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MAKER

MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.

Installation

MAKER can be installed from the Bioconda Anaconda channel by loading the Miniforge module and then creating a Conda environment and installing MAKER into it (output below truncated):

$ module load miniforge
$ mamba create --quiet --yes --name maker_env
$ mamba activate maker_env
(maker_env) $ mamba install bioconda::maker

Looking for: ['bioconda::maker']
...
  Updating specs:
   - bioconda::maker
...
Confirm changes: [Y/n] Y
...
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Usage

To run MAKER, simply load the miniforge module and activate the Conda environment you previously created (see above for details):

$ module load miniforge
$ mamba activate maker_env
(maker_env) $ maker --help
MAKER version X.Y.Z

Usage:

     maker [options] <maker_opts> <maker_bopts> <maker_exe>

For usage documentation, run maker --help.

Example job

Serial job

Here is an example job to perform a gene-based annotation, running on 1 core and 1GB of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load miniforge
mamba activate maker_env

maker maker_opts.ctl \
      maker_bopts.ctl \
      maker_exe.ctl

Reference