Web lists-archives.com

Re: User-installable Debian packages?




Hi Benda,

On 30.07.17 09:37, Benda Xu wrote:
> Hi Steffen,
>
> Steffen Möller <steffen_moeller@xxxxxx> writes:
>
>> I just had a quick look and it seems really nice, indeed! Thank you tons for
>> pointing that out to us. Has anybody already tried that with Debian?
> I am one of a few guys behind that project.  Gentoo Prefix with its own
> libc runs on Debian very well, the explicity tested distributions are
> listed at,
>
>   https://wiki.gentoo.org/wiki/Prefix/libc#Tested_distributions
>
> The highlights are:
>
>   1. you can compile almost any package available in Gentoo.
>   2. you can run x86 Gentoo Prefix on a amd64 Debian, thus another form
>      of multiarch.
>
> The downside compared to Debian and any binary distribution is that,
> everything need to be compiled from source.  That's slow.
>
>
> A preliminary draft has been prepared to discuss its use on HPC
> environments:
>
>   https://arxiv.org/abs/1610.02742
>
>
> Alternative projects are _spack_ and _easybuild_, with slightly
> different motivations and implementations.
>

This is good to hear. While I like all that I read about Gentoo, I do
not know about how well equipped it is with packages in computational
biology [edit: I had a look at
https://packages.gentoo.org/categories/sci-biology and am impressed,
well done!]. This is where BioConda (bioconda.github.io) is very strong
now. And while the Conda community gets increasingly sophisticated with
their packaging, we can decide to either just let them go for it or to
find ways to compete. These folks start as low as libz, i.e. just above
libc, really. I hence tend to think that it is something that we as a
Linux distribution should care about.

I have followed Johanness' link to
https://wiki.debian.org/Teams/Dpkg/Spec/InstallBootstrap but frankly do
not yet know how to transform that into something computational
biologists would like to use and trust more than Conda. It would all
start with cross-distribution packages of dpkg, right? And the testing
infrastructure of Debian would need to care for such
off-root-experiences, too. I do not see that just around the corner.

Best,

Steffen