Difference between revisions of "Braker"
| (One intermediate revision by one other user not shown) | |||
| Line 5: | Line 5: | ||
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
| Line 34: | Line 34: | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#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 | ||
|}} | |}} | ||
Latest revision as of 18:49, 19 August 2024
Description
BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes
Environment Modules
Run module spider braker to find out what environment modules are available for this application.
System Variables
- HPC_BRAKER_DIR - installation directory
- HPC_BRAKER_BIN - executable directory
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
Citation
If you publish research that uses braker you have to cite it as follows:
https://github.com/Gaius-Augustus/BRAKER#citing-braker-and-software-called-by-braker