Hi all,
    I am setting up our own galaxy instance here (or trying to).  We'd like to use fastqc, but I have run into a problem implementing it.  Any suggestions would be most welcome, as to what might be wrong.

1. fastqc runs fine outside of galaxy.  But when I try the same file inside galaxy, I get errors.

2. I can look to the shell script generated by galaxy inside ~/galaxy-dist/database/pbs/ .  When I run that python command inside the sh script, generated by galaxy, to execute fastqc -- it works fine, without errors.

Therefore, it seems as if there is some sort of permission or path problem when galaxy runs fastqc.  I have fastqc in the main path, and also installed it in the "jars" directory where the fastqc tool looks for it.  However, I still can't understand this, since when outside of galaxy, I can run the python command generated by galaxy successfully.


 The output/error inside galaxy is here:
Exception in thread "main" java.lang.NoClassDefFoundError: uk.ac.bbsrc.babraham.FastQC.Sequence.FastQFile
   at java.lang.Class.initializeClass(libgcj.so.7rh)
   at uk.ac.bbsrc.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:83)
   at uk.ac.bbsrc.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:113)
   at uk.ac.bbsrc.babraham.FastQC.Analysis.OfflineRunner.(OfflineRunner.java:84)
   at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:308)
Caused by: java.lang.ClassFormatError: org.itadaki.bzip2.BZip2InputStream (unrecognized class file version)
   at java.lang.VMClassLoader.defineClass(libgcj.so.7rh)
   at java.lang.ClassLoader.defineClass(libgcj.so.7rh)
   at java.security.SecureClassLoader.defineClass(libgcj.so.7rh)
   at java.net.URLClassLoader.findClass(libgcj.so.7rh)
   at java.lang.ClassLoader.loadClass(libgcj.so.7rh)
   at java.lang.ClassLoader.loadClass(libgcj.so.7rh)
   at java.lang.Class.forName(libgcj.so.7rh)
   at java.lang.Class.initializeClass(libgcj.so.7rh)
   ...4 more



Any clues/advice most appreciated!

Todd 
-- 
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Todd Oakley, Professor
Ecology Evolution and Marine Biology
University of California, Santa Barbara
Santa Barbara, CA 93106 USA

NEWLY UPDATED LAB WEBSITE: http://labs.eemb.ucsb.edu/oakley/todd/
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