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Re: Packging jModelTest for Debian and versioning



Hi Diego,

it took some time since the last mail exchange but as I mentioned before
we need to work on the third party JARs to build them from source as
separate packages.  I managed to do this now for alter.jar, pal.jar and
prottest.jar (fetching latest version 3.4 instead of 3.0 - hope this is
fine).  The only remaining bio-related JAR is lib/readseq.jar.

We had some previous discussion on the Debian Med mailing list[2] which
lead to the conclusion that this code could at best shipped under
non-free if the authors are not responsive.  Since we did not got any
response from the authors we somehow assume that the readseq2 project is
possibly dead.

You might check whether jmodeltest would be able to use

    https://github.com/rdpstaff/ReadSeq

instead to not relay on a non-free project with uncertain maintenance
status.

Kind regards

     Andreas.


[2] https://lists.debian.org/debian-med/2014/02/msg00205.html

On Thu, Aug 27, 2015 at 03:51:40PM +0200, Diego Darriba wrote:
> Hi Andreas,
> 
> As you said, jModelTest has been officially migrated to github, since
> google code is going away:
> 
>   https://github.com/ddarriba/jmodeltest
> 
> I tagged the last releases, available at Google Drive together with the
> PhyML binaries. jModelTest requires PhyML to be available, but it can be
> configured for using a system wide installed version by setting  the flag
> `global-phyml-exe` in the configuration file:
> 
> https://github.com/ddarriba/jmodeltest2/blob/v2.1.7r20150222/src/main/resources/conf/jmodeltest.conf
> 
> Don't hesitate on asking me if you have any question or you need me to do
> any further change in the code.
> 
> Best Regards,
> Diego.
> 
> On 27.08.2015 14:18, Andreas Tille wrote:
> > Hi,
> > 
> > I'm writing you on behalf of the Debian Med team that has the objective
> > to package all free software that is relevant in the field of medicine
> > and biology.  You can find an overview about the biological software we
> > have just packaged for Debian on our biology task page[1].
> > 
> > Since I was asked to package jModelTest I checked what might be the
> > latest version.  At
> > 
> >    https://code.google.com/p/jmodeltest2/wiki/Updates 
> > 
> > I found
> > 
> >    "20 Feb 2015 Version 2.1.7 rev 20150220"
> > 
> > which seems to be the latest download that is available at your Google
> > drive download location.  In addition at Github a release
> > jModelTest-2.1.7-20141120 is available.  While I would really prefer
> > releases from Github since this simplifies things a lot this does not
> > seem to be tha lastet release.
> > 
> > It would help if you could confirm that the codebase officially moved
> > from Google Code to Github and if so if all released states would be
> > properly tagged.
> > 
> > Kind regards
> > 
> >        Andreas.
> > 
> > [1] http://blends.debian.org/med/tasks/bio
> > 
> 
> 

-- 
http://fam-tille.de


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