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

[Andreas Tille]

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