Re: guix-based installation of pigx-rnaseq - works
Hi Simon,
Am 02.03.21 um 14:52 schrieb zimoun:
> Hi,
>
> On Sat, 27 Feb 2021 at 19:55, Steffen Möller <steffen_moeller@gmx.de> wrote:
>
>>>> We keep mentioning conda also the time, while guix is somewhat left
>>>> aside, but https://guix.gnu.org/packages/ is truly impressive. Somewhat
>>>> annoying, if we ever decide to also reference guix packages in
>>>> d/u/metadata, then there are only versioned web pages like
>>>> https://guix.gnu.org/de/packages/bc-1.07.1/, so we would only have
>>>> moving targets point to.
>>> What do you mean exactly?
>> In d/u/metadata we give references to the bio.tools registry,
>> SciCrunch's RRIDs and conda. But we should also give one to guix if we
>> know about an "ortholog" package. These references point up as URLs on
>> our task pages for the various blends. There is however no page for a
>> package in guix that is not versioned if I get this right.
> Just to understand, since I am not totally familiar with the debian/
> folder, you are speaking about this file, for instance,
>
> https://salsa.debian.org/med-team/pigx-rnaseq/-/blob/master/debian/upstream/metadata
yes
> What would be nice for Debian instead of
> <https://guix.gnu.org/en/packages/pigx-rnaseq-0.0.10/>?
The updates of Debian's packages and those of guix are not synchronized.
And once something is in a regular Debian release, the Debian package
likely points to an older version of the same in guix. It would hence be
preferable to have an unversioned page to point to - which then lists
all the versions available for that package.
> And where could I find a an example on how the others do?
https://tracker.debian.org/pkg/vim
https://anaconda.org/conda-forge/vim
>> The fun part is, and this is where this shot on guix comes in, that we
>> can compare a Debian based implementation with an image that upstream
>> provides. Or compare with conda/brew/...guix. We are currently team
>> building and collect ideas what we want to achieve.
> I am not sure how the image upstream provides is built,
> probably with
> "guix pack -f docker":
>
> <http://bioinformatics.mdc-berlin.de/pigx/supplementary-materials.html>
Ah, there is is. Many thanks. I knew I had seen this somewhere :)
>> Hm. Not so sure. My interpretation was some general incompatibility of
>> above docker-approach with GUIX, so I happily adopt the "guix pack".
> There is another level to build Docker images using Guix: "guix system
> docker-image" but it is more complicated and probably not the correct
> path to distribute packages in a container.
>
> <http://guix.gnu.org/manual/devel/en/html_node/Invoking-guix-system.html#Invoking-guix-system>
Hm. Would be interesting to learn about differences between different
ways to come up with an image.
Best,
Steffen
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