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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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1 Galaxy wrapper for OpenMS
2 =========================
3
4 OpenMS is an open-source software C++ library for LC/MS data management and analyses.
5 It offers an infrastructure for the rapid development of mass spectrometry related software.
6 OpenMS is free software available under the three clause BSD license and runs under Windows, MacOSX and Linux.
7
8 More informations are available at:
9
10 * https://github.com/OpenMS/OpenMS
11 * http://open-ms.sourceforge.net
12
13
14 Installation
15 ============
16
17 Galaxy should be able to automatically install the dependencies, i.e.
18 'package_openms_2_0' or 'package_qt_4_8' repository.
19
20 The wrappers are included in https://testtoolshed.g2.bx.psu.edu/view/bgruening/openms.
21
22
23 Generating OpenMS wrappers
24 ==========================
25
26 * install OpenMS (you can do this automatically through the Tool Shed)
27 * create a folder called CTD
28 * inside of your new installed openms/bin folder, execute the following command:
29
30 ```bash
31 for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done;
32 ```
33
34 * clone or install CTDopts
35
36 ```bash
37 git clone https://github.com/genericworkflownodes/CTDopts
38 ```
39
40 * add CTDopts to your `$PYTHONPATH`
41
42 ```bash
43 export PYTHONPATH=/home/user/CTDopts/
44 ```
45
46 * clone or install GalaxyConfigGenerator
47
48 ```bash
49 git clone https://github.com/TorHou/GalaxyConfigGenerator.git
50 ```
51
52 * If you have CTDopts and GalaxyConfigGenerator installed you are ready to generate Galaxy Tools from CTD definitions
53
54 ```bash
55 python ./galaxyconfiggenerator/generator.py \
56 -i /PATH/TO/YOUR/CTD*.ctd \
57 -o ./wrappers -t tool.conf \
58 -d OpenMS -g proteomics \
59 -b version log debug test no_progress threads \
60 in_type exe executable myrimatch_executable \
61 omssa_executable pepnovo_executable \
62 xtandem_executable \
63 -l ListOfNeededTools.txt
64 ```
65
66 The list of needed Tools is a whitelist of all Tools that you want to create. It's simply a list of all tools separated by line breaks.
67 An example file is located under https://gist.github.com/bgruening/421f97d36c27443e5f35
68
69
70 * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example:
71
72 ```
73 sed -i '10 a\-exe fido' wrappers/FidoAdapter.xml
74 sed -i '10 a\-executable msgfplus.jar' wrappers/MSGFPlusAdapter.xml
75 sed -i '10 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml
76 sed -i '10 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml
77 sed -i '10 a\-pepnovo_executable pepnovo' wrappers/PepNovoAdapter.xml
78 sed -i '10 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml
79 ```
80
81 Licence (MIT)
82 =============
83
84 Permission is hereby granted, free of charge, to any person obtaining a copy
85 of this software and associated documentation files (the "Software"), to deal
86 in the Software without restriction, including without limitation the rights
87 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
88 copies of the Software, and to permit persons to whom the Software is
89 furnished to do so, subject to the following conditions:
90
91 The above copyright notice and this permission notice shall be included in
92 all copies or substantial portions of the Software.
93
94 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
95 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
96 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
97 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
98 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
99 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
100 THE SOFTWARE.
101