Purdue University

Commands

• run_sepp.py
• run_upp.py
• split_sequences.py
• sumlabels.py
• sumtrees.py

Module

You can load the modules by:

module load biocontainers
module load sepp

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 Sepp on our clusters:

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

module --force purge
ml biocontainers sepp

run_sepp.py -t mock/rpsS/sate.tre \
    -r mock/rpsS/sate.tre.RAxML_info \
    -a mock/rpsS/sate.fasta \
    -f mock/rpsS/rpsS.even.fas \
    -o rpsS.out.default