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author | lz_hust |
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date | Sat, 01 Jun 2019 07:20:41 -0400 |
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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 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 | |
25 .. _toolshed: http://toolshed.g2.bx.psu.edu/view/iuc/gatk2 | |
26 | |
27 Galaxy should be able to install samtools dependencies automatically | |
28 for you. GATK2, and its new licence model, does not allow us to distribute the GATK binaries. | |
29 As a consequence you need to install GATK2 by your own, please see the GATK website for more information: | |
30 | |
31 http://www.broadinstitute.org/gatk/download | |
32 | |
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: | |
35 | |
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: | |
41 | |
42 <tool_dependency_dir>/environment_settings/GATK2_SITE_OPTIONS/iuc/gatk2/<hash_string>/env.sh | |
43 | |
44 to deactivate the 'call home feature' of GATK with something like: | |
45 | |
46 GATK2_SITE_OPTIONS='-et NO_ET -K /data/gatk2_key_file' | |
47 | |
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: | |
52 http://www.broadinstitute.org/gatk/guide/article?id=1250 | |
53 | |
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 | |
57 | |
58 Note that due to the manual nature of the GATK2 installation you will be getting the | |
59 following warnings in the Galaxy log (unless you specified the env.sh in the previous paragraph): | |
60 :: | |
61 Failed to resolve dependency on 'gatk2', ignoring. | |
62 | |
63 This is because the | |
64 :: | |
65 <requirement type="package">gatk2</requirement> | |
66 is specified but never resolved in the tool_dependencies.xml. It is safe to ignore. | |
67 | |
68 Finally, you should fill in additional information about your genomes and | |
69 annotations in the gatk2_picard_index.loc and gatk2_annotations.txt. | |
70 You can find them in the tool-data/ Galaxy directory. | |
71 | |
72 History | |
73 ======= | |
74 | |
75 * v0.1 - Initial public release | |
76 * v2.8.0 - Bugfix release, increase version number to reflect the underlying GATK version | |
77 | |
78 | |
79 Licence (MIT) | |
80 ============= | |
81 | |
82 Permission is hereby granted, free of charge, to any person obtaining a copy | |
83 of this software and associated documentation files (the "Software"), to deal | |
84 in the Software without restriction, including without limitation the rights | |
85 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
86 copies of the Software, and to permit persons to whom the Software is | |
87 furnished to do so, subject to the following conditions: | |
88 | |
89 The above copyright notice and this permission notice shall be included in | |
90 all copies or substantial portions of the Software. | |
91 | |
92 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
93 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
94 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
95 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
96 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
97 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
98 THE SOFTWARE. |