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Solar on BiowulfSOLAR 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):
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 |
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This document is available as http://biowulf.nih.gov/apps/solar.html |
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