Biowulf High Performance Computing at the NIH
OSCA on Biowulf

OSCA (OmicS-data-based Complex trait Analysis) is a software tool written in C/C++ for the analysis of complex traits using multi-omics data.

Functions currently supported are:

Note: Although this software tool is designed for gene expression and DNA methylation data, it can be applied to any other source of omics data including microbiome, proteome and brain connectome.

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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 ~]$ module load osca

[user@cn3144 ~]$ cp $OSCA_EXAMPLES/* .
[user@cn3144 ~]$ osca --efile test.txt --make-bod --out test --methylation-beta

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

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

#!/bin/bash
module load osca
osca --reml --orm myorm --pheno my.phen --reml-pred-rand --out myblp

Submit this job using the Slurm sbatch command.

sbatch osca.sh