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Uploaded v0.0.8, MIT licence, RST for README, citation information, development moved to GitHub
author peterjc
date Wed, 18 Sep 2013 06:15:33 -0400
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2:9ec94203d895 3:b2e648e55ed7
1 Galaxy wrapper for NLStradamus v1.7 or v1.8 (C++ version)
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 (MIT licence).
7
8 NLStradamus is a command line tool for predicting nuclear localization
9 signals (NLSs) in a FASTA file of proteins using a Hidden Markov Model (HMM).
10
11 This wrapper is available from the Galaxy Tool Shed at:
12 http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
13
14 A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses.
15 NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction.
16 BMC Bioinformatics. 2009 Jun 29;10(1):202.
17 http://dx.doi.org/10.1186/1471-2105-10-202
18
19 http://www.moseslab.csb.utoronto.ca/NLStradamus
20
21 Early versions of NLStradamus did not have a native tabular output format, this
22 was added in version 1.7. Additionally a fast C++ implementation was added at
23 this point (early versions of NLStradamus came as a perl script only).
24
25 Version 1.8 fixed a C++ compilation issue on modern compilers, but is otherwise
26 unchanged.
27
28
29 Automated Installation
30 ======================
31
32 This should be straightforward, Galaxy should automatically download and install
33 the C++ implementation of NLStradamus v1.8, and run the unit tests.
34
35
36 Manual Installation
37 ===================
38 This wrapper expects the compiled C++ binary "NLStradamus" to be on the system
39 PATH.
40
41 To install the wrapper copy or move the following files under the Galaxy tools
42 folder, e.g. in a tools/protein_analysis folder:
43
44 * nlstradamus.xml (the Galaxy tool definition)
45 * nlstradamus.txt (this README file)
46
47 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
48 tool. If you are using other protein analysis tools like TMHMM or SignalP, put
49 it next to them. Just add the line (matching the chosen install path)::
50
51 <tool file="protein_analysis/nlstradamus.xml" />
52
53 If you wish to run the unit tests, also add this to tools_conf.xml.sample
54 and move/copy the test-data files under Galaxy's test-data folder. Then::
55
56 $ ./run_functional_tests.sh -id nlstradamus
57
58 That's it.
59
60
61 History
62 =======
63
64 ======= ======================================================================
65 Version Changes
66 ------- ----------------------------------------------------------------------
67 v0.0.3 - Initial public release
68 v0.0.4 - Adding DOI link to reference
69 (Documentation change only)
70 v0.0.5 - Assume non-zero return codes are errors
71 v0.0.6 - Show output help text using a table
72 - Added unit tests
73 v0.0.7 - Automatic installation of the NLStradamus binary when installed
74 via the Galaxy Tool Shed
75 v0.0.8 - Link to Tool Shed added to help text and this documentation.
76 - Use reStructuredText for this README file.
77 - Adopted standard MIT licence.
78 - Updated citation information (Cock et al. 2013).
79 - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
80 ======= ======================================================================
81
82
83 Developers
84 ==========
85
86 This script and related tools are being developed on the following hg branch:
87 http://bitbucket.org/peterjc/galaxy-central/src/tools
88
89 Development has now moved to a dedicated GitHub repository:
90 https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus
91
92 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
93 the following command from the Galaxy root folder::
94
95 $ tar -czf nlstradmus.tar.gz tools/nlstradamus/README.rst tools/nlstradamus/nlstradamus.xml tools/nlstradamus/tool_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.nlstradamus.tabular test-data/empty.fasta test-data/empty_nlstradamus.tabular
96
97 Check this worked::
98
99 $ tar -tzf nlstradmus.tar.gz
100 tools/nlstradamus/README.rst
101 tools/nlstradamus/nlstradamus.xml
102 tools/nlstradamus/tool_dependencies.xml
103 test-data/four_human_proteins.fasta
104 test-data/four_human_proteins.nlstradamus.tabular
105 test-data/empty.fasta
106 test-data/empty_nlstradamus.tabular
107
108
109 Licence (MIT)
110 =============
111
112 Permission is hereby granted, free of charge, to any person obtaining a copy
113 of this software and associated documentation files (the "Software"), to deal
114 in the Software without restriction, including without limitation the rights
115 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
116 copies of the Software, and to permit persons to whom the Software is
117 furnished to do so, subject to the following conditions:
118
119 The above copyright notice and this permission notice shall be included in
120 all copies or substantial portions of the Software.
121
122 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
123 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
124 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
125 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
126 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
127 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
128 THE SOFTWARE.