Hi all, I am setting up our own galaxy instance here. 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