Purdue University

Commands

• create_dbs.py
• download_eggnog_data.py
• emapper.py
• hmm_mapper.py
• hmm_server.py
• hmm_worker.py
• vba_extract.py

Module

You can load the modules by:

module load biocontainers
module load eggnog-mapper

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 Eggnog-mapper on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=eggnog-mapper
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers eggnog-mapper

emapper.py -i proteins.faa --cpu 24 -o protein.out
emapper.py -m diamond --itype CDS -i cDNA.fasta -o cdna.out --cpu 24