Some (minimal?) Java help needed (Was: Bug#670353: ITP: fastqc -- quality control for next generation sequencing data)

[Andreas Tille <andreas@an3as.eu>]

Hi,

I stumbled upon this one and did some work on it in

   Vcs-Svn: http://svn.debian.org/debian-med/trunk/packages/babraham/fastqc/trunk/

It is close to lintian clean now but there is some CLASSPATH issue
which is probably very easy for Java experts:

$ fastqc 
Exception in thread "main" java.lang.NoClassDefFoundError: uk/ac/babraham/FastQC/FastQCApplication
Caused by: java.lang.ClassNotFoundException: uk.ac.babraham.FastQC.FastQCApplication
        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)
Could not find the main class: uk.ac.babraham.FastQC.FastQCApplication. Program will exit.

or when trying manually what the wrapper tries to do

$ java -jar /usr/share/fastqc/fastqc.jar uk.ac.babraham.FastQC.FastQCApplication
Skipping 'uk.ac.babraham.FastQC.FastQCApplication' which didn't exist, or couldn't be read


My suspicion is that simply specifying the Main-Class in debian/manifest
is not sufficient.  Something might be wrong with the Debian home brewn
Makefile as quilt patch and ant+built.xml might do a better job to build
the Jar functionally.  Any hint for doing this properly?

Note to obtain the source as easy as possible:  Just use the uscan from

   http://anonscm.debian.org/gitweb/?p=users/tille/devscripts.git;a=blob;f=scripts/uscan.pl

to call

   uscan.pl --verbose --force-download --repack-compression xz

which gives you a properly stripped source tarball.

Kind regards and thanks for any help

       Andreas.

On Wed, Apr 25, 2012 at 01:08:54AM +0200, Steffen Moeller wrote:
> Package: wnpp
> Severity: wishlist
> Owner: Steffen Moeller <steffen_moeller@gmx.de>
> 
> * Package name    : fastqc
> * URL             : http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
> * License         : GPL-3
>   Programming Lang: Java
>   Description     : quality control for next generation sequencing data
> 
> The Debian Med source code repository has some functional (not lintian clean) package in
> trunk/packages/babraham/fastqc.
> 

-- 
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