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date Mon, 02 Dec 2013 06:18:36 -0500
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1 Galaxy wrapper for GATK2
2 ========================
3
4 This wrapper is copyright 2013 by Björn Grüning, Jim Johnson & the Galaxy Team.
5
6 The Genome Analysis Toolkit or GATK is a software package developed at the
7 Broad Institute to analyse next-generation resequencing data. The toolkit offers
8 a wide variety of tools, with a primary focus on variant discovery and
9 genotyping as well as strong emphasis on data quality assurance. Its robust
10 architecture, powerful processing engine and high-performance computing features
11 make it capable of taking on projects of any size.
12
13 http://www.broadinstitute.org/gatk
14 http://www.broadinstitute.org/gatk/about/citing-gatk
15
16
17 GATK is Free for academics, and fee for commercial use. Please study the GATK licensing website:
18 http://www.broadinstitute.org/gatk/about/#licensing
19
20
21 Installation
22 ============
23
24 The recommended installation is by means of the toolshed_.
25
26 .. _toolshed: http://toolshed.g2.bx.psu.edu/view/bjoern-gruening/augustus
27
28 Galaxy should be able to automatically install samtools dependencies automatically
29 for you. GATK2, and its new licence model, does not allow us to distribute the GATK binaries.
30 As a consequence you need to install GATK2 by your own, please see the GATK website for more informations:
31
32 http://www.broadinstitute.org/gatk/download
33
34 Once you have installed GATK2 you need to edit the env.sh file that is installed with these wrappers.
35 You will find this env.sh file under:
36
37 <tool_dependency_dir>/gatk2/<version>/iuc/<hash_string>/env.sh
38
39 You should edit the GATK2_PATH environment variable to point to the folder you have installed GATK2
40 and if you want to deactivate the 'call home feature' from GATK you can set
41
42 GATK2_SITE_OPTIONS='-et "NO_ET" -K "/data/gatk2_key_file"'
43
44 GATK2_SITE_OPTIONS can be used to insert specific options into every GATK2 wrapper
45 during runtime, without changing the actuall wrapper.
46
47 Read more about the "Phone Home" problem under:
48 http://www.broadinstitute.org/gatk/guide/article?id=1250
49
50
51 Finally, you should fill in additional information about your genomes and
52 annotations in the gatk2_picard_index.loc and gatk2_annotations.txt.
53 You can find them under ./tool-data/.
54
55
56
57 History
58 =======
59
60 v0.1 - Initial public release
61
62
63 Licence (MIT)
64 =============
65
66 Permission is hereby granted, free of charge, to any person obtaining a copy
67 of this software and associated documentation files (the "Software"), to deal
68 in the Software without restriction, including without limitation the rights
69 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
70 copies of the Software, and to permit persons to whom the Software is
71 furnished to do so, subject to the following conditions:
72
73 The above copyright notice and this permission notice shall be included in
74 all copies or substantial portions of the Software.
75
76 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
77 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
78 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
79 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
80 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
81 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
82 THE SOFTWARE.
83
84