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1 Galaxy wrapper for GATK2
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2 ========================
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3
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4 This wrapper is copyright 2013 by Björn Grüning, Jim Johnson & the Galaxy Team.
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5
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6 The Genome Analysis Toolkit or GATK is a software package developed at the
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7 Broad Institute to analyse next-generation resequencing data. The toolkit offers
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8 a wide variety of tools, with a primary focus on variant discovery and
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9 genotyping as well as strong emphasis on data quality assurance. Its robust
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10 architecture, powerful processing engine and high-performance computing features
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11 make it capable of taking on projects of any size.
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12
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13 http://www.broadinstitute.org/gatk
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14 http://www.broadinstitute.org/gatk/about/citing-gatk
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15
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16 GATK is Free for academics, and fee for commercial use. Please study the GATK licensing website:
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17 http://www.broadinstitute.org/gatk/about/#licensing
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18
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19
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20 Installation
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21 ============
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22
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23 The recommended installation is by means of the toolshed_.
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24
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25 .. _toolshed: http://toolshed.g2.bx.psu.edu/view/iuc/gatk2
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26
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27 Galaxy should be able to install samtools dependencies automatically
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28 for you. GATK2, and its new licence model, does not allow us to distribute the GATK binaries.
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29 As a consequence you need to install GATK2 by your own, please see the GATK website for more information:
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30
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31 http://www.broadinstitute.org/gatk/download
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32
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33 Once you have installed GATK2, you need to edit the env.sh files that are installed together with the wrappers.
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34 You must edit the GATK2_PATH environment variable in the file:
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35
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36 <tool_dependency_dir>/environment_settings/GATK2_PATH/iuc/gatk2/<hash_string>/env.sh
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37
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38 to point to the folder where you have installed GATK2.
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39
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40 Optionally, you may also want to edit the GATK2_SITE_OPTIONS environment variable in the file:
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41
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42 <tool_dependency_dir>/environment_settings/GATK2_SITE_OPTIONS/iuc/gatk2/<hash_string>/env.sh
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43
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44 to deactivate the 'call home feature' of GATK with something like:
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45
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46 GATK2_SITE_OPTIONS='-et NO_ET -K /data/gatk2_key_file'
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47
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48 GATK2_SITE_OPTIONS can be also used to insert other specific options into every GATK2 wrapper
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49 at runtime, without changing the actual wrapper.
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50
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51 Read more about the "Phone Home" problem at:
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52 http://www.broadinstitute.org/gatk/guide/article?id=1250
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53
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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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55 ::
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56 <tool_dependency_dir>/gatk2/default/env.sh
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57
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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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59 following warnings in the Galaxy log (unless you specified the env.sh in the previous paragraph):
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60 ::
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61 Failed to resolve dependency on 'gatk2', ignoring.
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62
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63 This is because the
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64 ::
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65 <requirement type="package">gatk2</requirement>
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66 is specified but never resolved in the tool_dependencies.xml. It is safe to ignore.
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67
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68 Finally, you should fill in additional information about your genomes and
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69 annotations in the gatk2_picard_index.loc and gatk2_annotations.txt.
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70 You can find them in the tool-data/ Galaxy directory.
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71
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72 History
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73 =======
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74
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75 * v0.1 - Initial public release
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76 * v2.8.0 - Bugfix release, increase version number to reflect the underlying GATK version
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77
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78
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79 Licence (MIT)
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80 =============
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81
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82 Permission is hereby granted, free of charge, to any person obtaining a copy
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83 of this software and associated documentation files (the "Software"), to deal
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84 in the Software without restriction, including without limitation the rights
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85 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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86 copies of the Software, and to permit persons to whom the Software is
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87 furnished to do so, subject to the following conditions:
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88
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89 The above copyright notice and this permission notice shall be included in
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90 all copies or substantial portions of the Software.
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91
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92 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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93 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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94 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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95 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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96 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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97 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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98 THE SOFTWARE.
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