Mercurial > repos > galaxyp > openms_featurelinkerunlabeledkd
comparison readme.md @ 0:b73b578a6c11 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author | galaxyp |
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date | Wed, 09 Aug 2017 09:34:25 -0400 |
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children | 1e9edcc25bbe |
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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 Generating OpenMS wrappers | |
15 ========================== | |
16 | |
17 * install OpenMS (you can do this automatically through Conda) | |
18 * create a folder called CTD | |
19 * if you installed openms as a binary in a specific directory, execute the following command in the `openms/bin` directory: | |
20 | |
21 ```bash | |
22 for binary in `ls`; do ./$binary -write_ctd /PATH/TO/YOUR/CTD; done; | |
23 ``` | |
24 | |
25 * if there is no binary release (e.g. as with version 2.2), download and unpack the Conda package, find the `bin` folder and create a list of the tools as follow: | |
26 | |
27 ```bash | |
28 ls >> tools.txt | |
29 ``` | |
30 | |
31 * search for the `bin` folder of your conda environment containing OpenMS and do: | |
32 | |
33 ```bash | |
34 while read p; do | |
35 ./PATH/TO/BIN/$p -write_ctd /PATH/TO/YOUR/CTD; | |
36 done <tools.txt | |
37 ``` | |
38 | |
39 * You should have all CTD files now. `MetaProSIP.ctd` includes a not supported character: To use it, search for `²` and replace it (e.g. with `^2`). | |
40 | |
41 * clone or install CTDopts | |
42 | |
43 ```bash | |
44 git clone https://github.com/genericworkflownodes/CTDopts | |
45 ``` | |
46 | |
47 * add CTDopts to your `$PYTHONPATH` | |
48 | |
49 ```bash | |
50 export PYTHONPATH=/home/user/CTDopts/ | |
51 ``` | |
52 | |
53 * clone or install CTD2Galaxy | |
54 | |
55 ```bash | |
56 git clone https://github.com/WorkflowConversion/CTD2Galaxy.git | |
57 ``` | |
58 | |
59 * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it. | |
60 | |
61 ```bash | |
62 python generator.py \ | |
63 -i /PATH/TO/YOUR/CTD/*.ctd \ | |
64 -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \ | |
65 -d datatypes_conf.xml -g openms \ | |
66 -b version log debug test no_progress threads \ | |
67 in_type executable myrimatch_executable \ | |
68 fido_executable fidocp_executable \ | |
69 omssa_executable pepnovo_executable \ | |
70 xtandem_executable param_model_directory \ | |
71 java_executable java_memory java_permgen \ | |
72 -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \ | |
73 -s PATH/TO/SKIP_TOOLS_FILES.txt | |
74 ``` | |
75 | |
76 | |
77 * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example: | |
78 | |
79 ``` | |
80 sed -i '13 a\-fido_executable fido' wrappers/FidoAdapter.xml | |
81 sed -i '13 a\-fidocp_executable fido_choose_parameters' wrappers/FidoAdapter.xml | |
82 sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml | |
83 sed -i '13 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml | |
84 sed -i '13 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml | |
85 ``` | |
86 | |
87 * For some tools, additional work has to be done. In `MSGFPlusAdapter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where): | |
88 | |
89 ``` | |
90 <command><![CDATA[ | |
91 | |
92 ## check input file type | |
93 #set $in_type = $param_in.ext | |
94 | |
95 ## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files | |
96 ln -s '$param_in' 'param_in.${in_type}' && | |
97 ln -s '$param_database' param_database.fasta && | |
98 ## find location of the MSGFPlus.jar file of the msgf_plus conda package | |
99 MSGF_JAR=\$(msgf_plus -get_jar_path) && | |
100 | |
101 MSGFPlusAdapter | |
102 -executable \$MSGF_JAR | |
103 #if $param_in: | |
104 -in 'param_in.${in_type}' | |
105 #end if | |
106 #if $param_out: | |
107 -out $param_out | |
108 #end if | |
109 #if $param_mzid_out: | |
110 -mzid_out $param_mzid_out | |
111 #end if | |
112 #if $param_database: | |
113 -database param_database.fasta | |
114 #end if | |
115 | |
116 [...] | |
117 ]]> | |
118 ``` | |
119 | |
120 * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where): | |
121 | |
122 ``` | |
123 <command><![CDATA[ | |
124 | |
125 ## check input file type | |
126 #set $in_type = $param_in.ext | |
127 | |
128 ## create the symlinks to set the proper file extension, since IDFileConverter uses them to choose how to handle the input files | |
129 ln -s '$param_in' 'param_in.${in_type}' && | |
130 | |
131 IDFileConverter | |
132 | |
133 #if $param_in: | |
134 -in 'param_in.${in_type}' | |
135 #end if | |
136 | |
137 [...] | |
138 ]]> | |
139 ``` | |
140 | |
141 * In `IDFileConverter.xml` and `FileConverter.xml` add `auto_format="true"` to the output, e.g.: | |
142 | |
143 - `<data name="param_out" auto_format="true"/>` | |
144 - `<data name="param_out" metadata_source="param_in" auto_format="true"/>` | |
145 | |
146 * To add an example test case to `DecoyDatabase.xml` add the following after the output section. If standard settings change you might have to adjust the options and/or the test files. | |
147 | |
148 ``` | |
149 <tests> | |
150 <test> | |
151 <param name="param_in" value="DecoyDatabase_input.fasta"/> | |
152 <output name="param_out" file="DecoyDatabase_output.fasta"/> | |
153 </test> | |
154 </tests> | |
155 ``` | |
156 | |
157 | |
158 * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in Galaxy-stable and are therefore in `SKIP_TOOLS_FILES.txt`: | |
159 * SeedListGenerator | |
160 * SpecLibSearcher | |
161 * MapAlignerIdentification | |
162 * MapAlignerPoseClustering | |
163 * MapAlignerSpectrum | |
164 * MapAlignerRTTransformer | |
165 | |
166 * Additionally cause of lacking dependencies, the following adapters have been removed in `SKIP_TOOLS_FILES.txt` as well: | |
167 * OMSSAAdapter | |
168 * MyrimatchAdapter | |
169 | |
170 * Additionally cause of a problematic parameter (-model_directory), the following adapter has been removed: | |
171 * PepNovoAdapter | |
172 | |
173 | |
174 Licence (MIT) | |
175 ============= | |
176 | |
177 Permission is hereby granted, free of charge, to any person obtaining a copy | |
178 of this software and associated documentation files (the "Software"), to deal | |
179 in the Software without restriction, including without limitation the rights | |
180 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
181 copies of the Software, and to permit persons to whom the Software is | |
182 furnished to do so, subject to the following conditions: | |
183 | |
184 The above copyright notice and this permission notice shall be included in | |
185 all copies or substantial portions of the Software. | |
186 | |
187 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
188 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
189 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
190 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
191 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
192 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
193 THE SOFTWARE. | |
194 |