[Debian-med-packaging] Bug#697604: Templates/Icons is not found

[Andreas Tille]

Hi Ognyan,

sorry for the late reply (I've though I would have answered immediately
but BTS does not show something ...)

Can you please specify what exactly you did after starting fastqc to
enable us reproducing the problem.  I admit I'm not a user of this program
myself so I need some additional information.  Olivier, do you have some
additional hints how to tackle this?

Thanks for the bug report in any case

      Andreas.

On Mon, Jan 07, 2013 at 04:44:09PM +0200, Ognyan Kulev wrote:
> Package: fastqc
> Version: 0.10.1+dfsg-1
> Severity: grave
> 
> Non-interactive fastqc always fails with
> 
> java.lang.NullPointerException
>         at
> uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:170)
>         at
> uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:60)
>         at
> uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:157)
>         at
> uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:108)
>         at java.lang.Thread.run(Thread.java:679)
> 
> It's this line:
> 
> File templatesDir = new
> File(URLDecoder.decode(ClassLoader.getSystemResource("Templates/Icons").getFile(),"UTF-8"));
> 
> So it tries to find /usr/share/fastqc/Templates/Icons and don't succeed.
> I tried various things to add /usr/share/fastqc to CLASSPATH in
> /usr/bin/fastqc but it's not enough.
> 
> I downloaded upstream FastQC and there was no such problem. The only
> difference that I see is that in Debian a fastqc.jar is used while in
> upstream it's unpacked in the root directory. My conclusion is that this
> specific way with getSystemResource searches only the location where
> main class resides. In Debian's case it's fastqc.jar and in upstream
> it's FastQC directory.
> 
> The easiest solution is to include all /usr/share/fastqc/* in the jar
> file. (Well, you could not use jar file at all but I don't think it's a
> good idea.)
> 
> Regards,
> Ognyan Kulev

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