|
0
|
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
|
