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