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comparison tools/protein_analysis/nlstradamus.txt @ 1:f93ad4882338 draft

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Uploaded v0.0.6, adds unit tests and minor documentation changes.
author peterjc
date Wed, 17 Apr 2013 08:26:25 -0400
parents 0ad90e5eb390
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0:0ad90e5eb390 1:f93ad4882338
1 Galaxy wrapper for NLStradamus v1.7 (C++ version) 1 Galaxy wrapper for NLStradamus v1.7 or v1.8 (C++ version)
2 ================================================= 2 =========================================================
3 3
4 This wrapper is copyright 2011 by Peter Cock, The James Hutton Institute 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. 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below. 6 See the licence text below.
7 7
8 NLStradamus is a command line tools for predicting nuclear localization 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). 9 signals (NLSs) in a FASTA file of proteins using a Hidden Markov Model (HMM).
10 10
11 A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses. 11 A. N. Nguyen Ba, A. Pogoutse, N. Provart, A. M. Moses.
12 NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction. 12 NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction.
13 BMC Bioinformatics. 2009 Jun 29;10(1):202. 13 BMC Bioinformatics. 2009 Jun 29;10(1):202.
14 http://dx.doi.org/10.1186/1471-2105-10-202
14 15
15 http://www.moseslab.csb.utoronto.ca/NLStradamus 16 http://www.moseslab.csb.utoronto.ca/NLStradamus
16 17
17 Early versions of NLStradamus did not have a native tabular output format, this 18 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 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 this point (early versions of NLStradamus came as a perl script only).
20 wrapper expects the compiled C++ binary "NLStradamus" to be on the system PATH.
21 21
22 To install the wrapper installed the following files under the Galaxy tools 22 Version 1.8 fixed a C++ compilation issue on modern compilers, but is otherwise
23 unchanged.
24
25
26 Installation
27 ============
28 This wrapper expects the compiled C++ binary "NLStradamus" to be on the system
29 PATH.
30
31 To install the wrapper copy or move the following files under the Galaxy tools
23 folder, e.g. in a tools/protein_analysis folder: 32 folder, e.g. in a tools/protein_analysis folder:
24 33
25 * nlstradamus.xml (the Galaxy tool definition) 34 * nlstradamus.xml (the Galaxy tool definition)
26 * nlstradamus.txt (this README file) 35 * nlstradamus.txt (this README file)
27 36
29 tool. If you are using other protein analysis tools like TMHMM or SignalP, put 38 tool. If you are using other protein analysis tools like TMHMM or SignalP, put
30 it next to them. Just add the line: 39 it next to them. Just add the line:
31 40
32 <tool file="protein_analysis/nlstradamus.xml" /> 41 <tool file="protein_analysis/nlstradamus.xml" />
33 42
43 If you wish to run the unit tests, also add this to tools_conf.xml.sample
44 and move/copy the test-data files under Galaxy's test-data folder.
45
34 That's it. 46 That's it.
35 47
36 48
37 History 49 History
38 ======= 50 =======
39 51
40 v0.0.3 - Initial public release 52 v0.0.3 - Initial public release
53 v0.0.4 - Adding DOI link to reference
54 (Documentation change only)
55 v0.0.5 - Assume non-zero return codes are errors
56 v0.0.6 - Show output help text using a table
57 - Added unit tests
41 58
42 59
43 Developers 60 Developers
44 ========== 61 ==========
45 62
46 This script and related tools are being developed on the following hg branch: 63 This script and related tools are being developed on the following hg branch:
47 http://bitbucket.org/peterjc/galaxy-central/src/tools 64 http://bitbucket.org/peterjc/galaxy-central/src/tools
48 65
49 For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use 66 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
50 the following command from the Galaxy root folder: 67 the following command from the Galaxy root folder:
51 68
52 tar -czf nlstradmus.tar.gz tools/protein_analysis/nlstradum.xml tools/protein_analysis/nlstradum.txt 69 $ tar -czf nlstradmus.tar.gz tools/protein_analysis/nlstradamus.xml tools/protein_analysis/nlstradamus.txt test-data/four_human_proteins.fasta test-data/four_human_proteins.nlstradamus.tabular test-data/empty.fasta test-data/empty_nlstradamus.tabular
53 70
54 Check this worked: 71 Check this worked:
55 72
56 $ tar -tzf nlstradmus.tar.gz 73 $ tar -tzf nlstradmus.tar.gz
57 filter/seq_filter_by_id.py 74 tools/protein_analysis/nlstradamus.xml
58 filter/seq_filter_by_id.txt 75 tools/protein_analysis/nlstradamus.txt
59 filter/seq_filter_by_id.xml 76 test-data/four_human_proteins.fasta
77 test-data/four_human_proteins.nlstradamus.tabular
78 test-data/empty.fasta
79 test-data/empty_nlstradamus.tabular
60 80
61 81
62 Licence (MIT/BSD style) 82 Licence (MIT/BSD style)
63 ======================= 83 =======================
64 84