JohannesWiesner / csp_docker

A repository for creating Docker and Singularity files using Neurodocker
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Conda environment should be already activated when starting the container #16

Closed JohannesWiesner closed 1 year ago

JohannesWiesner commented 1 year ago

Might be related to https://github.com/ReproNim/neurodocker/issues/354

JohannesWiesner commented 1 year ago

What happened to activate=True? Can't find it anymore in the current neurodocker docs . But with older images, it was there (see nipype_tutorial)

JohannesWiesner commented 1 year ago

Checked again with docker run --rm kaczmarj/neurodocker:0.7.0 generate docker --help, here it is still found.

JohannesWiesner commented 1 year ago

Opened an issue for that: https://github.com/ReproNim/neurodocker/issues/506

JohannesWiesner commented 1 year ago

With this commit (1171de5100f258b530ae4d96701bbd265830d022), the problem is still not solved but at least we can already activate the csp env once the container is running using source activate csp (conda activate csp will not work!)

JohannesWiesner commented 1 year ago

https://stackoverflow.com/questions/55123637/activate-conda-environment-in-docker

JohannesWiesner commented 1 year ago

Can we use ENTRYPOINT to execute "source activate csp"? https://stackoverflow.com/questions/21553353/what-is-the-difference-between-cmd-and-entrypoint-in-a-dockerfile

JohannesWiesner commented 1 year ago

Difference between source activate and conda activate: https://stackoverflow.com/q/49600611/8792159

JohannesWiesner commented 1 year ago

https://stackoverflow.com/questions/64323539/docker-run-interactive-with-conda-environment-already-activated