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psyc_7102_statistical-genetics [2015/11/13 13:48] scott |
psyc_7102_statistical-genetics [2015/12/07 20:43] (current) scott |
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- | Here are some useful | + | |
+ | ======= Homework ======= | ||
+ | |||
+ | [[homework_6_ancestry]] | ||
+ | |||
+ | [[homework_7_functional_annotation]] | ||
+ | |||
+ | |||
+ | ======= Final Exam ======= | ||
+ | |||
+ | [[final_exam]] | ||
+ | |||
+ | |||
+ | ======= Command Line and Other Coding Resources ======= | ||
+ | |||
+ | |||
+ | ====== Command Line ====== | ||
+ | |||
+ | [[https:// | ||
+ | |||
+ | [[https:// | ||
+ | |||
+ | |||
+ | ====== Regular Expressions (Regex) ====== | ||
+ | |||
+ | [[http:// | ||
+ | |||
+ | [[http:// | ||
+ | |||
+ | |||
+ | ======= Code Samples (Please add!) ======= | ||
+ | |||
+ | |||
+ | ====== Server and file management tools ====== | ||
+ | |||
+ | |||
+ | df -h ### Show space availability in all directories | ||
+ | df -h / | ||
+ | |||
+ | | ||
+ | | ||
+ | |||
+ | ls -lhrt ### list the contents of a directory sorted from oldest to newest | ||
+ | |||
+ | ### Is your command taking a very long time and you can't keep your computer open for hours? | ||
+ | ### Just prepend your command with ' | ||
+ | ### This will prevent the system from killing your job when your computer disconnects from | ||
+ | ### the server. | ||
+ | ### | ||
+ | nohup plink --vcf myvcf.vcf.gz --maf .05 & # Run plink | ||
+ | nohup zgrep -v '#' | ||
+ | |||
+ | |||
+ | |||
+ | ====== Logging into vieques from home without using VPN ====== | ||
+ | |||
+ | |||
+ | ssh < | ||
+ | ### for an account if you don't already have one). | ||
+ | ssh < | ||
+ | |||
+ | |||
+ | |||
+ | ====== PBS batch queuing (used on vieques and research computing) ====== | ||
- | df -h ### Show space availability in all directories | ||
- | df -h / | ||
- | ### | ||
- | | ||
- | | ||
- | ### | ||
### PBS batch system utilities | ### PBS batch system utilities | ||
- | | + | |
watch qstat ### Refreshes " | watch qstat ### Refreshes " | ||
+ | |||
+ | ### Submit interactive pbs job in the short queue for 23 hours on 1 node with 22 CPUs | ||
+ | ### | ||
+ | qsub -I -q short -l walltime=23: | ||
+ | |||
+ | qdel <job number> | ||
+ | qdel all ### Kill all your PBS jobs | ||