PSYC 7102: Statistical-Genetics

Homework

Homework 6: Ancestry

Homework 7: Functional Annotation

Final Exam

Final Exam

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