Purdue University

Commands

• transvar

Module

You can load the modules by:

module load biocontainers
module load transvar

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 Transvar on our clusters:

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

module --force purge
ml biocontainers transvar

# set up databases
transvar config --download_anno --refversion hg19

# in case you don't have a reference
transvar config --download_ref --refversion hg19

transvar panno -i 'PIK3CA:p.E545K' --ucsc --ccds