glimmerhmm
Link to section 'Introduction' of 'glimmerhmm' Introduction
Glimmerhmm is a new gene finder based on a Generalized Hidden Markov Model (GHMM).
For more information, please check its website: https://biocontainers.pro/tools/glimmerhmm and its home page: https://ccb.jhu.edu/software/glimmerhmm/.
Link to section 'Versions' of 'glimmerhmm' Versions
- 3.0.4
Link to section 'Commands' of 'glimmerhmm' Commands
- glimmerhmm
- glimmhmm.pl
- trainGlimmerHMM
Link to section 'Module' of 'glimmerhmm' Module
You can load the modules by:
module load biocontainers
module load glimmerhmm
Link to section 'Example job' of 'glimmerhmm' Example job
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 Glimmerhmm on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=glimmerhmm
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers glimmerhmm
trainGlimmerHMM Asperg.fasta Asperg.cds -d Asperg
glimmerhmm Asperg.fasta -d Asperg -o Asperg_glimmerhmm_out