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--- psyc_7102_statistical-genetics [2015/11/14 03:52] – /* Code Samples (Please add!) */ scott
+++ psyc_7102_statistical-genetics [2015/12/08 03:43] (current) – scott
@@ Line 3: / Line 3: @@
 [[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]]
@@ Line 15: / Line 32: @@
-====== Server management tools ======
+====== 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 &
@@ Line 29: / Line 56: @@
-   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.
-PBS batch queuing (used on vieques and research computing)
+====== PBS batch queuing (used on vieques and research computing) ======
  ### PBS batch system utilities
@@ Line 47: / Line 76: @@
  qdel all                    ### Kill all your PBS jobs