Mercurial > repos > geert-vandeweyer > mutect_wrapper
comparison readme.rst @ 5:f9a746877f6c draft
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| author | geert-vandeweyer |
|---|---|
| date | Thu, 13 Feb 2014 09:27:26 -0500 |
| parents | |
| children | 3b2782fc9610 |
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| 4:e774395351f5 | 5:f9a746877f6c |
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| 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 |