[Debian-med-packaging] Qualimap into Debian - Missing sources of bioinfo.org libraries (Was: Seeking for Java source code of org.bioinfo.*)

[Andreas Tille]

Hi again,

is there any chance that we will find the missing sources or is this a
lost case and we need to seek for alternatives for Qualimap? 

Kind regards

       Andreas.

On Thu, Jan 14, 2016 at 05:27:46PM +0100, Andreas Tille wrote:
> Hola,
>  
> I'd like to summarise my understanding of the issue and hope this migth
> lead to a soonish solution of the issue.
>  
> Fernando once was working at CIPF where the Java classes for bioinfo.org
> were developed.  The JARs resulting from the bioinfo.org code are used
> by Qualimap (which is my final target for the Debian packaging).  For
> some reason the Java source code of the bioinfo.org classes where never
> published on any public repository nor taken over into Qualimap
> maintenance.
> 
> We are seeking now for a kind soul who might find the according code on
> some local hard disk or if all fails on a backup and would be able to
> publish it (preferable on Github or any other public repository).
> 
> The thing is that Debian requires the full source to build a programm
> and without these bits of code Qualimap can not enter Debian.
> 
> The only alternative would be to find other Open Source Java classes
> that might provide the functionality of bioinfo.org and could replace
> the missing code.
> 
> I hope this summary describes the current situation correctly and leads
> to a solution of the current dead lock.
> 
> Muchas gracias
> 
>        Andreas.
>  
> 2016-01-05 12:29 GMT+01:00 Garcia-Alcalde, Fernando <
> fernando.garcia-alcalde at roche.com>:
> 
> > Dear Ximo,
> >
> > I hope this email finds you well! I am writing to you regarding a request
> > from Andreas Tille (Cc here), who is aiming to package Qualimap for
> > official Debian.
> >
> > I short, he is in need of all the sources needed to build Qualimap and he
> > has had no luck in finding the source code of the dependencies of the
> > bioinfo.org CIPF repository (please note that we use directly the
> > associated JARs to build Qualimap which is not sufficient in this case).
> >
> > Unfortunately nor me nor Konstantin have access to these sources. Could
> > you please inform us who is the appropriate person of contact?
> >
> > Muchas gracias!
> > Fernando
> >
> > --
> > Fernando Garcia-Alcalde, PhD
> > Senior Scientist, Infectious Diseases
> > Roche Pharmaceutical Research and Early Development
> >
> >
> > Roche Innovation Center Basel
> >
> >
> > F. Hoffmann-La Roche Ltd
> >
> > Grenzacherstrasse 124
> > 4070 Basel
> > Switzerland
> > Tel: +41 (0)616878987
> > email: fernando.garcia-alcalde at roche.com
> 
> -- 
> http://fam-tille.de
> 
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