SOLAR is a package of software to perform several kinds of statistical genetic analysis, including linkage analysis, quantitative genetic analysis, and covariate screening. The name SOLAR stands for "Sequential Oligogenic Linkage Analysis Routines."
Solar was developed by researchers at the Southwest Foundation for Biomedical Research. Solar website.
New Solar users should send email to staff@hpc.nih.gov asking to be registered as a Solar user. The Solar package requires each user to be registered.
- Module Name: solar (see the modules page for more information)
- Singlethreaded
- Example files in /usr/local/apps/solar/examples
As of September 2021, users looking to take advantage of new GPU capabilities should load the solar/8.5.1b module and allocate a GPU node as necessary
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 ~]$ cp -r /usr/local/apps/solar/examples ./solar_examples [user@cn3144 ~]$ cd solar_examples [user@cn3144 ~]$ $ solar SOLAR Eclipse version 8.3.2 (General), last updated on October 31, 2016 Copyright (c) 1995-2016 Maryland Psychiatric Research Center Visit our website www.solar-eclipse-genetics.org For questions email: pkochunov@gmail.com Enter help for help, exit to exit, doc to browse documentation. solar> load pedigree plains_ped.txt Unloading current pedigree data ... Unloading current marker data ... Loading pedigree data from the file plains_ped.txt ... solar> verbosity min solar> load marker plainschr16_mrk.txt Getting initial estimates of allele freqs from the marker data ... Loading marker data from the file plainschr16_mrk.txt ... solar> load map plainschr16_map.txt solar> mibd prep loki Preparing input files for Loki multipoint IBD computation ... The following files have been created: lkmibd.data - pedigree/genotype data lkmibd.prep - prep parameter file lkmibd.loki - loki parameter file mibdchr16.loc - map file for SOLAR plots Move the file mibdchr16.loc to the directory where the Loki-computed IBDs will be stored. [...etc...] solar> quit [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Create a batch input file (e.g. solar.sh). For example:
#!/bin/bash set -e module load solar cp /usr/local/apps/solar/examples/* . solar << EOF load pedigree gaw10.ped load phenotypes phen trait Q4 covariate sex age age*sex polygenic quit EOF
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] solar.sh
1. First create different directories for each solar run. Put all the required input files under the created directories.
2. For each directory, create a script file which contains the solar commands as below:
-----------/data/$USER/solar/run1/script ---------- module load solar cd /data/$USER/solar/run1 solar << EOF load pedigree ped.txt load marker mrk.txt verbosity min freq mle load map map.txt ....... .... ... return "" quit EOF -------------------------------------------------
3. Now prepare the swarm command file with one line for each Solar run, e.g.
#------- cmdfile ------------- /data/$USER/solar/run1/script /data/$USER/solar/run2/script /data/$USER/solar/run3/script /data/$USER/solar/run4/script ..... .... /data/$USER/solar/runX/script #---- end of cmdfile ---------
Submit this swarm of Solar jobs with
swarm -f cmdfile --g #] --module solar
-f cmdfile | swarm command file |
-g # | # of Gigabytes of memory required for a single Solar run |