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psyc_7102_statistical-genetics [2015/11/13 20:55]
scott /* Server and file management tools */ 		psyc_7102_statistical-genetics [2015/12/02 11:51]
scott /* Homework */
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 [[homework_6_ancestry]] [[homework_6_ancestry]]
 +
 +[[homework_7_functional_annotation]]
  
  
 ======= 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]]
 +
 +
 +====== 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]]
  
  
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-   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. 
 +   htop           ### Souped-up "top"
        
-   top                ### Show resource utilization and job status, etc. +   ls -lhrt       ### list the contents of a directory sorted from oldest to newest
-   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 &
        
  
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-   ssh <uniquename>@statgen.colorado.edu  ### log into statgen a server at IBG (ask Jeff +   ssh <uniquename>@statgen.colorado.edu  ### Log into statgen a server at IBG (ask Jeff Lessem 
-                                                                      ###   Lessem for an account if you don't already have one).+                                          ###     for an account if you don't already have one).
    ssh <uniquename>@vieques.colorado.edu  ### Once on statgen, then log into vieques from statgen.    ssh <uniquename>@vieques.colorado.edu  ### Once on statgen, then log into vieques from statgen.
        
psyc_7102_statistical-genetics.txt · Last modified: 2015/12/07 20:43 by scott

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