Solar on Biowulf

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 should be run interactively on the Biowulf interactive nodes. If you have multiple Solar jobs to run, the swarm utility is recommended. Below are sample sessions for three submission methods. Please see User Documentation for more information about calculations of genetic variance analysis.

Swarm Sample Session:

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, 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

Interactive Sample Session (user input is in bold):

<biowulf>% qsub -I -l nodes=1

qsub: waiting for job 593807.biobose to start
qsub: job 593807.biobose ready

<p2>% cd mydir

<p2>% solar

Copyright (c) 1995-2006 Southwest Foundation for Biomedical Research
Enter help for help, exit to exit, doc to browse documentation.

solar> example
Loading pedigree data from the file example.ped ...
Getting initial estimates of allele freqs from the marker data ...
Loading marker data from the file example.mrk ...
Running allfreq for marker D6S477 ... iter  20  delta loglike =     1.1031 
Running allfreq for marker D6S1006 ... iter  20  delta loglike =     3.9962 
Running allfreq for marker D6S1019 ... iter  26  delta loglike =     4.0122 
Running allfreq for marker D6S1018 ... iter  22  delta loglike =     1.2878 
[...]
solar> quit

<p2>% exit
qsub: job 593807.biobose completed

<biowulf>%

Submit A Single Solar Batch Job(s):

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

This document is available as http://biowulf.nih.gov/apps/solar.html
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