annogesic
Link to section 'Introduction' of 'annogesic' Introduction
ANNOgesic is the swiss army knife for RNA-Seq based annotation of bacterial/archaeal genomes.
Docker hub: https://hub.docker.com/r/silasysh/annogesic
Home page: https://github.com/Sung-Huan/ANNOgesic
Link to section 'Versions' of 'annogesic' Versions
- 1.1.0
Link to section 'Commands' of 'annogesic' Commands
- annogesic
Link to section 'Module' of 'annogesic' Module
You can load the modules by:
module load biocontainers
module load annogesic
Link to section 'Example job' of 'annogesic' Example job
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