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comparison tools/protein_analysis/nlstradamus.txt @ 0:0ad90e5eb390

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Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 17:39:58 -0400
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1 Galaxy wrapper for NLStradamus v1.7 (C++ version)
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 NLStradamus is a command line tools for predicting nuclear localization
9 signals (NLSs) in a FASTA file of proteins using a Hidden Markov Model (HMM).
10
11 A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses.
12 NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction.
13 BMC Bioinformatics. 2009 Jun 29;10(1):202.
14
15 http://www.moseslab.csb.utoronto.ca/NLStradamus
16
17 Early versions of NLStradamus did not have a native tabular output format, this
18 was added in version 1.7. Additionally a fast C++ implementation was added at
19 this point (early versions of NLStradamus came as a perl script only). This
20 wrapper expects the compiled C++ binary "NLStradamus" to be on the system PATH.
21
22 To install the wrapper installed the following files under the Galaxy tools
23 folder, e.g. in a tools/protein_analysis folder:
24
25 * nlstradamus.xml (the Galaxy tool definition)
26 * nlstradamus.txt (this README file)
27
28 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
29 tool. If you are using other protein analysis tools like TMHMM or SignalP, put
30 it next to them. Just add the line:
31
32 <tool file="protein_analysis/nlstradamus.xml" />
33
34 That's it.
35
36
37 History
38 =======
39
40 v0.0.3 - Initial public release
41
42
43 Developers
44 ==========
45
46 This script and related tools are being developed on the following hg branch:
47 http://bitbucket.org/peterjc/galaxy-central/src/tools
48
49 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
50 the following command from the Galaxy root folder:
51
52 tar -czf nlstradmus.tar.gz tools/protein_analysis/nlstradum.xml tools/protein_analysis/nlstradum.txt
53
54 Check this worked:
55
56 $ tar -tzf nlstradmus.tar.gz
57 filter/seq_filter_by_id.py
58 filter/seq_filter_by_id.txt
59 filter/seq_filter_by_id.xml
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. NLStradamus
84 is available and licenced separately.