IBG Wiki

User Tools

Site Tools

Trace:
psyc_7102_statistical-genetics

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision 		Previous revision
Last revision Both sides next revision
psyc_7102_statistical-genetics [2015/11/13 13:52]
scott 		psyc_7102_statistical-genetics [2015/12/02 11:51]
scott /* Homework */
Line 1: Line 1:
-Here are some useful server management tools+ 
 +======= Homework ======= 
 + 
 +[[homework_6_ancestry]] 
 + 
 +[[homework_7_functional_annotation]] 
 + 
 + 
 +======= 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               ### 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.txt · Last modified: 2015/12/07 20:43 by scott

Page Tools

Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial-Share Alike 4.0 International
CC Attribution-Noncommercial-Share Alike 4.0 International Donate Powered by PHP Valid HTML5 Valid CSS Driven by DokuWiki