Mercurial > repos > bgruening > glimmer3
comparison readme.rst @ 0:841357e0acbf draft
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author | bgruening |
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date | Sat, 06 Jul 2013 10:09:30 -0400 |
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1 ======================================= | |
2 Galaxy wrapper for Glimmer gene calling | |
3 ======================================= | |
4 | |
5 This wrapper is copyright 2012-2013 by Björn Grüning. | |
6 | |
7 This is a wrapper for the command line tool of Glimmer3_. | |
8 | |
9 .. _Glimmer: http://www.cbcb.umd.edu/software/glimmer/ | |
10 | |
11 Glimmer is a system for finding genes in microbial DNA, | |
12 especially the genomes of bacteria, archaea, and viruses. | |
13 Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated | |
14 Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. | |
15 | |
16 S. Salzberg, A. Delcher, S. Kasif, and O. White. Microbial gene identification using interpolated Markov models, Nucleic Acids Research 26:2 (1998), 544-548. | |
17 | |
18 A.L. Delcher, D. Harmon, S. Kasif, O. White, and S.L. Salzberg. Improved microbial gene identification with GLIMMER, Nucleic Acids Research 27:23 (1999), 4636-4641. | |
19 | |
20 A.L. Delcher, K.A. Bratke, E.C. Powers, and S.L. Salzberg. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (Advance online version) (2007). | |
21 | |
22 | |
23 ============ | |
24 Installation | |
25 ============ | |
26 | |
27 Since version 0.2 the recommended installation procedure is via the `Galaxy Tool Shed`. | |
28 | |
29 .. _`Galaxy Tool Shed`: http://toolshed.g2.bx.psu.edu/view/bjoern-gruening/glimmer3 | |
30 | |
31 To install Glimmer3 manually, please download Glimmer3 from:: | |
32 | |
33 http://www.cbcb.umd.edu/software/glimmer/glimmer302.tar.gz | |
34 | |
35 and follow the installation instructions. You can also use packages from your distribution like http://packages.debian.org/stable/science/tigr-glimmer | |
36 | |
37 To install the wrapper copy the glimmer3 folder in the galaxy tools | |
38 folder and modify the tools_conf.xml file to make the tool available to Galaxy. | |
39 For example:: | |
40 | |
41 <tool file="gene_prediction/tools/glimmer3/glimmer_w_icm.xml" /> | |
42 <tool file="gene_prediction/tools/glimmer3/glimmer_wo_icm.xml" /> | |
43 <tool file="gene_prediction/tools/glimmer3/glimmer_build-icm.xml" /> | |
44 | |
45 ======= | |
46 History | |
47 ======= | |
48 | |
49 - v0.1: Initial public release | |
50 - v0.2: Add tool shed integration | |
51 | |
52 =============================== | |
53 Wrapper Licence (MIT/BSD style) | |
54 =============================== | |
55 | |
56 Permission to use, copy, modify, and distribute this software and its | |
57 documentation with or without modifications and for any purpose and | |
58 without fee is hereby granted, provided that any copyright notices | |
59 appear in all copies and that both those copyright notices and this | |
60 permission notice appear in supporting documentation, and that the | |
61 names of the contributors or copyright holders not be used in | |
62 advertising or publicity pertaining to distribution of the software | |
63 without specific prior permission. | |
64 | |
65 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL | |
66 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED | |
67 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE | |
68 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT | |
69 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS | |
70 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE | |
71 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE | |
72 OR PERFORMANCE OF THIS SOFTWARE. | |
73 |