Purdue University

Commands

• clone_filter
• count_fixed_catalog_snps.py
• cstacks
• denovo_map.pl
• gstacks
• integrate_alignments.py
• kmer_filter
• phasedstacks
• populations
• process_radtags
• process_shortreads
• ref_map.pl
• sstacks
• stacks-dist-extract
• stacks-gdb
• stacks-integrate-alignments
• tsv2bam
• ustacks

Module

You can load the modules by:

module load biocontainers
module load stacks

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 Stacks on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=stacks
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers stacks

denovo_map.pl -T 8 -M 4 -o ./stacks/  \
    --samples ./samples --popmap ./popmaps/popmap