[Debian-med-packaging] Bug#693655: ugene: Please update ugene to the latest version 1.11.3

['Andreas Tille']

Hi Ivan,

On Tue, Nov 27, 2012 at 01:48:40PM +0700, Ivan Efremov wrote:
> 
> I see your point, but most of 3rd-party plugins including ball, hmmer,
> phylip, psipred etc. are integrated into UGENE at the source level.
> Typically that means that we modified the original code, provided adapters
> and so on. For instance, you can take a look at HMMER3 code in the UGENE
> tarball - it differs significantly form the original (e.g. we had to replace
> all abort()'s and exit()'s). So for tools contained in src/plugins_3rdparty
> there is almost no way to reuse original binaries.

Well, I do not want to suggest you should change your development model
right now.  However, in the long run you might profit from the fact that
there is no need to patch third party software for any of their new
version.  We will try to package Ugene as it is provided from your side
but it is also our duty as Debian maintainer to raise our opinion about
possible advancements in the long run - and so I did.
 
> The good news is that we have a bunch of algorithms integrated as truly
> external tools, i.e. UGENE depends on the original binaries (see
> http://ugene.unipro.ru/external.html). In this case we can modify
> ubuntu/debian installer to "recommend" these packages and at the source code
> level check if needed binaries are installed to system-wide directories.

Yes, this is what we definitely should do and I will try to work on this.

> So, may I ask you to file a bug at http://ugene.unipro.ru/tracker to make
> sure our engineers will handle the issue with external tools?

https://ugene.unipro.ru/tracker/browse/UGENE-1335

(I admit I had some trouble creating a working login - immediate login was
not possible, needed to request a password change first;  also submitting the
issue was not straightforeward - the session was ended and I needed to restart
the action :-()

Kind regards

      Andreas.

-- 
http://fam-tille.de