Mercurial > repos > peterjc > clinod
comparison tools/clinod/README.rst @ 3:6a9debe4b860 draft
Uploaded v0.0.6, MIT licence, reStructuredText README, citation information, development moved to GitHub
author | peterjc |
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date | Wed, 18 Sep 2013 06:09:33 -0400 |
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children | 4d9a4a43861b |
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1 Galaxy wrapper for Command line NoD predictor (v1.3) | |
2 ==================================================== | |
3 | |
4 This wrapper is copyright 2011-2013 by Peter Cock, The James Hutton Institute | |
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. | |
6 See the licence text below. | |
7 | |
8 Command line NoD predictor is a tool for predicting nucleolar localization | |
9 sequences (NoLSs) in a FASTA file of proteins using a neural network. There | |
10 is also a webtool version at http://www.compbio.dundee.ac.uk/www-nod/ | |
11 | |
12 This NoD wrapper is available from the Galaxy Tool Shed at: | |
13 http://toolshed.g2.bx.psu.edu/view/peterjc/clinod | |
14 | |
15 | |
16 Automated Installation | |
17 ====================== | |
18 | |
19 This should be straightforward, Galaxy should automatically download and install | |
20 the JAR file for clinod v1.3 and the batchman executable from the Stuttgart | |
21 Neural Network Simulator (SNNS), and set the $CLINOD to their folder. | |
22 | |
23 | |
24 Manual Installation | |
25 =================== | |
26 This wrapper expects the java binary to be on the system PATH, and to be able | |
27 to access command line NoD as $CLINOD/clinod-1.3.jar which means if you used | |
28 /opt/clinod/clinod-1.3.jar set the environment variable $CLINOD to /opt/clinod | |
29 | |
30 Internally NoD calls the binary batchman v1.0 from the Stuttgart Neural Network | |
31 Simulator (SNNS) v4.2 or 4.3 software suite. This binary can either be on the | |
32 system path or located next to the JAR file, i.e. /opt/clinod/batchman | |
33 | |
34 To install the wrapper copy or move the following files under the Galaxy tools | |
35 folder, e.g. in a tools/clinod folder: | |
36 | |
37 * clinod.xml (the Galaxy tool definition) | |
38 * README.rst (this file) | |
39 | |
40 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the | |
41 tool. If you are using other protein analysis tools like TMHMM or SignalP, put | |
42 it next to them. Just add the line:: | |
43 | |
44 <tool file="clinod/clinod.xml" /> | |
45 | |
46 If you wish to run the unit tests, also add this to tools_conf.xml.sample | |
47 and move/copy the test-data files under Galaxy's test-data folder. Then:: | |
48 | |
49 $ ./run_functional_tests.sh -id clinod | |
50 | |
51 That's it. | |
52 | |
53 | |
54 History | |
55 ======= | |
56 | |
57 ======= ====================================================================== | |
58 Version Changes | |
59 ------- ---------------------------------------------------------------------- | |
60 v0.0.1 - Initial public release | |
61 v0.0.2 - Treat non-zero return codes as errors | |
62 v0.0.3 - Describe output table in help | |
63 v0.0.4 - Added unit test | |
64 v0.0.5 - Link to Tool Shed added to help text and this documentation. | |
65 - Automated tool installation. | |
66 v0.0.6 - Adopted standard MIT licence. | |
67 - Use reStructuredText for this README file. | |
68 - Updated citation information (Cock et al. 2013). | |
69 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy | |
70 ======= ====================================================================== | |
71 | |
72 | |
73 Developers | |
74 ========== | |
75 | |
76 This script and related tools were initially developed on the following hg branch: | |
77 http://bitbucket.org/peterjc/galaxy-central/src/tools | |
78 | |
79 Development has now moved to a dedicated GitHub repository: | |
80 https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod | |
81 | |
82 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use | |
83 the following command from the Galaxy root folder:: | |
84 | |
85 $ tar -czf clinod.tar.gz tools/clinod/README.rst tools/clinod/clinod.xml tools/clinod/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.clinod-1.3.tabular | |
86 | |
87 Check this worked:: | |
88 | |
89 $ tar -tzf clinod.tar.gz | |
90 tools/clinod/README.rst | |
91 tools/clinod/clinod.xml | |
92 tools/clinod/tool_dependencies.xml | |
93 test-data/four_human_proteins.fasta | |
94 test-data/four_human_proteins.clinod-1.3.tabular | |
95 | |
96 | |
97 Licence (MIT) | |
98 ============= | |
99 | |
100 Permission is hereby granted, free of charge, to any person obtaining a copy | |
101 of this software and associated documentation files (the "Software"), to deal | |
102 in the Software without restriction, including without limitation the rights | |
103 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
104 copies of the Software, and to permit persons to whom the Software is | |
105 furnished to do so, subject to the following conditions: | |
106 | |
107 The above copyright notice and this permission notice shall be included in | |
108 all copies or substantial portions of the Software. | |
109 | |
110 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
111 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
112 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
113 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
114 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
115 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
116 THE SOFTWARE. | |
117 | |
118 NOTE: This is the licence for the Galaxy Wrapper only. Command line | |
119 NoD is available and licenced separately. |