PLINK

To use the plink module, add it to your environment. Use:

module spider plink

to see how to load the module and the needed prerequisites.

Example, loading Plink version 1.07

ml GCC/6.3.0-2.27
ml OpenMPI/2.0.2
ml PLINK/1.07

You can read more about loading modules on our Accessing software with Lmod page and our Using modules (Lmod) page.

Loading the module should set any needed environmental variables as well as the path. 

See http://zzz.bwh.harvard.edu/plink/ for more information about the usage of plink.

Make a job-script similar to this example:

#!/bin/bash
# Project to run under
#SBATCH -A SNICXXXX-YY-ZZ
# name of the error file
#SBATCH --error=my_plink_job_%J.err
# name of the output file
#SBATCH --output=my_plink_job_%J.out
# when to send email
#SBATCH --mail-type=ALL

# asking for 1 node, 8 processors 
#SBATCH -N 1
#SBATCH -n 8 
# the job may to use up to 30 minutes to run
#SBATCH -t 00:30:00

# Purge any loaded modules and then load the PLINK module and its prerequisites  
ml GCC/6.3.0-2.27 
ml OpenMPI/2.0.2 
ml PLINK/1.07

# run the job
plink <options>

Submit it with

sbatch <jobscript>

where <jobscript> is the name you give your batch-script.