Purdue University

Commands

• cegma2zff
• chado2gff3
• compare
• cufflinks2gff3
• evaluator
• fasta_merge
• fasta_tool
• genemark_gtf2gff3
• gff3_merge
• iprscan2gff3
• iprscan_wrap
• ipr_update_gff
• maker
• maker2chado
• maker2eval_gtf
• maker2jbrowse
• maker2wap
• maker2zff
• maker_functional
• maker_functional_fasta
• maker_functional_gff
• maker_map_ids
• map2assembly
• map_data_ids
• map_fasta_ids
• map_gff_ids
• tophat2gff3

Module

You can load the modules by:

module load biocontainers
module load maker/2.31.11 # OR maker/3.01.03  

Prerequisites

1. After loading MAKER modules, users can create MAKER control files by the following comand:

   maker -CTL
   

   This will generate three files:

• maker_opts.ctl (required to be modified)
• maker_exe.ctl (do not need to modify this file)
• maker_bopts.ctl (optionally modify this file)

1. maker_opts.ctl: - If not using RepeatMasker, modify model_org=all to model_org= - If not using RepeatMasker, modify model_org=all to an appropriate family/genus/species.

Example job non-mpi

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 MAKER on our cluster:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 10:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=MAKER
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers maker/2.31.11  # or maker/3.01.03 

maker -c 24

Example job mpi

To use MAKER in MPI mode, we cannot use the maker modules. Instead we have to use the singularity image files stored in /apps/biocontainers/images:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 5:00:00
#SBATCH -N 2
#SBATCH -n 24
#SBATCH -c 8
#SBATCH --job-name=MAKER_mpi
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --mail-user=UserID@purdue.edu
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
 
## MAKER2
mpirun -n 24 singularity exec /apps/biocontainers/images/maker_2.31.11.sif maker -c 8

## MAKER3
mpirun -n 24 singularity exec /apps/biocontainers/images/maker_3.01.03.sif maker -c 8