Hello, The easiest way to ensure that dependencies are set up correctly is to install tool dependencies directly from the Tool Shed: http://wiki.galaxyproject.org/DefiningRepositoryDependencies#Complex_reposit... You will want to use: http://toolshed.g2.bx.psu.edu/ "package_picard_1_56_0" For local instance help, please post to the galaxy-dev@bx.psu.edu mailing list, as that is the best way to reach the development community. I am going to double post this reply, to resolve the question on the original galaxy-user and to give it visibility on the galaxy-dev list, but going forward on this thread (if needed) please remove galaxy-user from future replies. Best! Jen Galaxy team On 8/31/13 11:19 AM, Nicolas Quizon wrote:

Dear Galaxy Gurus,

I am a student and still new to Galaxy. I am encountering an error when trying to run the Picard Paired Read Mate Fixer with default settings on Galaxy. The code only runs for a few seconds before failing and displaying the error message.

## exit code=1; stdout= [Mon Aug 19 16:46:15 EDT 2013] net.sf.picard.sam.FixMateInformation INPUT=[/usr/lib/galaxy-server/database/files/000/dataset_85.dat] OUTPUT=/usr/lib/galaxy-server/database/tmp/tmpxhbz3T SORT_ORDER=coordinate VALIDATION_STRINGENCY=LENIENT VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false [Mon Aug 19 16:46:15 EDT 2013] Executing as root@biolinux-pbcn6 on Linux 3.2.0-43-generic amd64; OpenJDK 64-Bit Server VM 1.6.0_27-b27; Picard version: 1.91() [Mon Aug 19 16:46:15 EDT 2013] net.sf.picard.sam.FixMateInformation done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=378470400 To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp Exception in thread "main" java.lang.NoClassDefFoundError: org/itadaki/bzip2/BZip2InputStream at net.sf.picard.sam.FixMateInformation.doWork(FixMateInformation.java:84) 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.FixMateInformation.main(FixMateInformation.java:76) Caused by: java.lang.ClassNotFoundException: org.itadaki.bzip2.BZip2InputStream 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

For input I am using data that I have successfully mapped with BWA for Illumina. I currently have Python version 2.7.3 and Java version 1.6.0_27, and an working on a machine running Ubuntu 12.04.2 LTS.

Any help is greatly appreciated!

Thanks!

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