Purdue University

Commands

• shorah
• b2w
• diri_sampler
• fil

Module

You can load the modules by:

module load biocontainers
module load shorah

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 Shorah on our clusters:

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

module --force purge
ml biocontainers shorah

shorah amplicon -b ampli_sorted.bam -f reference.fasta
shorah shotgun -b test_aln.cram -f test_ref.fasta
shorah shotgun -a 0.1 -w 42 -x 100000 -p 0.9 -c 0 -r REF:42-272 -R 42 -b test_aln.cram -f ref.fasta