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Re: Request for discussion - what should bio.tools et al. do for us?



Hi Steffen,

On Wed, Jun 16, 2021 at 07:38:37PM +0200, Steffen Möller wrote:
> Hallo,
> 
> I had joined the bio.tools folks this afternoon for a pre-meeting of an
> EU project to give the registries a boost. I was asked what Debian would
> want from them. And while I do not think that my answer was completely
> off, we should possibly come up with a consensus on this list. Here my
> shot, hoping to seed further discussions, not only among current
> contributors to Debian Med:
> 
>  * Awareness - something better than our task lists

I'd say s/better/other/ in the sense that it is more focussed on user
needs.  The tasks lists are fullfilling a some needs from a Debian
perspective but they are weak in terms of a bioinformatican view
(regarding better categorisation etc. which is probably a strength of
bio.tools).  I'd love to repeat that I personally do not consider this
a problem of the technique behind but rather the fact that our data
are pretty weakly maintained.

>     - of Debian as a whole
>     - of packages Debian offers
>     - for the possibiliy that
>       + Debian can be joined and that there is mentoring for newbies
>       + companies offer support for Debian/Ubuntu where this is desired
> 
>  * Guidance - something better than our Excel sheet

I'd love if you would use the term "Spreadsheet" since the program you
are mentioning is neither used nor needed to work with this sheet.  I'm
also not sure if the term "better" should be replaced by "more visible"
and may be "easier to maintain".

>     - packages that Debian offers for particular tasks/problems/workflows
>     - packages that Debian misses (but conda/guix have or workflow X
> depends on that is already 90% covered with Debian packages)
>     - pointers to new technical developments that Debian should look at
> 
>  * workflows meta-continuous integration testing
>     - workflows should come with examples how to run them
>     - Debian has reproducible builds - can we have repoducible workflow
> tests
>     - Some distribution-independent testing environment should compare
> results between conda/guix/Debian/brew...
> 
>  * Improved compatibility
>     - "apt-get install conda", please. We are not too far from that but
> need some guidance for the last meters.

When I was laying down my work on this it was just some build time tests
away but I was simply lacking knowledge whether these were ignorable or
not.  However, I fail to see in how far bio.tools can help us getting
conda packaged.

>     - avoid "which python installation"-hassle with /usr/bin/python* vs
> conda installation shebang lines

I also do not see any connection to bio.tools here - but may be I'm
misleaded about their scope.
 
Kind regards

      Andreas.

-- 
http://fam-tille.de


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