On Tue, Feb 23, 2021 at 09:28:48PM +0100, Steffen Möller wrote: > Hello, > > sudo apt-get install guix > guix install pigx-rnaseq
:) > indeed installs the pigx-rnaseq library with its R dependencies. It > installs it all in /gnu, which is somewhat inconvenient, as in "my root > partition complained", and it takes painstakingly long, but it works. > > The system finds STAR and other executables in the regular system path, > only pigx-rnaseq was installed: > > $ guix package -l > Generation 1 Feb 23 2021 18:27:42 (current) > pigx-rnaseq 0.0.10 out > /gnu/store/nlknrjmm2knbr8i5m5qj94788arfb14n-pigx-rnaseq-0.0.10 > > The full install "pigx" I have not tried, yet. Will do. > > 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. > > But otherwise, Debian's guix package has formidably done its job. It is > about time we get the conda packages into a similar state, just maybe > the / partition should be spared by default, but then again, it was only > 6.5GB. > > I had tried in vain to create a dockerfile with this setup which gets a > permission error in the moment that the installation of the packages starts: > > FROM debian:unstable > ENV TERM=xterm > RUN apt-get update -qq > RUN apt-get install -y guix > #RUN (/usr/bin/guix-daemon --build-users-group=_guixbuild & ) && guix > install pigx-rnaseq > #RUN (/usr/bin/guix-daemon & ) && guix install pigx-rnaseq # too big to fail > RUN (/usr/bin/guix-daemon & ) && guix install vim # still takes long and > fails The guix-daemon needs full privileges by default, but it does not need to run inside a container. Just build a docker or guix container and you'll get a minimal dependency tree inside the container. I wrote some stuff up here: https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org mostly because I don't trust my memory ;) > Should this trigger any idea among those reading this - some RTFM plus a > small pointer would be much appreciated. Note that Guix is a rolling distribution. It can do that because versions do not interfere with each other. You can have an unlimited number of glibcs, pythons etc. The reason it installs software in /gnu/store is because of reproducibility. All paths are hard coded in binaries and libs. There is no search path to look up libs, for example. Install a package once and you'll get identical paths between machines, containers etc. I love Debian, but Guix packages and containers are the cats whiskers! It is brilliant to have them both. I have no need for conda. Pj.
