Bug#670353: Some (minimal?) Java help needed (Was: Bug#670353: ITP: fastqc -- quality control for next generation sequencing data)
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.
>
--
http://fam-tille.de
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