Commit Graph

5 Commits (187b464ded542582a2749bf3947df7ea9f022b50)

Author SHA1 Message Date
chartl 80a5ddfa2f Memory string added
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3771 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-12 20:43:19 +00:00
chartl 2e4377b1cf Awesome: JobDispatcher can now dispatch jobs by gene from a target .design file found in /seq/references.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3170 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-14 18:17:41 +00:00
chartl fab31e1d53 Check in so I don't lose this code -- spawning of jobs by genes
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3137 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 16:18:40 +00:00
chartl 687fd477ff Just some code I want to freeze. If you ever need to estimate the % of bases covered by exon, given an interval list, give it to getTargetedGenes. Not the best name for this function, but I don't expect anyone to use it but me.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3111 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 20:21:50 +00:00
chartl ac9c335cd2 This is a python job dispatcher I've been using, which builds on Mark's FarmJob utility, and an example script of how I'm using it. Basically I wrote it to smartly break up analysis over an interval list, givin a maximum number of bases per job, a list of available queues, and a limit on each queue. It handles going over these limits in three ways:
1) [default]: Fail
  - No jobs are actually spawned

2) Space
  - User provides a string of the form A:B:C where A is the number of days to wait before scheduling jobs over
    the queue limits; B the number of hours, C the number of minutes. Exceeding the queue limits again will
    increment the space by another A:B:C

3) Stop-Resume
 - Spawns the maximum number of jobs, and writes a file describing the next job, and a hash code of the remaining jobs.
   The next time the script is run, it spawns the next set of jobs starting with what's written in the file. If the 
   hash code (and thus the command string) changes between runs, the dispatcher fails-fast.

The base job dispatcher class is also capable of dealing with dependencies if it is used correctly.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3102 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-31 19:53:13 +00:00