Hi, Todd. The error message: > Exception in thread "main" java.lang.NoClassDefFoundError: > uk.ac.bbsrc.babraham.FastQC.Sequence.FastQFile makes me guess that the fastqc perl script is not being executed from the root of a complete FastQC distribution directory substructure by the Galaxy tool wrapper.
The FastQC Galaxy tool has very specific installation requirements - a system install won't work - even though FastQC works from the command line. The FastQC java applications use a perl wrapper to set up the classpaths, and it expects to be executed from inside the root of the complex FastQC distribution folder structure. Having a system wide installation will allow the various phenomena you describe, but won't work when the Galaxy tool tries to run, because the tool expects to find the entire FastQC distribution layout in the [galaxy root]/tool-data/shared/jars/FastQC directory. Please run the following command from your [galaxy-root]/tool-data/shared/jars/ directory: ls -l FastQC/uk/ac/bbsrc/babraham/FastQC I'm guessing you'll see " No such file or directory" - but if you untar the distribution to where the tool expects it, you should see something like: (vgalaxy)galaxy@omics:~/tool-data/shared$ ls -l jars/FastQC/uk/ac/bbsrc/babraham/FastQC total 68 drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Analysis drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Dialogs -rwxr-xr-x 1 galaxy galaxy 1080 2011-09-19 14:13 FastQCApplication$1.class -rwxr-xr-x 1 galaxy galaxy 1080 2011-09-19 14:13 FastQCApplication$2.class -rwxr-xr-x 1 galaxy galaxy 9366 2011-09-19 14:13 FastQCApplication.class -rwxr-xr-x 1 galaxy galaxy 3661 2011-09-19 14:13 FastQCMenuBar.class drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 FileFilters drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Graphs drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Help drwxr-xr-x 3 galaxy galaxy 4096 2011-09-19 14:13 Modules drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Report drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Resources drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Results drwxr-xr-x 3 galaxy galaxy 4096 2011-09-19 14:13 Sequence drwxr-xr-x 2 galaxy galaxy 4096 2011-09-19 14:13 Statistics Note that it would be possible to change the xml wrapper to expect to find the distribution on the path if there is community preference for requiring the FastQC distribution to be on the execution host path but having it the way it is allows explicit control of the version the tool uses within the layout of the Galaxy installation root, as is done for other fussy java packages. Suggestions welcomed. On Thu, Oct 20, 2011 at 6:03 AM, Todd Oakley <todd.oak...@lifesci.ucsb.edu> wrote: > 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 > > -- > ************************************* > 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/ > ************************************** > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
