Mercurial > repos > galaxyp > openms
comparison readme.md @ 0:3070d71e0e5c draft
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author | bgruening |
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date | Thu, 16 Apr 2015 08:37:04 -0400 |
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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 |