phyml for Debian
----------------

The wrapper /usr/bin/phyml is detecting whether the machine is able
to use MPI and if so it uses the parallelised version which is installed
to /usr/lib/phyml/bin/phyml-mpi.

In case you might experience problems with the MPI version you can
switch this of by using the PHYMLCPUS variable.  If it is set to an
integer number > 1 this number of processors will be used.  If it is set
to something else (either 1 or any other string) the single processor
version is used.  Example:

   If you set

      export PHYMLCPUS=16

   set in your environment 16 processors are used for phyml.


Regarding the packaged version upstream provided the following information

Date: Wed, 18 Mar 2015 20:35:10 +1300
From: Stephane Guindon <s.guindon@auckland.ac.nz>
To: Andreas Tille <andreas@an3as.eu>
Subject: Re: What version of PHyML should be distributed by Debian

I must admit I am not familiar with Github's approach of versioning,
hence my own ad-hoc technique.
The most suitable version of PhyML is probably the Development one.
It should be fairly stable.

Regards,

-Stephane-


On 17/03/2015 04:53, Andreas Tille wrote:
> Hi Stéphane,
>
> I'm writing you on behalf of the Debian Med team who tries to integrate free
> software that is relevant in medicine and biology into official Debian.  As
> you can see we also have packaged PHyML:
>
>    http://blends.debian.org/med/tasks/bio#phyml
>
> I noticed that the source code went from Google Code to Github and is now
> maintained at
>
>    https://github.com/stephaneguindon/phyml
>
> I also noticed that there exist a separate location for releases:
>
>    https://github.com/stephaneguindon/phyml-downloads/releases
>
> This is a bit unusual since most projects use a major.minor.subminor (or
> some other versioning scheme) release tagging inside the Git repository
> and Github creates downloadable archives from those release tags.  But
> you might have your reasons to do so.  However, the content of your
> separate release area shows three different releases one is named
> stable, one development and one "latest patch" (which is not as late as
> development).
>
> I wonder which of these three you personally would consider best suited
> for being distributed by Debian - in other word you want to be used by
> the "generic user of PHyML.
>
> Kind regards
>
>          Andreas.
>


 -- Andreas Tille <tille@debian.org>  Wed, 31 Jul 2013 13:55:11 +0200

