using snappy java in picard tools

doc.ramses · 09-13-2011, 09:59 AM

Hey,

I have a problem using picard-tools on large files. It tells me that I don't have snappyjava in java.library.
I'm not so familiar with java. Can anyone please point me on how to fix this.
I've already come across this:

http://sourceforge.net/apps/mediawik...appy_in_Picard

documentation, but don't really get.
I'm on a mac os x 10.6.8

Thank you for your help!

nilshomer · 09-13-2011, 06:29 PM

A quick fix is to run "java -Dsnappy.disable=true -jar ...", which will disable snappy, making Picard slower. But at least you don't have to run around trying to get snappy installed correctly!

doc.ramses · 10-04-2011, 03:34 AM

Thanks for the quick fix, that works for me. Although really slow

Graham Etherington · 10-04-2011, 08:17 AM

Snappy comes distributed with the most recent versions of picard-tools (v1.53 - http://sourceforge.net/projects/picard/files/)
It's in the top-level directory by itself. The remaining picard jar files are in a sub-directory.

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09-13-2011, 09:59 AM	#1
doc.ramses Member Location: Planet Earth Join Date: Jan 2011 Posts: 26	using snappy java in picard tools Hey, I have a problem using picard-tools on large files. It tells me that I don't have snappyjava in java.library. I'm not so familiar with java. Can anyone please point me on how to fix this. I've already come across this: http://sourceforge.net/apps/mediawik...appy_in_Picard documentation, but don't really get. I'm on a mac os x 10.6.8 Thank you for your help!

09-13-2011, 06:29 PM	#2
nilshomer Nils Homer Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,285	A quick fix is to run "java -Dsnappy.disable=true -jar ...", which will disable snappy, making Picard slower. But at least you don't have to run around trying to get snappy installed correctly!

10-04-2011, 03:34 AM	#3
doc.ramses Member Location: Planet Earth Join Date: Jan 2011 Posts: 26	Thanks for the quick fix, that works for me. Although really slow

10-04-2011, 08:17 AM	#4
Graham Etherington Member Location: Norwich, England. Join Date: Apr 2010 Posts: 22	Snappy comes distributed with the most recent versions of picard-tools (v1.53 - http://sourceforge.net/projects/picard/files/) It's in the top-level directory by itself. The remaining picard jar files are in a sub-directory.