[Debian-med-packaging] Bug#895765: IGV

[Olivier Sallou]

On 10/18/2018 08:25 PM, Andreas Tille wrote:
> Hi Olivier,
>
> On Thu, Oct 18, 2018 at 06:18:58PM +0200, Olivier Sallou wrote:
>> testing with your removals, you only need to add to build gradle file
>> the ref to htsjdk
> I've now pushed the freshly stripped upstream version since we
> both agree that a competing htsjdk is not a good idea.
>  
>> I pushed the update on patch (but your copyright patch is not yet there)
>>
>> With this compile "com.github.samtools:htsjdk:debian" and htsjdk jar
>> removed from upstream source, it compiles fine for me.
> I confirm it compiles fine now.  However:
>
>
> $ LC_ALL=C igv
> Error: Unable to initialize main class org.broad.igv.ui.Main
> Caused by: java.lang.NoClassDefFoundError: htsjdk/samtools/seekablestream/ISeekableStreamFactory

I just pulled from git, rebuilt and tried with new deb, and got no
issue, GUI started as expected.
This kind of error suggest that it did not found in igv classpath the
htsjdk.jar (not installed or not in in command classpath).

>
>
> Sorry to admit that we seem to need another iteration to get igv out.
>  
> Thanks a lot for your effort
>
>       Andreas.
>

-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

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