Purdue University

Commands

• augustify.py
• bamToWig.py
• cleanup-blastdb-volumes.py
• edirect.py
• executeTestCGP.py
• extractAnno.py
• findRepetitiveProtSeqs.py
• fix_in_frame_stop_codon_genes.py
• generate_plot.py
• getAnnoFastaFromJoingenes.py
• hist_plot.py
• pd_config.py
• run_abundance.py
• run_purge_dups.py
• run_sepp.py
• run_tipp.py
• run_tipp_tool.py
• run_upp.py
• split_sequences.py
• stringtie2fa.py
• sumlabels.py
• sumtrees.py

Module

You can load the modules by:

module load biocontainers
module load purge_dups

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 purge_dups on our clusters:

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

module --force purge
ml biocontainers purge_dups