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Uploaded wrapper v0.0.1 (for clinod v1.3)
author peterjc
date Tue, 02 Aug 2011 06:51:52 -0400
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-1:000000000000 0:b8be455c27d1
1 Galaxy wrapper for Command line NoD predictor (v1.3)
2 ====================================================
3
4 This wrapper is copyright 2011 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
13 Installation
14 ============
15 This wrapper expects the java binary to be on the system PATH, and to be able
16 to access command line NoD as /opt/clinod/clinod-1.3.jar (edit clinod.xml if
17 you wish to use a different location).
18
19 Internally NoD calls the binary batchman from the Stuttgart Neural Network
20 Simulator (SNNS) v 4.2 software suite. This binary can either be on the system
21 path or located next to the JAR file, i.e. /opt/clinod/batchman
22
23 To install the wrapper copy or move the following files under the Galaxy tools
24 folder, e.g. in a tools/protein_analysis folder:
25
26 * clinod.xml (the Galaxy tool definition)
27 * clinod.txt (this README file)
28
29 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
30 tool. If you are using other protein analysis tools like TMHMM or SignalP, put
31 it next to them. Just add the line:
32
33 <tool file="protein_analysis/clinod.xml" />
34
35 That's it.
36
37
38 History
39 =======
40
41 v0.0.1 - Initial public release
42
43
44 Developers
45 ==========
46
47 This script and related tools are being developed on the following hg branch:
48 http://bitbucket.org/peterjc/galaxy-central/src/tools
49
50 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
51 the following command from the Galaxy root folder:
52
53 $ tar -czf clinod.tar.gz tools/protein_analysis/clinod.xml tools/protein_analysis/clinod.txt
54
55 Check this worked:
56
57 $ tar -tzf clinod.tar.gz
58 tools/protein_analysis/clinod.xml
59 tools/protein_analysis/clinod.txt
60
61
62 Licence (MIT/BSD style)
63 =======================
64
65 Permission to use, copy, modify, and distribute this software and its
66 documentation with or without modifications and for any purpose and
67 without fee is hereby granted, provided that any copyright notices
68 appear in all copies and that both those copyright notices and this
69 permission notice appear in supporting documentation, and that the
70 names of the contributors or copyright holders not be used in
71 advertising or publicity pertaining to distribution of the software
72 without specific prior permission.
73
74 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
75 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
76 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
77 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
78 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
79 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
80 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
81 OR PERFORMANCE OF THIS SOFTWARE.
82
83 NOTE: This is the licence for the Galaxy Wrapper only. Command line
84 NoD is available and licenced separately.