guix-based installation of pigx-rnaseq - works
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
Should this trigger any idea among those reading this - some RTFM plus a
small pointer would be much appreciated.
Best,
Steffen
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