Genemarks-2
Introduction
GeneMarkS-2 combines GeneMark.hmm (prokaryotic) and GeneMark (prokaryotic) with a self-training procedure that determines parameters of the models of both GeneMark.hmm and GeneMark.
For more information, please check:
The users need to download your own licence key from GeneMark website and copy key “gm_key” into users’ home directory as: cp gm_key ~/.gm_key | Home page: http://opal.biology.gatech.edu/GeneMark/
Versions
1.14_1.25
Commands
gms2.pl
biogem
compp
gmhmmp2
Module
You can load the modules by:
module load biocontainers
module load genemarks-2
Example job
Warning
Using #!/bin/sh -l
as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash
instead.
To run genemarks-2 on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=genemarks-2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers genemarks-2