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

[Ognyan Kulev]

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