rsnt_translations
56,430
edits
GATK: Difference between revisions
no edit summary
No edit summary |
No edit summary |
||
| Line 34: | Line 34: | ||
<!--T:5--> | <!--T:5--> | ||
More specific information of any given version can be | More specific information of any given version can be accessed with: | ||
<!--T:6--> | <!--T:6--> | ||
| Line 42: | Line 42: | ||
<!--T:7--> | <!--T:7--> | ||
As you can see, this module only has nixpkgs/16.09 module as prerequisite | As you can see, this module only has the nixpkgs/16.09 module as prerequisite | ||
so it can be loaded by: | so it can be loaded by: | ||
| Line 59: | Line 59: | ||
==General usage == <!--T:11--> | ==General usage == <!--T:11--> | ||
The later versions of GATK (>=4.0.0.0) provide a wrapper over the | The later versions of GATK (>=4.0.0.0) provide a wrapper over the Java executables (.jar). Loading the GATK modules will automatically set most of the environmental variables you will need to successfully run GATK. | ||
<!--T:12--> | <!--T:12--> | ||
The module spider command also provides you with usage and examples of that wrapper: | The <code>module spider</code> command also provides you with usage and examples of that wrapper: | ||
<pre> | <pre> | ||
Usage | Usage | ||
| Line 75: | Line 75: | ||
<!--T:13--> | <!--T:13--> | ||
As you probably notice, there are some arguments to be passed directly to java through the | As you probably notice, there are some arguments to be passed directly to java through the <code>--java-options</code> such as the maximum heap memory (<code>-Xmx8G</code> in the example, reserving 8 Gb of memory for the virtual machine). We recommend that you <b>always</b> use <code>-DGATK_STACKTRACE_ON_USER_EXCEPTION=true</code> since it will give you more information in case the program fails. This information can help you or us (in case you needed support) to solve the issue. | ||
Note that all options passed to <code>--java-options</code> have to be within quotation marks. | Note that all options passed to <code>--java-options</code> have to be within quotation marks. | ||