Hi Ross,
    Thanks for your advice.

Yes, something like this seems logical. However, after I installed system-wide before, I noticed that galaxy was expecting fastqc in the 'jars' directory. So, I copied the full directory structure over there. As such, when I look at the directory you suggest, I do indeed see files there:


[galaxy@node95 jars]$ ls -l FastQC/uk/ac/bbsrc/babraham/FastQC/
total 68
drwxr-xr-x 2 galaxy hpuser  4096 Oct 18 20:18 Analysis
drwxr-xr-x 2 galaxy hpuser  4096 Oct 18 20:18 Dialogs
-rw-r--r-- 1 galaxy hpuser  1054 Oct 18 20:18 FastQCApplication$1.class
-rw-r--r-- 1 galaxy hpuser 10075 Oct 18 20:18 FastQCApplication.class
-rw-r--r-- 1 galaxy hpuser  3624 Oct 18 20:18 FastQCMenuBar.class
drwxr-xr-x 2 galaxy hpuser  4096 Oct 18 20:18 FileFilters
drwxr-xr-x 2 galaxy hpuser  4096 Oct 18 20:18 Graphs
drwxr-xr-x 2 galaxy hpuser  4096 Oct 18 20:18 Help
drwxr-xr-x 3 galaxy hpuser  4096 Oct 18 20:18 Modules
drwxr-xr-x 2 galaxy hpuser  4096 Oct 18 20:18 Report
drwxr-xr-x 2 galaxy hpuser  4096 Oct 18 20:18 Resources
drwxr-xr-x 2 galaxy hpuser  4096 Oct 18 20:18 Results
drwxr-xr-x 4 galaxy hpuser  4096 Oct 18 20:18 Sequence
drwxr-xr-x 2 galaxy hpuser  4096 Oct 18 20:18 Statistics
drwxr-xr-x 2 galaxy hpuser  4096 Oct 18 20:18 Utilities



Perhaps I will remove my system installation, and also try untaring fastqc anew in the jars file, in case something didn't copy. But at first glance, it seems to be something else...

Todd



On 10/19/2011 2:51 PM, Ross wrote:
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/
**************************************

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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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in your mail client.  To manage your subscriptions to this
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