pixi activation in a docker container

[colindaven]

Dear all,

I like pixi, it's fast, but I don't know how to activate it easily in a docker container so the installed binaries like Rscript, libraries and R packages can be found.

This is my code - which works.

I create a docker container, then a singularity container from this. I can run a binary such as Rscript if I use the full path in the container,
eg /opt/pixi/.pixi/env/bin/Rscript
but not with just Rscript

Am I missing something obvious or has someone got an example?
Thanks

# Try out pixi for software env 

RUN apt update && apt install -y curl tar  

RUN mkdir /opt/pixi && cd /opt/pixi && curl -fsSL https://pixi.sh/install.sh | bash

#channel order correct for r packages?
RUN cd /opt/pixi && pixi init --channel conda-forge --channel bioconda && \
  pixi add bioconductor-deseq2==1.34.0 r-dplyr r-ggbeeswarm r-ashr bioconductor-rhdf5 bioconductor-tximport bioconductor-reportingtools r-hwriter r-ini r-ggrepel r-png bioconductor-complexheatmap r-circlize pandas numpy

# how do I activate the pixi env in the container ?

[baszalmstra]

You cannot globally activate a shell like you can with mamba/micromamba. If you want to run a command in a container you can simply do:

pixi run <your command goes here>

I would recommend adding pixi install to the RUN command in your docker to cache the installation of all dependencies.

[bcm0]

You could try SHELL in the Dockerfile https://docs.docker.com/engine/reference/builder/#shell but I don't know the exact pixi command. I opened a similar discussion for bash scripts #690