Annogesic

Introduction

ANNOgesic is the swiss army knife for RNA-Seq based annotation of bacterial/archaeal genomes.

For more information, please check:

Docker hub: https://hub.docker.com/r/silasysh/annogesic

Home page: https://github.com/Sung-Huan/ANNOgesic

Versions

• 1.1.0

Commands

• annogesic

Module

You can load the modules by:

module load biocontainers
module load annogesic

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 annogesic on our clusters:

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

module --force purge
ml biocontainers annogesic

ANNOGESIC_FOLDER=ANNOgesic
annogesic \
    update_genome_fasta \
    -c $ANNOGESIC_FOLDER/input/references/fasta_files/NC_009839.1.fa \
    -m $ANNOGESIC_FOLDER/input/mutation_tables/mutation.csv \
    -u NC_test.1 \
    -pj $ANNOGESIC_FOLDER