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Re: Packging jModelTest for Debian and versioning

Hi Diego,

thanks a lot for your support.  Prottest now builds fine under Debian
stable and I'll upload a backport to Jessie soon.  I also noticed that
jmodeltest now can be build easily and I'm in the process of preparing
packages.  When doing so I noticed some glitches you might be interested

  1. Please review the patch I'm using at
     The original build.xml removes executable bit from every file
     in /usr/bin which is probably not what you want and if the
     user that builds jmodeltest has root permissions (and is not
     in a chrooted system where Debian builds are happening) the
     system in question might become disfunctional.

  2. When I start runjmodeltest-gui the window displays:

WARNING: PhyML binary is not in the list of compatibility: 
/usr/bin/phyml v3:320+dfsg-2~bpo8+1
Compatible versions: 20130103 20131022 20141009 20141029 20150501 20151222 
jModelTest will try to continue execution anyway, but it might fail.

     I have no idea how you do ther version verfification in
     jmodeltest.  I just can say that we packaged what can be
     found here:


     Could you confirm that this phyml version would work?

I'll probably come up with more questions regarding proper usage
of mpj but that's it for now.

Thanks a lot for your cooperation


On Mon, May 09, 2016 at 04:58:06PM +0200, Diego Darriba wrote:
> Hi Andreas,
> Sorry for the delay. The netbeans dependencies where removed time ago, but I could not work in the
> new release. It is now ready and you can find it in the github repository. Hopefully everything is
> OK now. The only thing to be taken into account is that you would need to set "global-phyml-exe =
> true" in prottest.properties in order to use PhyML from the path.
> Kind Regards,
> Diego.
> On 07.05.2016 15:57, Andreas Tille wrote:
> > Hi Diego,
> > 
> > I wonder whether I missed something but I have not found any new
> > protest3 version which is not using netbeans.  May be you simply
> > forgot to tag it on Github?
> > 
> > Kind regards and thanks for your cooperation
> > 
> >     Andreas.
> > 
> > On Mon, Jan 18, 2016 at 01:45:59PM +0100, Andreas Tille wrote:
> >> Hi Diego,
> >>
> >> On Sat, Jan 16, 2016 at 02:30:58AM +0100, Diego Darriba López wrote:
> >>> I though I have already answered. Sorry for that. Effectively, that is the project for BrowserLauncher.
> >>
> >> OK, I've packaged this and uploaded to the Debian new queue.
> >>  
> >>> I will upload the next release for ProtTest in the next days. The dependency has been removed, but there is also a recently found bug I need to fix.
> >>
> >> Sounds good!
> >>
> >> Thanks for your kind cooperation
> >>
> >>       Andreas.
> >>
> >> -- 
> >> http://fam-tille.de
> >>
> >>
> > 


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