Purdue University

Commands

• gseapy
• python
• python3

Module

You can load the modules by:

module load biocontainers
module load gseapy

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 Gseapy on our clusters:

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

module --force purge
ml biocontainers gseapy

gseapy ssgsea -d ./data/testSet_rand1200.gct \
            -g data/temp.gmt \
            -o test/ssgsea_report2  \
            -p 4 --no-plot --no-scale
gseapy replot -i data -o test/replot_test