Re: Bio-Linux

[Andreas Tille <andreas@an3as.eu>]

Hi Steffen,

On Wed, Aug 15, 2018 at 05:40:51PM +0200, Steffen Möller wrote:
> >
> >     https://salsa.debian.org/blends-team/biolinux
> >
> > To have some content I have choosen a copy of med-bio for biolinux-desktop
> > and med-bio-dev for biolinux-server which is definitely *not* sensible, but
> > works as a test case.  Please adapt the tasks (including the Description in
> > the top) to your preference.  Once you have something reasonable I'll setup
> > the websentinel config to have tasks pages for BioLinux.
> 
> from my side I would be particularly interested to learn about the
> packages that Bio-Linux wants to see redistributed with them but that
> are yet not in Debian.

We actually have this kind of documentation since our latest sprint.
Unfortunately it seems to be in a simila maintenance situation that
overworked contributors do not find the time to care for it.  I now
finally removed what I once marked as "in Debian" - please double check
my latest commit:

    https://salsa.debian.org/med-team/community/bio-linux/commit/090871600b1f72a532a449d88af9f118b0d95868

It would be a really helpful contribution from BioLinux if you could
maintain this list to point package maintainers to the **urgently**
**needed** software to start with this to spent our time in a sensible
manner.  I'm also offering mentoring to learn how to properly package
inside the Debian Med team[1].
 
> The https://blends.debian.org/med/tasks/bio pages have that yellow
> section that lists a few bio-linux ones. How would you (Andreas and
> Tony) feel about moving them to the Bio-Linux list?

You mean to the the according task file?  Its currently in the desktop
task since its a stupic copy of or bio task.  I did not yet activated
the web rendering since I understood Bio-Linux developers wanted to
create something more sensible first.  Please let me know if you need
further help to accomplish this.  If you do not ask questions I have
no idea how to help. 

> >> As far as I can tell from the Debian documentation and what we've discussed,
> >> the complete set of Bio-Linux tasks would simply be Tim's original package
> >> list, divided into desktop and server tasks. I would ask your preference on
> >> whether we would use the reduced list I created which only has packages in
> >> sid (although this has some issues with virtual packages)

What are the issues with virtual packages?

> >> or the compete set.
> The complete list, I propose. The colouring to indicate what is
> available and what is on salsa etc is done in an automated fashion.

I'd also vote to keep the long list and show what is missing / what
we are working on.  The Blends toolset is dealing sensibly with the
missings when it will create the metapackages.

> >> I know that the documentation states the latter, but I don't know if
> >> all of the packages are still useful to Bio-Linux.
> I tend to agree that a refurbished Bio-Linux should address today's
> problems more than the ones of the past. But you can easily remove
> packages by just deleting a line, so, first let's have a look about how
> much we already cover.

I agree with Steffen that removals are very cheap to do.  If I were you
I would start with a sensible long list and reduce later in a second
rush.

> > Hope this helps over the first hurdle but keep on asking here.  I'll be
> > more responsive soon (just in the train back home from DebConf).
> >
> > Thanks for the effort to merge BioLinux and Debian Med - I'm positive
> > about a great and productive cooperation
> 
> Ok.  I am not sure about how far we are from everything. It would help
> if we just have something as a start.

+1

Kind regards

      Andreas.
 

[1] https://wiki.debian.org/DebianMed/MoM

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