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======= Homework =======

[[homework_6_ancestry]]

[[homework_7_functional_annotation]]


======= Final Exam =======

[[final_exam]]


======= Command Line and Other Coding Resources =======


====== Command Line ======

[[https://www.codecademy.com/learn/learn-the-command-line|Code Academy]]

[[https://www.coursera.org/course/gencommand|Coursera]]


====== Regular Expressions (Regex) ======

[[http://networking.ringofsaturn.com/Web/regular-expressions-cheat-sheet-v2.pdf|Regex Cheat Sheet]]

[[http://www.zytrax.com/tech/web/regex.htm|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
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