Mercurial > repos > jjohnson > augustus_dep
comparison readme.txt @ 0:807dc2efb781 draft
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| author | jjohnson |
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| date | Mon, 22 Oct 2012 13:25:19 -0400 |
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| -1:000000000000 | 0:807dc2efb781 |
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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 |