comparison readme.txt @ 0:e11e303c39a4 default tip

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author bjoern-gruening
date Wed, 11 Jan 2012 09:34:45 -0500
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1 Galaxy wrapper for RepeatMasker
2 =====================================
3
4 This wrapper is copyright 2012 by Björn Grüning.
5
6 This is a wrapper for the command line tool of Glimmer3.
7 http://www.cbcb.umd.edu/software/glimmer/
8
9 Glimmer is a system for finding genes in microbial DNA,
10 especially the genomes of bacteria, archaea, and viruses.
11 Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated
12 Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.
13
14 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.
15 S. Salzberg, A. Delcher, S. Kasif, and O. White. Microbial gene identification using interpolated Markov models, Nucleic Acids Research 26:2 (1998), 544-548.
16 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).
17
18
19
20 Installation
21 ============
22
23 To install Glimmer3, please download Glimmer3 from
24
25 http://www.cbcb.umd.edu/software/glimmer/glimmer302.tar.gz
26
27 and follow the installation instructions. You can also use packages from your distribution like
28
29 http://packages.debian.org/stable/science/tigr-glimmer
30
31
32 To install the wrapper copy the glimmer3 folder in the galaxy tools
33 folder and modify the tools_conf.xml file to make the tool available to Galaxy.
34 For example:
35
36 <tool file="gene_prediction/tools/glimmer3/glimmer3-main-wrapper.xml" />
37 <tool file="gene_prediction/tools/glimmer3/glimmer_predict.xml" />
38 <tool file="gene_prediction/tools/glimmer3/glimmer_orf_to_seq.xml" />
39 <tool file="gene_prediction/tools/glimmer3/glimmer2gff.xml" />
40 <tool file="gene_prediction/tools/glimmer3/gbktoorfWrapper.xml" />
41 <tool file="gene_prediction/tools/glimmer3/glimmer_acgt_content.xml" />
42 <tool file="gene_prediction/tools/glimmer3/glimmer3-build-icm-wrapper.xml" />
43 <tool file="gene_prediction/tools/glimmer3/glimmer3-extract-wrapper.xml" />
44 <tool file="gene_prediction/tools/glimmer3/glimmer3-long-orfs-wrapper.xml" />
45
46
47 History
48 =======
49
50 v0.1 - Initial public release
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