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psyc_7102_statistical-genetics [2015/11/13 17:43] scott |
psyc_7102_statistical-genetics [2015/12/02 11:51] scott /* Homework */ |
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[[homework_6_ancestry]] | [[homework_6_ancestry]] | ||
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+ | [[homework_7_functional_annotation]] | ||
======= Command Line and Other Coding Resources ======= | ======= Command Line and Other Coding Resources ======= | ||
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+ | |||
+ | ====== Command Line ====== | ||
[[https:// | [[https:// | ||
+ | |||
[[https:// | [[https:// | ||
- | ======= Code Samples (students please | + | ====== Regular Expressions (Regex) ====== |
+ | |||
+ | [[http:// | ||
+ | |||
+ | [[http:// | ||
+ | |||
+ | |||
+ | ======= Code Samples (Please | ||
+ | |||
+ | |||
+ | ====== Server and file management tools ====== | ||
- | Here are some useful server management tools | ||
| | ||
- | df -h ### Show space availability in all directories | + | df -h |
- | df -h / | + | 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. | ||
+ | ### Here are a few toy examples | ||
+ | nohup plink --vcf myvcf.vcf.gz --maf .05 & # Run plink | ||
+ | nohup zgrep -v '#' | ||
- | PBS batch queuing (used on vieques and research computing) | + | |
+ | ====== Logging into vieques from home without using VPN ====== | ||
+ | |||
+ | |||
+ | ssh < | ||
+ | ### for an account if you don't already have one). | ||
+ | ssh < | ||
+ | |||
+ | |||
+ | |||
+ | ====== | ||
### PBS batch system utilities | ### PBS batch system utilities | ||
- | | + | |
watch qstat ### Refreshes " | watch qstat ### Refreshes " | ||
- | ### | + | ### |
- | qsub -I -q short -l walltime=23: | + | ### |
+ | qsub -I -q short -l walltime=23: | ||
+ | |||
+ | qdel <job number> | ||
+ | qdel all ### Kill all your PBS jobs | ||
- |