|
0
|
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 GATK is Free for academics, and fee for commercial use. Please study the GATK licensing website:
|
|
|
17 http://www.broadinstitute.org/gatk/about/#licensing
|
|
|
18
|
|
|
19
|
|
|
20 Installation
|
|
|
21 ============
|
|
|
22
|
|
|
23 The recommended installation is by means of the toolshed_.
|
|
|
24
|
|
2
|
25 .. _toolshed: http://toolshed.g2.bx.psu.edu/view/iuc/gatk2
|
|
0
|
26
|
|
2
|
27 Galaxy should be able to install samtools dependencies automatically
|
|
0
|
28 for you. GATK2, and its new licence model, does not allow us to distribute the GATK binaries.
|
|
2
|
29 As a consequence you need to install GATK2 by your own, please see the GATK website for more information:
|
|
0
|
30
|
|
|
31 http://www.broadinstitute.org/gatk/download
|
|
|
32
|
|
2
|
33 Once you have installed GATK2, you need to edit the env.sh files that are installed together with the wrappers.
|
|
|
34 You must edit the GATK2_PATH environment variable in the file:
|
|
0
|
35
|
|
2
|
36 <tool_dependency_dir>/environment_settings/GATK2_PATH/iuc/gatk2/<hash_string>/env.sh
|
|
|
37
|
|
|
38 to point to the folder where you have installed GATK2.
|
|
|
39
|
|
|
40 Optionally, you may also want to edit the GATK2_SITE_OPTIONS environment variable in the file:
|
|
0
|
41
|
|
2
|
42 <tool_dependency_dir>/environment_settings/GATK2_SITE_OPTIONS/iuc/gatk2/<hash_string>/env.sh
|
|
0
|
43
|
|
2
|
44 to deactivate the 'call home feature' of GATK with something like:
|
|
0
|
45
|
|
2
|
46 GATK2_SITE_OPTIONS='-et NO_ET -K /data/gatk2_key_file'
|
|
0
|
47
|
|
2
|
48 GATK2_SITE_OPTIONS can be also used to insert other specific options into every GATK2 wrapper
|
|
|
49 at runtime, without changing the actual wrapper.
|
|
|
50
|
|
|
51 Read more about the "Phone Home" problem at:
|
|
0
|
52 http://www.broadinstitute.org/gatk/guide/article?id=1250
|
|
|
53
|
|
2
|
54 Optionally, you may also want to add some commands to be executed before GATK (e.g. to load modules) to the file:
|
|
|
55
|
|
|
56 <tool_dependency_dir>/gatk2/default/env.sh
|
|
0
|
57
|
|
|
58 Finally, you should fill in additional information about your genomes and
|
|
|
59 annotations in the gatk2_picard_index.loc and gatk2_annotations.txt.
|
|
2
|
60 You can find them in the tool-data/ Galaxy directory.
|
|
0
|
61
|
|
|
62
|
|
|
63 History
|
|
|
64 =======
|
|
|
65
|
|
|
66 v0.1 - Initial public release
|
|
|
67
|
|
|
68
|
|
|
69 Licence (MIT)
|
|
|
70 =============
|
|
|
71
|
|
|
72 Permission is hereby granted, free of charge, to any person obtaining a copy
|
|
|
73 of this software and associated documentation files (the "Software"), to deal
|
|
|
74 in the Software without restriction, including without limitation the rights
|
|
|
75 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
|
|
76 copies of the Software, and to permit persons to whom the Software is
|
|
|
77 furnished to do so, subject to the following conditions:
|
|
|
78
|
|
|
79 The above copyright notice and this permission notice shall be included in
|
|
|
80 all copies or substantial portions of the Software.
|
|
|
81
|
|
|
82 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
|
|
83 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
|
|
84 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
|
|
85 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
|
|
86 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
|
|
87 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
|
|
|
88 THE SOFTWARE.
|
