Mercurial > repos > peterjc > nlstradamus
comparison tools/nlstradamus/nlstradamus.txt @ 2:9ec94203d895 draft
Uploaded v0.0.7 with automatic installation of the C++ binary.
| author | peterjc |
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| date | Tue, 23 Apr 2013 11:59:14 -0400 |
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| 1:f93ad4882338 | 2:9ec94203d895 |
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| 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. | |
| 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 http://dx.doi.org/10.1186/1471-2105-10-202 | |
| 15 | |
| 16 http://www.moseslab.csb.utoronto.ca/NLStradamus | |
| 17 | |
| 18 Early versions of NLStradamus did not have a native tabular output format, this | |
| 19 was added in version 1.7. Additionally a fast C++ implementation was added at | |
| 20 this point (early versions of NLStradamus came as a perl script only). | |
| 21 | |
| 22 Version 1.8 fixed a C++ compilation issue on modern compilers, but is otherwise | |
| 23 unchanged. | |
| 24 | |
| 25 | |
| 26 Automated Installation | |
| 27 ====================== | |
| 28 | |
| 29 This should be straightforward, Galaxy should automatically download and install | |
| 30 the C++ implementation of NLStradamus v1.8, and run the unit tests. | |
| 31 | |
| 32 | |
| 33 Manual Installation | |
| 34 =================== | |
| 35 This wrapper expects the compiled C++ binary "NLStradamus" to be on the system | |
| 36 PATH. | |
| 37 | |
| 38 To install the wrapper copy or move the following files under the Galaxy tools | |
| 39 folder, e.g. in a tools/protein_analysis folder: | |
| 40 | |
| 41 * nlstradamus.xml (the Galaxy tool definition) | |
| 42 * nlstradamus.txt (this README file) | |
| 43 | |
| 44 You will also need to modify the tools_conf.xml file to tell Galaxy to offer the | |
| 45 tool. If you are using other protein analysis tools like TMHMM or SignalP, put | |
| 46 it next to them. Just add the line (matching the chosen install path): | |
| 47 | |
| 48 <tool file="protein_analysis/nlstradamus.xml" /> | |
| 49 | |
| 50 If you wish to run the unit tests, also add this to tools_conf.xml.sample | |
| 51 and move/copy the test-data files under Galaxy's test-data folder. Then: | |
| 52 | |
| 53 $ ./run_functional_tests.sh -id nlstradamus | |
| 54 | |
| 55 That's it. | |
| 56 | |
| 57 | |
| 58 History | |
| 59 ======= | |
| 60 | |
| 61 v0.0.3 - Initial public release | |
| 62 v0.0.4 - Adding DOI link to reference | |
| 63 (Documentation change only) | |
| 64 v0.0.5 - Assume non-zero return codes are errors | |
| 65 v0.0.6 - Show output help text using a table | |
| 66 - Added unit tests | |
| 67 v0.0.7 - Automatic installation of the NLStradamus binary when installed | |
| 68 via the Galaxy Tool Shed | |
| 69 | |
| 70 | |
| 71 Developers | |
| 72 ========== | |
| 73 | |
| 74 This script and related tools are being developed on the following hg branch: | |
| 75 http://bitbucket.org/peterjc/galaxy-central/src/tools | |
| 76 | |
| 77 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use | |
| 78 the following command from the Galaxy root folder: | |
| 79 | |
| 80 $ tar -czf nlstradmus.tar.gz tools/nlstradamus/nlstradamus.xml tools/nlstradamus/nlstradamus.txt 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 | |
| 81 | |
| 82 Check this worked: | |
| 83 | |
| 84 $ tar -tzf nlstradmus.tar.gz | |
| 85 tools/nlstradamus/nlstradamus.xml | |
| 86 tools/nlstradamus/nlstradamus.txt | |
| 87 tools/nlstradamus/tool_dependencies.xml | |
| 88 test-data/four_human_proteins.fasta | |
| 89 test-data/four_human_proteins.nlstradamus.tabular | |
| 90 test-data/empty.fasta | |
| 91 test-data/empty_nlstradamus.tabular | |
| 92 | |
| 93 | |
| 94 Licence (MIT/BSD style) | |
| 95 ======================= | |
| 96 | |
| 97 Permission to use, copy, modify, and distribute this software and its | |
| 98 documentation with or without modifications and for any purpose and | |
| 99 without fee is hereby granted, provided that any copyright notices | |
| 100 appear in all copies and that both those copyright notices and this | |
| 101 permission notice appear in supporting documentation, and that the | |
| 102 names of the contributors or copyright holders not be used in | |
| 103 advertising or publicity pertaining to distribution of the software | |
| 104 without specific prior permission. | |
| 105 | |
| 106 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
| 107 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
| 108 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
| 109 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
| 110 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
| 111 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
| 112 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
| 113 OR PERFORMANCE OF THIS SOFTWARE. | |
| 114 | |
| 115 NOTE: This is the licence for the Galaxy Wrapper only. NLStradamus | |
| 116 is is available and licenced separately (under the GPL v3 or later). |