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author Bjoern Gruening <bjoern@gruenings.eu>
date Thu, 15 Mar 2012 10:09:28 +0100
parents augustus/readme.txt@9fb7ae02453c
children 02e9daf33c24
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1 Galaxy wrapper for Augustus
2 =====================================
3
4 This wrapper is copyright 2012 by Björn Grüning.
5
6 This is a wrapper for the command line tool of augustus.
7 http://bioinf.uni-greifswald.de/augustus/
8
9 AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
10
11 Oliver Keller, Martin Kollmar, Mario Stanke, Stephan Waack (2011)
12 A novel hybrid gene prediction method employing protein multiple sequence alignments
13 Bioinformatics, doi: 10.1093/bioinformatics/btr010
14
15 Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008)
16 Using native and syntenically mapped cDNA alignments to improve de novo gene finding
17 Bioinformatics, doi: 10.1093/bioinformatics/btn013
18
19 Mario Stanke and Stephan Waack (2003)
20 Gene Prediction with a Hidden-Markov Model and a new Intron Submodel.
21 Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225
22
23
24
25
26 Installation
27 ============
28
29 Install or downlaod augustus from:
30
31 http://bioinf.uni-greifswald.de/augustus/binaries/
32
33 and follow the installation instructions or copy the binaries into your $PATH
34
35 To install the wrapper copy the augustus folder in the galaxy tools
36 folder and modify the tools_conf.xml file to make the tool available to Galaxy.
37 For example:
38
39 <section name="Gene Prediction" id="gene_prediction">
40 <tool file="gene_prediction/tools/augustus/augustus.xml" />
41 </section>
42
43
44 Set the AUGUSTUS_CONFIG_PATH to /path_to_augustus/augustus/config with
45 export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
46 or modify the wrapper and use the following additional commandline switch:
47 --AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
48
49
50
51
52 History
53 =======
54
55 v0.1 - Initial public release
56
57
58 Wrapper Licence (MIT/BSD style)
59 ===============================
60
61 Permission to use, copy, modify, and distribute this software and its
62 documentation with or without modifications and for any purpose and
63 without fee is hereby granted, provided that any copyright notices
64 appear in all copies and that both those copyright notices and this
65 permission notice appear in supporting documentation, and that the
66 names of the contributors or copyright holders not be used in
67 advertising or publicity pertaining to distribution of the software
68 without specific prior permission.
69
70 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
71 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
72 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
73 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
74 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
75 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
76 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
77 OR PERFORMANCE OF THIS SOFTWARE.
78