Purdue University

Commands

• bed_to_gff.pl
• bp_seq_select.pl
• build_mod.pl
• calc_introns_from_gtf.pl
• change_path_in_perl_scripts.pl
• compare_intervals_exact.pl
• gc_distr.pl
• get_below_gc.pl
• get_sequence_from_GTF.pl
• gmes_petap.pl
• hc_exons2hints.pl
• histogram.pl
• make_nt_freq_mat.pl
• parse_ET.pl
• parse_by_introns.pl
• parse_gibbs.pl
• parse_set.pl
• predict_genes.pl
• reformat_gff.pl
• rescale_gff.pl
• rnaseq_introns_to_gff.pl
• run_es.pl
• run_hmm_pbs.pl
• scan_for_bp.pl
• star_to_gff.pl
• verify_evidence_gmhmm.pl

Academic license

To use GeneMark, users need to download license files by yourself.

Go to the GeneMark web site: http://exon.gatech.edu/GeneMark/license_download.cgi. Check the boxes for GeneMark-ES/ET/EP ver 4.69_lic and LINUX 64 next to it, fill out the form, then click "I agree". In the next page, right click and copy the link addresses for 64 bit licenss. Paste the link addresses in the commands below:

cd $HOME
wget "replace with license URL"
zcat gm_key_64.gz > .gm_key

Module

You can load the modules by:

module load biocontainers
module load genemark/4.68 

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 GeneMark on our cluster:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=genemark
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers genemark/4.68  

gmes_petap.pl --ES  --cores 24 --sequence scaffolds.fasta