Set environment variables using repo2docker

maaaaaaaartin · April 18, 2025, 9:44am

Hello,
I am trying to set an environment variables in a environment.yml file (cf. dolfin_warp-tutorials/.repo2docker/environment.yml at d652be8c959928b79e3c8cc47c283ac663910c49 · mgenet/dolfin_warp-tutorials · GitHub). The image is built using repo2docker in a GitHub Action (cf. Setting up Docker image and Jupyter book build and deploy on GitHub · mgenet/dolfin_warp-tutorials@945c219 · GitHub). Unfortunately the environment variable is not set (cf. Binder). Any idea? Thanks in advance!

fomightez · April 18, 2025, 4:53pm

It is the start configuration file you want to set environment variables in, see here.

From the documentation on start here:

“Use this to set environment variables that software installed in your container expects to be set.”

Example:

github.com/fomightez/RNArtistCore-binder

start

8989d573a

#!/bin/bash


# set environmental variables - this handles adding to path so works, see https://twitter.com/rnartist_app/status/1369181657727664128
export RNAVIEW="$HOME/RNAVIEW"
export PATH=$RNAVIEW/bin:$PATH
# need to be set in the start, too so survive to launching of session

# Was doing here so it always has most up to date public version but maybe build takes too long? And 
# so for now moving to postBuild to make sure at least works first and then decide if time tolerable 
# for building during start later
# retrieve rnartistcore and build  Kotlin library to describe and plot RNA secondary structures
#git clone https://github.com/fjossinet/RNArtistCore.git
#cd RNArtistCore/
#git pull
#mvn clean package


# this must be last line according to 
# https://repo2docker.readthedocs.io/en/latest/config_files.html#start-run-code-before-the-user-sessions-starts

This file has been truncated. show original

maaaaaaaartin · April 28, 2025, 7:39am

Thank you! Any idea why the environment variable defined in the .yml file is not set? I think it used to be taken into account.

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Set environment variables using repo2docker

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