Re: [svtoolkit-help] Java Library Path

[Bob H. <han...@br...>]

Hi, Eric,
I apologize for not responding sooner - the mailing list was messed up 
and I wasn't receiving these emails.
You need to have the bwa shared library on your library path (libbwa.so).
There's a suitable library in the bwa directory.
For example, in the scripts in the installtest directory, they have a 
line like this:

export LD_LIBRARY_PATH=${SV_DIR}/bwa:${LD_LIBRARY_PATH}

Running ComputeGenomeMask will only work on linux.

-Bob

On 3/28/11 6:34 PM, svt...@li... wrote:
> Subject:
> Java Library Path
> From:
> "Fritz, Eric R [AN S]" <er...@ia...>
> Date:
> Mon, 28 Mar 2011 17:32:48 -0500
>
> To:
> "svt...@li..." 
> <svt...@li...>
>
>
> Hello,
>
> I am getting the following error when trying to run the ComputeGenomeMask portion of the SVToolkit.
>
> INFO  17:32:10,456 HelpFormatter - ----------------------------------------------------------
> INFO  17:32:10,459 HelpFormatter - Program Name: org.broadinstitute.sv.apps.ComputeGenomeMask
> INFO  17:32:10,460 HelpFormatter - Program Args: -R Chr12.fa -O Chr12.mask.fa -readLength 83
> INFO  17:32:10,460 HelpFormatter - Date/Time: 2011/03/28 17:32:10
> INFO  17:32:10,460 HelpFormatter - ----------------------------------------------------------
> INFO  17:32:10,461 HelpFormatter - ----------------------------------------------------------
> INFO  17:32:10,525 GenomeMaskAlgorithm - Initializing bwa ...
> Exception in thread "main" java.lang.UnsatisfiedLinkError: no bwa in java.library.path
> 	at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1754)
> 	at java.lang.Runtime.loadLibrary0(Runtime.java:823)
> 	at java.lang.System.loadLibrary(System.java:1045)
> 	at org.broadinstitute.sting.alignment.bwa.c.BWACAligner.<clinit>(BWACAligner.java:21)
> 	at org.broadinstitute.sv.mask.GenomeMaskAlgorithm.getAligner(GenomeMaskAlgorithm.java:206)
> 	at org.broadinstitute.sv.mask.GenomeMaskAlgorithm.getAlignmentCode(GenomeMaskAlgorithm.java:119)
> 	at org.broadinstitute.sv.mask.GenomeMaskAlgorithm.generateMaskForSequence(GenomeMaskAlgorithm.java:93)
> 	at org.broadinstitute.sv.mask.GenomeMaskAlgorithm.generateMask(GenomeMaskAlgorithm.java:75)
> 	at org.broadinstitute.sv.apps.ComputeGenomeMask.run(ComputeGenomeMask.java:63)
> 	at org.broadinstitute.sv.commandline.CommandLineProgram.execute(CommandLineProgram.java:33)
> 	at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239)
> 	at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:23)
> 	at org.broadinstitute.sv.apps.ComputeGenomeMask.main(ComputeGenomeMask.java:49)
>
>
> If anyone could tell me how to solve this issue that would be great.
>
> -Eric
>
>
> Eric Fritz
> Assistant Scientist II
> Iowa State University
> 2255G Kildee Hall
> Ames, IA 50014