Scientific Application – SOLAR

Overview

SOLAR is an extensive, flexible software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, SNP association analysis (QTN and QTLD), and covariate screening. Operations are included for calculation of marker-specific or multipoint identity-by-descent (IBD) matrices in pedigrees of arbitrary size and complexity, and for linkage analysis of multiple quantitative traits and/or discrete traits which may involve multiple loci (oligogenic analysis), dominance effects, household effects, and interactions.

Research Computing Server(s): Kure, KillDevil
Default Version: 4.3.1
Installed Version(s): 4.2.7, 4.3.1

Setting up your Environment and Invoking

SOLAR can be accessed through the Research Computing server KillDevil.

1. To invoke Solar you must be running an X windows session, you can do this by using the –X or –Y option on your ssh command line when you login to KillDevil.unc.edu

ssh –X onyen@KillDevil.unc.edu
ssh –Y onyen@KillDevil.unc.edu

Using the –X option is preferred, it offers a more secure connection, but not all systems support –X.

2. At the linux machine prompt, type the following module command. Skip this step if you have done it before.

module initadd solar

and to load Verdi just for your current session use

module add solar

The shell scripts in the home directory are then modified. The PATH to access SOLAR and all necessary environment variables are set up properly.

3. To check if your startup scripts have been setup for SOLAR, type the following command at the prompt.

module list

A line “solar” is shown which indicates the environment is set.

4. After the PATH and environment variables for SOLAR are set up properly, SOLAR can then be accessed. At the Linux machine prompt, type the following LSF command to invoke the software.

bsub –q day –Ip solar

where “-q day –Ip” specifies the interactive session through the “day” queue on KillDevil.

Links

  • For more information and up-to-date documentation, check out the SOLAR Home Page.

Additional Help

Research Computing home page