Re: cwl - ok for me to document my progress on wiki.d.o?
Hi Afif,
On Mon, Feb 15, 2016 at 12:23:27AM -0800, Afif Elghraoui wrote:
>
> :) So is there no problem to edit tasks pages for other blends to add
> packages we maintain?
I'd like to avoid the term "other" when we talk about Blends. A Blend
should make sense and if we packaged something in our Vcs that might
help any Blend it should be mentioned there (as well as out tasks
contain packages maintained by DebiChem, NeuroDebian and Debian
Science).
> I always wondered why Debian Med didn't maintain
> the science-bio metapackage directly. I thought that med-bio was created
> and added as a dependency to science-bio just so that it could be
> managed directly by Debian Med. I never got around asking about that, I
> guess until now. Was the reason for this just historical?
Its rather a matter of maintenance. The point of the implicite
dependencies solves the issue of reaching (basically) the same effect by
maintaining one file rather than two. I think the idea to "resolve"
Dependencies on the tasks pages by rather displaying the dependencies
of med-bio and med-bio-dev on the science-biology tasks page is now
probably 10 years old and with the upcoming new implementation of the
tasks pages finally not that hard to reach any more.
> > I do not see any reason to add quite generic tools like make & makepp.
>
> As you wish,
Its not about my wish - may be it makes sense to discuss this on the
Debian Science list.
> though they do have relevance for scientific research. I
> personally use Make for all my bioinformatics pipelining. It's
> especially nice since you can change the SHELL/.SHELLFLAGS for different
> targets. If you wanted, you can have one rule execute in R, one in
> Bourne shell, another in SQL, and others in Python, Perl, and so on. You
> might think of snakemake almost as running a regular GNU Makefile that
> sets `SHELL=python` and declares `.ONESHELL`.
If you add the tools to the Debian Science tasks (perhaps with some
additional comment) that's perfectly fine for me.
> > However, despite the fact that I think these tools are well placed in
> > science-tools tasks are not exclusive. A task should give a hint to a
> > user looking at the task matching the own field of work. So there is no
> > point in putting snakemake and cwl into only science-tools. We could
> > decide that it is not that important for med-bio / med-imaging and just
> > use a "Suggests" relation.
> >
>
> Or should med-bio/med-imaging just suggest science-tools itself?
Why not?
> I think
> the other things in there may also be of interest and we wouldn't need
> to add Suggests one at a time. I have no problem either way; just a
> suggestion.
I like your suggestions ... and you are a memeber of Debian Blends team
so you have proper permissions to implement these. ;-)
Kind regards
Andreas.
--
http://fam-tille.de
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