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
in:
1. Please review the patch I'm using at
https://anonscm.debian.org/git/debian-med/jmodeltest.git/tree/debian/patches/do_not_chmod_anything_in_usr_bin.patch
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:
https://github.com/stephaneguindon/phyml/releases
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
Andreas.
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
> >>
> >>
> >
>
>
--
http://fam-tille.de
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