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lecture_notes:04-28-2010 [2010/05/01 22:42]
galt
lecture_notes:04-28-2010 [2010/05/02 09:22] (current)
karplus added workaround for campusrocks filesystem problem
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 === Misc Notes: === === Misc Notes: ===
  
-**campusrocks is broken!**+**campusrocks is broken!** ​ The head node has the file system mounted as /​campusdata,​ but the client nodes have it mounted as /​campus. ​ The workaround is to use the trick in assemblies/​Pog/​map-colorspace5/​Makefile 
 +<​code>​ 
 +CWD ?= $(subst campusdata,​campus,​$(shell pwd)) 
 +</​code>​ 
 +Then instead of  
 +<​code>​ 
 +        qsub -cwd 
 +</​code>​ use  
 +<​code>​ 
 +        qsub -wd ${CWD} 
 +</​code>​ 
  
 //Pog// has 2 repeats: ~1k & 1.1k \\ //Pog// has 2 repeats: ~1k & 1.1k \\
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 Took about 50 minutes for all.\\ Took about 50 minutes for all.\\
-For comparison, Newbler took 18 minutes and about 40 contigs.+For comparison, Newbler took 18 minutes and 31 non-overlapping ​contigs.
  
-Just qsub them with no arguments, and it runs everything.\\+Just qsub them with no arguments, and it runs everything. ​("​Them"?​ "​it"?​ What does this sentence mean? FIXME  --- //​[[karplus@soe.ucsc.edu|Kevin Karplus]] 2010/05/02 09:14//)
  
  
lecture_notes/04-28-2010.1272778937.txt.gz · Last modified: 2010/05/01 22:42 by galt