BRAKER
Description
BRAKER is a tool for eukaryotic genome annotation. It uses genomic and RNA-Seq data to automatically generate full gene structure annotations in novel genome. BRAKER is based on GeneMark-ET R2 and AUGUSTUS pipelines.
License
Free to use and open source under [Artistic License] (https://opensource.org/licenses/artistic-license-1.0)
Version
Version on CSC's Servers
Puhti: 2.1.6, 3.0.7
Setting up BRAKER
BRAKER needs some additional setting up steps before using it for the first time.
CSC BRAKER installations do not contain GeneMark or ProtHint softaware packages. While they are free for individual use, their licensing terms do not allow CSC to make a public installation of them. Each user needs to license and install them for their own use.
GeneMark
Go to GeneMark download page, and fill in the form. The version you need is "GeneMark-ES/ET/EP+" for "LINUX 64 kernel 3.10 - 5". Download the program file and yhe license key. To uncompress the packages:
tar xf gmes_linux_64_4.tar.gz
gunzip gm_key_64.gz
To tell BRAKER where to find GeneMark, set environment variable $GENEMARK_PATHto point to install location or use command line option --GENEMARK_PATH.
export GENEMARK_PATH=/path/to/gmes_linux_64_4
BRAKER module contains all the necessary dependencies.
ProtHint
Download and uncompress ProtHint.
wget https://github.com/gatech-genemark/ProtHint/releases/download/v2.6.0/ProtHint-2.6.0.tar.gz
tar xf ProtHint-2.6.0.tar.gz
Set environment variable $PROTHINT_PATHto point to install location or use command line option --PROTHINT_PATH.
export PROTHINT_PATH=/path/to/ProtHint-2.6.0/bin
BRAKER module contains all the necessary dependencies.
AUGUSTUS
AUGUSTUS is included in the installation, but you will need your own copy of AUGUSTUS config directory, as it needs to be writable by the user. You can create this by running command:
copy_config
It will create directory config in your current directory.
Set environment variable $AUGUSTUS_CONFIG_PATH to print to the config directory or use command line option --AUGUSTUS_CONFIG_PATH
Usage
In Puhti BRAKER should be used only in batch jobs. Either in normal batch jobs or in interactive batch jobs.
Interactive usage
You can start interactive batch job with command:
sinteractive -i
BRAKER can utilize several computing cores and can require significant amount of memory so you should reserve more than the default resources for your interactive batch job. For example 4 cores and 32 GB of memory.
In batch job, you can initialize BRAKER environment with command
module load braker
After that you can launch a BRAKER job with command:
braker.pl
To see the options, run command:
braker.pl --help
Sample BRAKER command in Puhti:
braker.pl --species=sp1 --genome=Drosophila.dna.fa --prot_seq=Drosophila.pep.fa --prg=gth --trainFromGth --AUGUSTUS_ab_initio --cores=$SLURM_CPUS_PER_TASK
Batch jobs
Sample batch job scrip for BRAKER:
#!/bin/bash
#SBATCH --job-name=BRAKER_Job
#SBATCH --account=project_2012345
#SBATCH --time=24:00:00
#SBATCH --mem=32000
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --partition=small
# load braker
module load braker
# Use correct paths instead of "/path/to"
export GENEMARK_PATH=/path/to/gmes_linux_64_4
export PROTHINT_PATH=/path/to/ProtHint-2.6.0/bin
export AUGUSTUS_CONFIG_PATH=/path/to/config
# start the job
braker.pl --species=sp1 --genome=Drosophila.dna.fa --prot_seq=Drosophila.pep.fa \
--prg=gth --trainFromGth --AUGUSTUS_ab_initio --cores=$SLURM_CPUS_PER_TASK
In the batch job example above one task (--ntasks 1) is executed. The BRAKER job uses 8 cores (--cpus-per-task=8 ) with total of 32 GB of memory (--mem=32000). The maximum duration of the job is ten hours (--time 10:00:00 ). All the cores are assigned from one computing node (--nodes=1 ). In the example the project that will be used is project_2012345. This value shuold be replaced by the name of your computing project.
You can submit the batch job file to the batch job system with command:
sbatch batch_job_file.bash
See the Puhti user guide for more information about running batch jobs.