Maker

Introduction

Maker is a portable and easily configurable genome annotation pipeline. Note: To run MAKER MPI, please use the below two lines: export SINGULARITYENV_LIBDIR”/depot/itap/datasets/Maker/RepeatMasker/Libraries” srun -n XX singularity exec /apps/biocontainers/images/maker_3.01.03.sif maker

For more information, please check:
Home page: https://www.yandell-lab.org/software/maker.html

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

2.31.11, 3.01.03

BELL

2.31.11, 3.01.03

GAUTSCHI

2.31.11, 3.01.03

NEGISHI

2.31.11, 3.01.03

SCHOLAR

2.31.11, 3.01.03

Commands

  • AED_cdf_generator.pl

  • TACC.PL

  • cegma2zff

  • chado2gff3

  • compare_gff3_to_chado

  • cufflinks2gff3

  • fasta_merge

  • fasta_tool

  • genemark_gtf2gff3

  • gff3_merge

  • ipr_update_gff

  • iprscan2gff3

  • maker

  • maker2chado

  • maker2eval_gtf

  • maker2jbrowse

  • maker2wap

  • maker2zff

  • maker_functional_fasta

  • maker_functional_gff

  • maker_map_ids

  • map2assembly

  • map_data_ids

  • map_fasta_ids

  • map_gff_ids

  • match2gene.pl

  • quality_filter.pl

  • split_gff3

  • tophat2gff3

  • train_augustus.pl

  • zff2genbank.pl

Module

You can load the modules by:

module load biocontainers
module load maker

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 maker on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers maker

# Your maker workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers maker

# Your maker workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers maker

# Your maker workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers maker

# Your maker workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#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
module biocontainers maker

# Your maker workflow...