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date Sun, 09 Jun 2013 07:54:25 -0400
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1 Galaxy wrapper for Augustus
2 ===========================
3
4 This wrapper is copyright 2012-2013 by Björn Grüning.
5
6 This is a wrapper for the command line tool of Augustus_.
7
8 .. _augustus: http://bioinf.uni-greifswald.de/augustus/
9
10 AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
11
12 Oliver Keller, Martin Kollmar, Mario Stanke, Stephan Waack (2011)
13 A novel hybrid gene prediction method employing protein multiple sequence alignments
14 Bioinformatics, doi: 10.1093/bioinformatics/btr010
15
16 Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008)
17 Using native and syntenically mapped cDNA alignments to improve de novo gene finding
18 Bioinformatics, doi: 10.1093/bioinformatics/btn013
19
20 Mario Stanke and Stephan Waack (2003)
21 Gene Prediction with a Hidden-Markov Model and a new Intron Submodel.
22 Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225
23
24
25 Installation
26 ============
27
28 The recommended installation is by means of the toolshed_.
29 If you need to install it manually here is a short introduction.
30
31 .. _toolshed: http://toolshed.g2.bx.psu.edu/view/bjoern-gruening/augustus
32
33
34 Install or downlaod augustus from::
35
36 http://bioinf.uni-greifswald.de/augustus/binaries/
37
38 and follow the installation instructions or copy the binaries into your $PATH. To install the wrapper copy the augustus folder in the galaxy tools folder and modify the tools_conf.xml file to make the tool available to Galaxy.
39
40 For example::
41
42 <section name="Gene Prediction" id="gene_prediction">
43 <tool file="gene_prediction/tools/augustus/augustus.xml" />
44 </section>
45
46
47 Set the *AUGUSTUS_CONFIG_PATH* to /path_to_augustus/augustus/config with::
48
49 export AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
50
51 or modify the wrapper and use the following additional commandline switch::
52
53 --AUGUSTUS_CONFIG_PATH=/path_to_augustus/augustus/config
54
55
56 History
57 =======
58
59 - v0.1: Initial public release
60 - v0.2: Added tool_dependencies.xml file and update the augustus version (thanks to James Johnson)
61 - v0.3: upgrade to augustus 2.7, added new organisms and new parameters, output additional sequence files
62
63 Wrapper Licence (MIT/BSD style)
64 ===============================
65
66 Permission to use, copy, modify, and distribute this software and its
67 documentation with or without modifications and for any purpose and
68 without fee is hereby granted, provided that any copyright notices
69 appear in all copies and that both those copyright notices and this
70 permission notice appear in supporting documentation, and that the
71 names of the contributors or copyright holders not be used in
72 advertising or publicity pertaining to distribution of the software
73 without specific prior permission.
74
75 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
76 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
77 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
78 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
79 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
80 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
81 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
82 OR PERFORMANCE OF THIS SOFTWARE.
83