PRSice (pronounced 'precise') is a Polygenic Risk Score software for calculating, applying, evaluating and plotting the results of polygenic risk scores (PRS) analyses.

References:

• PRSice: Polygenic Risk Score software, Euesden, Lewis, O'Reilly, Bioinformatics (2015) 31 (9):1466-1468. doi: 10.1093/bioinformatics/btu848

• PRSice Main Site
• User Support Group

• Module Name: prsice (see the modules page for more information)
• Environment variables set
  • PRSICE_HOME

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job
[user@cn3144 ~]$ cd /data/$USER
[user@cn3144 ~]$ mkdir TEST
[user@cn3144 ~]$ cd TEST
[user@cn3144 ~] cp /usr/local/apps/prsice/TEST_DATA/* .
[user@cn3144 ~]$ module load prsice
[user@cn3144 ~]$ PRSice.R \
    --prsice $(which PRSice) \
    --base TOY_BASE_GWAS.assoc \
    --target TOY_TARGET_DATA \
    --thread 1 \
    --stat OR \
    --binary-target T
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. prsice.sh). For example:

#!/bin/sh
set -e
module load prsice

test -n "$SLURM_CPUS_PER_TASK" || SLURM_CPUS_PER_TASK=1
PRSice.R \
 --prsice $(which PRSice) \
 --base TOY_BASE_GWAS.assoc \
 --target TOY_TARGET_DATA \
 --thread $SLURM_CPUS_PER_TASK \
 --stat OR
 --binary-target T

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] prsice.sh

Create a swarmfile (e.g. prsice.swarm). For example:

PRSice.R \
 --prsice $(which PRSice) \
 --base TOY_BASE_GWAS.assoc \
 --target TARGET_DATA_1 \
 --thread $SLURM_CPUS_PER_TASK \
 --stat OR
 --binary-target T
PRSice.R \
 --prsice $(which PRSice) \
 --base TOY_BASE_GWAS.assoc \
 --target TARGET_DATA_2 \
 --thread $SLURM_CPUS_PER_TASK \
 --stat OR
 --binary-target T
PRSice.R \
 --prsice $(which PRSice) \
 --base TOY_BASE_GWAS.assoc \
 --target TARGET_DATA_3 \
 --thread $SLURM_CPUS_PER_TASK \
 --stat OR
 --binary-target T

Submit this job using the swarm command.

swarm -f prsice.swarm [-g #] -t # --module prsice