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author iuc
date Sat, 18 Jan 2014 07:21:33 -0500
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11 make it capable of taking on projects of any size. 11 make it capable of taking on projects of any size.
12 12
13 http://www.broadinstitute.org/gatk 13 http://www.broadinstitute.org/gatk
14 http://www.broadinstitute.org/gatk/about/citing-gatk 14 http://www.broadinstitute.org/gatk/about/citing-gatk
15 15
16
17 GATK is Free for academics, and fee for commercial use. Please study the GATK licensing website: 16 GATK is Free for academics, and fee for commercial use. Please study the GATK licensing website:
18 http://www.broadinstitute.org/gatk/about/#licensing 17 http://www.broadinstitute.org/gatk/about/#licensing
19 18
20 19
21 Installation 20 Installation
22 ============ 21 ============
23 22
24 The recommended installation is by means of the toolshed_. 23 The recommended installation is by means of the toolshed_.
25 24
26 .. _toolshed: http://toolshed.g2.bx.psu.edu/view/bjoern-gruening/augustus 25 .. _toolshed: http://toolshed.g2.bx.psu.edu/view/iuc/gatk2
27 26
28 Galaxy should be able to automatically install samtools dependencies automatically 27 Galaxy should be able to install samtools dependencies automatically
29 for you. GATK2, and its new licence model, does not allow us to distribute the GATK binaries. 28 for you. GATK2, and its new licence model, does not allow us to distribute the GATK binaries.
30 As a consequence you need to install GATK2 by your own, please see the GATK website for more informations: 29 As a consequence you need to install GATK2 by your own, please see the GATK website for more information:
31 30
32 http://www.broadinstitute.org/gatk/download 31 http://www.broadinstitute.org/gatk/download
33 32
34 Once you have installed GATK2 you need to edit the env.sh file that is installed with these wrappers. 33 Once you have installed GATK2, you need to edit the env.sh files that are installed together with the wrappers.
35 You will find this env.sh file under: 34 You must edit the GATK2_PATH environment variable in the file:
36 35
37 <tool_dependency_dir>/gatk2/<version>/iuc/<hash_string>/env.sh 36 <tool_dependency_dir>/environment_settings/GATK2_PATH/iuc/gatk2/<hash_string>/env.sh
38 37
39 You should edit the GATK2_PATH environment variable to point to the folder you have installed GATK2 38 to point to the folder where you have installed GATK2.
40 and if you want to deactivate the 'call home feature' from GATK you can set
41 39
42 GATK2_SITE_OPTIONS='-et "NO_ET" -K "/data/gatk2_key_file"' 40 Optionally, you may also want to edit the GATK2_SITE_OPTIONS environment variable in the file:
43 41
44 GATK2_SITE_OPTIONS can be used to insert specific options into every GATK2 wrapper 42 <tool_dependency_dir>/environment_settings/GATK2_SITE_OPTIONS/iuc/gatk2/<hash_string>/env.sh
45 during runtime, without changing the actuall wrapper.
46 43
47 Read more about the "Phone Home" problem under: 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:
48 http://www.broadinstitute.org/gatk/guide/article?id=1250 52 http://www.broadinstitute.org/gatk/guide/article?id=1250
49 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
50 57
51 Finally, you should fill in additional information about your genomes and 58 Finally, you should fill in additional information about your genomes and
52 annotations in the gatk2_picard_index.loc and gatk2_annotations.txt. 59 annotations in the gatk2_picard_index.loc and gatk2_annotations.txt.
53 You can find them under ./tool-data/. 60 You can find them in the tool-data/ Galaxy directory.
54
55 61
56 62
57 History 63 History
58 ======= 64 =======
59 65
78 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 84 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
79 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 85 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
80 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 86 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
81 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 87 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
82 THE SOFTWARE. 88 THE SOFTWARE.
83
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