalaxyP Community 62 GalaxyP Community
64 ----------------- 63 -----------------
65 64
66 Current governing community policies for GalaxyP_ and other information can be found at: 65 Current governing community policies for GalaxyP_ and other information can be found at:
99 * Fred Sadler 98 * Fred Sadler
100 * John Chilton <jmchilton@gmail.com> 99 * John Chilton <jmchilton@gmail.com>
101 * Gerben Menschaert 100 * Gerben Menschaert
102 * Elvis Ndah 101 * Elvis Ndah
103 * Minnesota Supercomputing Institute, Univeristy of Minnesota 102 * Minnesota Supercomputing Institute, Univeristy of Minnesota
103 * Carlos Horro