Cegma

Introduction

CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virtually any eukaryotic genome.

For more information, please check:

Docker hub: https://hub.docker.com/r/chrishah/cegma

Home page: https://github.com/KorfLab/CEGMA_v2

Versions

• 2.5

Commands

• cegma

Module

You can load the modules by:

module load biocontainers
module load cegma

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 cegma on our clusters:

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

module --force purge
ml biocontainers cegma

cegma --genome genome.fasta -o output