Purdue University

Commands

• Rscript
• snphylo.sh
• convert_fasta_to_phylip.py
• convert_simple_to_hapmap.py
• determine_bs_tree.R
• draw_unrooted_tree.R
• generate_snp_sequence.R
• remove_low_depth_genotype_data.py
• remove_no_genotype_data.py

Module

You can load the modules by:

module load biocontainers
module load snphylo

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 snphylo on our clusters:

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

module --force purge
ml biocontainers snphylo