Re: [svtoolkit-help] no bwa in java.library.path

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

I think it's a fair question!
I currently don't support running any of the genome strip functions that 
require bwa (e.g. genome masking or alt allele alignments) on non-linux 
platforms.
You could try to build libbwa for macos and see if that works for you, 
but the binary in the distribution is a linux binary.
-Bob

On 11/22/11 12:01 PM, Mira Han wrote:
>
> Hi,
> I just asked this question at the GSA support website,
> but maybe it would be more appropriate for you.
> thanks in advance for your help.
> I'm trying to test my installation of svtoolkit using the test scripts 
> provided, but it fails and complains that it cannot find the bwa library.
> I am using Mac OS X Lion.
> I have the libbwa.so copied into /usr/lib/java/ as well as 
> /Library/Java/Extensions/.
> I have tried booting into both 64bit and 32bit mode and both failed.
> Would you have any clue why it's not finding the library?
> I know this question is not exactly about your software, but I'm 
> hoping maybe someone will have knowledge about this problem.
> thank you
>
> Miras-air:installtest mirahan$ java -Xmx1g 
> -Djava.io.tmpdir=/usr/local/src/svtoolkit/svtoolkit/installtest/tmpdir 
> -Djava.library.path=/usr/lib/java/ -cp 
> /usr/local/src/svtoolkit/svtoolkit/lib/SVToolkit.jar:/usr/local/src/svtoolkit/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/usr/local/src/svtoolkit/svtoolkit/lib/gatk/Queue.jar 
> org.broadinstitute.sting.gatk.CommandLineGATK -T SVAltAligner -R 
> /usr/local/src/svtoolkit/svtoolkit/installtest/data/human_b36_chr1.fasta 
> -I /usr/local/src/svtoolkit/svtoolkit/installtest/data/installtest.bam 
> -O 
> /usr/local/src/svtoolkit/svtoolkit/installtest/test2/altalign/installtest.alt.bam 
> -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference 
> test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true
> INFO 11:36:26,878 HelpFormatter - 
> --------------------------------------------------------------------------- 
>
> INFO 11:36:26,880 HelpFormatter - The Genome Analysis Toolkit (GATK) 
> v1.0.5039M, Compiled 2011/01/20 22:58:34
> INFO 11:36:26,880 HelpFormatter - Copyright (c) 2010 The Broad Institute
> INFO 11:36:26,880 HelpFormatter - Please view our documentation 
> athttp://www.broadinstitute.org/gsa/wiki
> INFO 11:36:26,881 HelpFormatter - For support, please view our support 
> site athttp://getsatisfaction.com/gsa
> INFO 11:36:26,881 HelpFormatter - Program Args: -T SVAltAligner -R 
> /usr/local/src/svtoolkit/svtoolkit/installtest/data/human_b36_chr1.fasta 
> -I /usr/local/src/svtoolkit/svtoolkit/installtest/data/installtest.bam 
> -O 
> /usr/local/src/svtoolkit/svtoolkit/installtest/test2/altalign/installtest.alt.bam 
> -md test2/metadata -U ALLOW_UNINDEXED_BAM -altReference 
> test2/altalign/installtest.sites.alt.fasta -alignUnmappedMates true
> INFO 11:36:26,881 HelpFormatter - Date/Time: 2011/11/22 11:36:26
> INFO 11:36:26,881 HelpFormatter - 
> --------------------------------------------------------------------------- 
>
> INFO 11:36:26,881 HelpFormatter - 
> --------------------------------------------------------------------------- 
>
> INFO 11:36:26,885 GenomeAnalysisEngine - Strictness is SILENT
> Exception in thread "main" java.lang.UnsatisfiedLinkError: no bwa in 
> java.library.path
> at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1758)
> at java.lang.Runtime.loadLibrary0(Runtime.java:823)
> at java.lang.System.loadLibrary(System.java:1045)
> at 
> org.broadinstitute.sting.alignment.bwa.c.BWACAligner.(BWACAligner.java:21) 
>
> at 
> org.broadinstitute.sv.breakpoint.BreakpointAligner.initialize(BreakpointAligner.java:46) 
>
> at 
> org.broadinstitute.sv.breakpoint.SVAltAlignerWalker.initialize(SVAltAlignerWalker.java:86) 
>
> at 
> org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:49) 
>
> at 
> org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217) 
>
> at 
> org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111) 
>
> at 
> org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239) 
>
> at 
> org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:87) 
>
> Miras-air:installtest mirahan$ ls /usr/lib/java/
> libbwa.so libjdns_sd.jnilib
> Miras-air:installtest mirahan$ ls /Library/Java/Extensions/
> libbwa.so
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure
> contains a definitive record of customers, application performance,
> security threats, fraudulent activity, and more. Splunk takes this
> data and makes sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-novd2d
>
>
> _______________________________________________
> svtoolkit-help mailing list
> svt...@li...
> https://lists.sourceforge.net/lists/listinfo/svtoolkit-help