View source for Braker

[[Category:Software]][[Category:Phylogenetics]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|braker}}
|{{#vardefine:url|https://github.com/Gaius-Augustus/BRAKER}}
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
|{{#vardefine:conf|}}           <!--CONFIGURATION-->
|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
|{{#vardefine:job|}}            <!--JOB SCRIPTS-->
|{{#vardefine:policy|}}         <!--POLICY-->
|{{#vardefine:testing|}}       <!--PROFILING-->
|{{#vardefine:faq|}}             <!--FAQ-->
|{{#vardefine:citation|1}}       <!--CITATION-->
|{{#vardefine:installation|}} <!--INSTALLATION-->
|}
<!--BODY-->
<!--Description-->
{{#if: {{#var: url}}|
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes

<!--Modules-->
==Environment Modules==
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory

<!--Configuration-->
{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
|}}
<!--Run-->
{{#if: {{#var: exe}}|==Additional Information==

Prior to running braker, you will need to copy the AUGUSTUS_CONFIG_PATH to your working directory:

$ cd /path/to/blue/working/directory

$ module load braker

$ cp -r $AUGUSTUS_CONFIG_PATH .


After loading the module in your job script, you will need to export the path to the config directory:

export AUGUSTUS_CONFIG_PATH=/path/to/blue/working/directory/config

|}}
<!--Job Scripts-->
{{#if: {{#var: job}}|==Job Script Examples==
See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.
|}}
<!--Policy-->
{{#if: {{#var: policy}}|==Usage Policy==

WRITE USAGE POLICY HERE (Licensing, usage, access).

|}}
<!--Performance-->
{{#if: {{#var: testing}}|==Performance==

WRITE_PERFORMANCE_TESTING_RESULTS_HERE

|}}
<!--Faq-->
{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
<!--Citation-->
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{#var:app}} you have to cite it as follows:

https://github.com/Gaius-Augustus/BRAKER#citing-braker-and-software-called-by-braker

|}}
<!--Installation-->
{{#if: {{#var: installation}}|==Installation==
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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