Re: Packging jModelTest for Debian and versioning
Hi Andreas,
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.
Best,
Diego.
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[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
>>>
>>
>>
>
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