Hi Andreas, Thanks for the advice. ReadSeq should be fine, even though according to its README file it does not parse PHYLIP format. I will check it within the next days and hopefully by the end of this week there will be a new release. I believe we can even proceed without readseq2/ReadSeq, using ALTER directly. I'll let you know.
Best Regards, 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 >>> >> >> >
