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psyc_7102_statistical-genetics [2015/11/14 00:43] – scottpsyc_7102_statistical-genetics [2015/12/08 03:43] (current) – scott
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 [[homework_6_ancestry]] [[homework_6_ancestry]]
 +
 +[[homework_7_functional_annotation]]
 +
 +
 +======= Final Exam =======
 +
 +[[final_exam]]
  
  
 ======= Command Line and Other Coding Resources ======= ======= Command Line and Other Coding Resources =======
 +
 +
 +====== Command Line ======
  
 [[https://www.codecademy.com/learn/learn-the-command-line|Code Academy]] [[https://www.codecademy.com/learn/learn-the-command-line|Code Academy]]
 +
 [[https://www.coursera.org/course/gencommand|Coursera]] [[https://www.coursera.org/course/gencommand|Coursera]]
  
  
-======= Code Samples (students please add) =======+====== 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 ======
  
-Here are some useful server management tools 
      
-   df -h              ### Show space availability in all directories +   df -h               ### Show space availability in all directories 
-   df -h /directory   ### Show disk space in /directory+   df -h /directory    ### Show disk space in /directory
        
-   top                ### Show resource utilization and job status, etc. +   top            ### Show resource utilization and job status, etc. 
-   htop               ### Souped up "top"+   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 &
        
  
-PBS batch queuing (used on vieques and research computing)+ 
 +====== 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  ### PBS batch system utilities
- qstat              ### On PBS batch system shows status of submitted jobs+ qstat                  ### On PBS batch system shows status of submitted jobs
  watch qstat        ### Refreshes "qstat" every second.  watch qstat        ### Refreshes "qstat" every second.
    
- ### submit interactive pbs job in the short queue for 23 hours on 1 node with 20 CPUs + ### Submit interactive pbs job in the short queue for 23 hours on 1 node with 22 CPUs 
- qsub -I -q short -l walltime=23:00:00 -l nodes=1:ppn=20 + ###   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
    
- 
psyc_7102_statistical-genetics.1447461809.txt.gz · Last modified: by scott