|
5
|
1 Galaxy wrapper for muTect
|
|
|
2 =========================
|
|
|
3
|
|
|
4 This wrapper is written by Geert Vandeweyer. MuTect is a software package developed at the
|
|
|
5 Broad Institute to analyse next-generation resequencing data.
|
|
|
6
|
|
|
7 The recommended installation is by means of the toolshed_.
|
|
|
8
|
|
|
9 .. _toolshed: http://toolshed.g2.bx.psu.edu/view/geert-vandeweyer/mutect_wrapper
|
|
|
10
|
|
|
11 Galaxy should be able to install samtools dependencies automatically
|
|
|
12 for you. muTect must be installed manually. After installation you need to edit the env.sh files that are installed together with the wrapper.
|
|
|
13
|
|
|
14 You must edit the MUTECT_PATH environment variable in the file:
|
|
|
15
|
|
|
16 <tool_dependency_dir>/environment_settings/MUTECT_PATH/geert-vandeweyer/mutect/<hash_string>/env.sh
|
|
|
17
|
|
|
18 to point to the folder where you have installed MUTECT.
|
|
|
19
|
|
|
20
|
