Re: Packging jModelTest for Debian and versioning
I added a new tagged revision after removing the dependency on ReadSeq. I also fixed the license in
several files where it was missing, and I removed the PhyML binaries from the repository. I am not
sure how you deal with that dependency, which is present also in ProtTest, but let me know if I
should do something about it. I replaced the binaries with a README file in
src/main/resources/exe/phyml that explains how to place the PhyML binary in the distribution.
On 19.10.2015 16:50, Andreas Tille wrote:
> 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 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
> instead to not relay on a non-free project with uncertain maintenance
> Kind regards
>  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:
>> 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:
>> 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,
>> On 27.08.2015 14:18, Andreas Tille wrote:
>>> 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.
>>> Since I was asked to package jModelTest I checked what might be the
>>> latest version. At
>>> 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
>>>  http://blends.debian.org/med/tasks/bio