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Re: snappy uploaded and picard-tools can be build against it



Le Tue, Aug 28, 2012 at 12:49:59PM +0200, olivier.sallou@codeless.fr a écrit :
> Hi,
> I have uploaded libsnappy1.0.3-java  package for picard-tools.
> I could successfully build picard-tools with this package.
> 
> picard-tools still need to be updated to get latest release and use
> snappy1.0.3-java.jar file (update of the patch)

Hi Olivier,

many thanks for all of this.

I built and installed libsnappy1.0.3-java.  It will need to conflict with
libsnappy-java, or the maven information will need to be renamed:

  Selecting previously unselected package libsnappy1.0.3-java.
  (Reading database ... 312719 files and directories currently installed.)
  Unpacking libsnappy1.0.3-java (from libsnappy1.0.3-java_1.0.3-rc3~dfsg-1_all.deb) ...
  dpkg: error processing libsnappy1.0.3-java_1.0.3-rc3~dfsg-1_all.deb (--install):
   trying to overwrite '/usr/share/maven-repo/org/xerial/snappy/snappy-java/debian/snappy-java-debian.pom', which is also in package libsnappy-java 1.0.4.1~dfsg-1
  Errors were encountered while processing:
   libsnappy1.0.3-java_1.0.3-rc3~dfsg-1_all.deb

On the source pakcage side, can you push the pristine-tar branch that contain
the version 1.0.3-rc3~dfsg ?

I then build and installed picard tools, but all the command I try to run fail
with an errror like the following.

 $ picard-tools EstimateLibraryComplexity I=testdata/net/sf/samtools/compressed.bam O=/dev/stdout
[Wed Aug 29 14:06:35 JST 2012] net.sf.picard.sam.EstimateLibraryComplexity INPUT=[testdata/net/sf/samtools/compressed.bam] OUTPUT=/dev/stdout    MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
[Wed Aug 29 14:06:35 JST 2012] Executing as charles@anx191 on Linux 3.2.0-2-amd64 amd64; OpenJDK 64-Bit Server VM 1.6.0_24-b24; Picard version: 1.75(exported)
[Wed Aug 29 14:06:35 JST 2012] net.sf.picard.sam.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=189071360
FAQ:  http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page
Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/tools/bzip2/CBZip2OutputStream
	at net.sf.picard.sam.EstimateLibraryComplexity.doWork(EstimateLibraryComplexity.java:217)
	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
	at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119)
	at net.sf.picard.sam.EstimateLibraryComplexity.main(EstimateLibraryComplexity.java:208)
Caused by: java.lang.ClassNotFoundException: org.apache.tools.bzip2.CBZip2OutputStream
	at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
	... 4 more

Installing libjbzip2-java did not solve the problem.  Do you have an idea ?

Have a nice day,

-- 
Charles Plessy
Tsurumi, Kanagawa, Japan


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