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.

Version 4.1.0 is currently installed on Biowulf.

New Solar users should send email to staff@helix.nih.gov asking to be registered as a Solar user. The Solar package requires each user to be registered.

Solar is not a parallel program. Single Solar jobs are most easily run interactively on Helix. It is useful to run on Biowulf only if you have multiple simultaneous Solar jobs to run.

The swarm program is a convenient way to submit large numbers of jobs all at once instead of manually submitting them one by one.

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 ----------
cd /data/user/solar/run1;/usr/local/bin/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 ---------

4. Now submit the Swarm job

biowulf% swarm -f cmdfile

1. Create a script file which contains the solar commands as below:

---------- /data/user/solar/run1/script --------------
#!/bin/csh -v
#PBS -N solar1
#PBS -m be
#PBS -k oe
cd /data/user/solar/run1;/usr/local/bin/solar <<EOF
load pedigree ped.txt
load marker mrk.txt
verbosity min
freq mle
load map map.txt
.......
....
analyzing commands
...
return ""
quit
EOF
----------------- end of script ----------------------

2. Now submit the script using the 'qsub' command, e.g.

qsub -l nodes=1 /data/user/solar/run1/script