PSYC 7102: Statistical-Genetics

Homework

Homework 6: Ancestry

Command Line and Other Coding Resources

Command Line

Code Academy

Coursera

Regular Expressions (Regex)

Regex Cheat Sheet

Regex Tutorial

Code Samples (Please add!)

Server and file management tools

 df -h               ### Show space availability in all directories
 df -h /directory    ### Show disk space in /directory
 
 top            ### Show resource utilization and job status, etc.
 htop           ### Souped-up "top"
 
 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 'nohup' and append it 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 '#' myvcf.vcf.gz | bgzip -c > newVcfMinusHeader.vcf.gz &

Logging into vieques from home without using VPN

 ssh <uniquename>@statgen.colorado.edu  ### Log into statgen a server at IBG (ask Jeff Lessem
                                        ###     for an account if you don't already have one).
 ssh <uniquename>@vieques.colorado.edu  ### Once on statgen, then log into vieques from statgen.

PBS batch queuing (used on vieques and research computing)

 ### PBS batch system utilities
 qstat                  ### On PBS batch system shows status of submitted jobs
 watch qstat        ### Refreshes "qstat" every second.
 
 ### Submit interactive pbs job in the short queue for 23 hours on 1 node with 22 CPUs
 ###   Having 22 or 23 CPUs is helpful when you're running per-chromosome jobs.
 qsub -I -q short -l walltime=23:00:00 -l nodes=1:ppn=22
 
 qdel <job number>  ### Kill a PBS job
 qdel all                    ### Kill all your PBS jobs