Mercurial > repos > iuc > gatk2
annotate readme.rst @ 15:a3247b69fa59 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 898393cb5c244c8fab2e965f003ae3991bcb655e
| author | iuc |
|---|---|
| date | Mon, 04 Apr 2016 06:33:05 -0400 |
| parents | 86007c982f00 |
| children |
| rev | line source |
|---|---|
| 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 | |
| 4 | 25 .. _toolshed: http://toolshed.g2.bx.psu.edu/view/iuc/gatk2 |
| 0 | 26 |
| 4 | 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. |
| 4 | 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 | |
| 4 | 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 |
| 4 | 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 |
| 4 | 42 <tool_dependency_dir>/environment_settings/GATK2_SITE_OPTIONS/iuc/gatk2/<hash_string>/env.sh |
| 0 | 43 |
| 4 | 44 to deactivate the 'call home feature' of GATK with something like: |
| 0 | 45 |
| 4 | 46 GATK2_SITE_OPTIONS='-et NO_ET -K /data/gatk2_key_file' |
| 0 | 47 |
| 4 | 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 | |
| 4 | 54 Optionally, you may also want to add some commands to be executed before GATK (e.g. to load modules) to the file: |
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86007c982f00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389
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55 :: |
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86007c982f00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389
iuc
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56 <tool_dependency_dir>/gatk2/default/env.sh |
| 4 | 57 |
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86007c982f00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389
iuc
parents:
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58 Note that due to the manual nature of the GATK2 installation you will be getting the |
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86007c982f00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389
iuc
parents:
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diff
changeset
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59 following warnings in the Galaxy log (unless you specified the env.sh in the previous paragraph): |
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86007c982f00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389
iuc
parents:
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diff
changeset
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60 :: |
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86007c982f00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389
iuc
parents:
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61 Failed to resolve dependency on 'gatk2', ignoring. |
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86007c982f00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389
iuc
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62 |
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86007c982f00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389
iuc
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63 This is because the |
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86007c982f00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389
iuc
parents:
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64 :: |
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86007c982f00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389
iuc
parents:
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changeset
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65 <requirement type="package">gatk2</requirement> |
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86007c982f00
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389
iuc
parents:
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diff
changeset
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66 is specified but never resolved in the tool_dependencies.xml. It is safe to ignore. |
| 0 | 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. | |
| 4 | 70 You can find them in the tool-data/ Galaxy directory. |
| 0 | 71 |
| 72 History | |
| 73 ======= | |
| 74 | |
| 6 | 75 * v0.1 - Initial public release |
| 76 * v2.8.0 - Bugfix release, increase version number to reflect the underlying GATK version | |
| 0 | 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. |