Difference between revisions of "PSYC 7102: Statistical-Genetics"
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= Homework = | = Homework = | ||
[[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] | ||
| + | |||
| + | == 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!) = | = Code Samples (Please add!) = | ||
| − | + | == Server and file management tools == | |
<syntaxhighlight lang="bash"> | <syntaxhighlight lang="bash"> | ||
| − | df -h | + | df -h ### Show space availability in all directories |
| − | df -h /directory | + | df -h /directory ### Show disk space in /directory |
| − | top | + | top ### Show resource utilization and job status, etc. |
| − | htop | + | 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 & | ||
</syntaxhighlight> | </syntaxhighlight> | ||
| − | + | == Logging into vieques from home without using VPN == | |
| − | Logging into vieques from home without using VPN | ||
<syntaxhighlight lang="bash"> | <syntaxhighlight lang="bash"> | ||
| − | ssh <uniquename>@statgen.colorado.edu ### | + | 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. | ssh <uniquename>@vieques.colorado.edu ### Once on statgen, then log into vieques from statgen. | ||
</syntaxhighlight> | </syntaxhighlight> | ||
| − | + | == PBS batch queuing (used on vieques and research computing) == | |
| − | PBS batch queuing (used on vieques and research computing) | ||
<syntaxhighlight lang="bash"> | <syntaxhighlight lang="bash"> | ||
### PBS batch system utilities | ### PBS batch system utilities | ||
| Line 34: | Line 54: | ||
### Having 22 or 23 CPUs is helpful when you're running per-chromosome jobs. | ### 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 | qsub -I -q short -l walltime=23:00:00 -l nodes=1:ppn=22 | ||
| + | |||
qdel <job number> ### Kill a PBS job | qdel <job number> ### Kill a PBS job | ||
qdel all ### Kill all your PBS jobs | qdel all ### Kill all your PBS jobs | ||
</syntaxhighlight> | </syntaxhighlight> | ||
Latest revision as of 03:43, 8 December 2015
Homework
Homework 7: Functional Annotation
Final Exam
Command Line and Other Coding Resources
Command Line
Regular Expressions (Regex)
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