[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

Re: Maybe sponsor package under debian-med umbrella?

Hi Benjamin,

thanks for contacting the Debian Med team.

On Tue, Mar 06, 2018 at 04:12:23PM -0500, Benjamin Redelings wrote:
>     I see that many bioinformatics programs such as muscle, mafft, and fsa
> (alignment) and mrbayes, beast-mcmc, and phyml (phylogenetics), etc. are
> maintained by the "Debian Med Packaging Team".

That's correct.

> I uploaded a package for
> bali-phy (which does simultaneous alignment) to mentors.debian.net. 
> (Disclaimer: I am the author). I was originally planning to try to maintain
> this on my own, but (supposing people are interesting in this package) would
> the Debian Med team be a better structure?

Definitely.  The Debian Med team has evolved to a strong group of people
interested in bioinformatics.  Upstream authors are more than welcome to
maintain their packages inside the team.
>     Many of the programs that I use (such as figtree) are available in
> Debian now, but a few (e.g. tracer:
> http://tree.bio.ed.ac.uk/software/tracer/,

So we should probably package tracer.

> canu:
> https://github.com/marbl/canu) are not.

Canu is packaged but not yet available in any release yet.  We might
consider a backport to stretch if this is helpful for you.  You can get
a full overview about all available packages in the so called "task
biology" (we have other tasks like biology-dev for development, medical
imaging and others).  Here is the deep link to canu[1]

> I would probably be interested in
> packaging tracer.  Like figtree, it is a java program, and it is by the same
> authors, so I presume I could use the figtree package as a template.
>     Thoughts?

The best idea would be you register on the new development platform


and ask for beeing added to the Debian Med team.  Once your application
is accepted please create a Git repository for bali-phy there and
somebody of our team will take over the sponsoring.

Kind regards


[1] https://blends.debian.org/med/tasks/bio#canu


Reply to: