Mybinder fails to launch, returns an internal server error : How to debug this?

Binder mybinder.org ops
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I’m trying to run the notebook in this repository : GitHub - vincent-noel/project_repo_ecm_simul: Project repository for the creation of jupyter notebook for PhysiCell simulation with extra cellular matrtix

The docker image builds without issue, but when launching it, mybinder tells me it’s taking too long, and ends up failing with an internal server error. The full log is the following :

Found built image, launching…
Launching server…
Internal Server Error

Link to the mybinder launcher

Is there a verbosity option somewhere to get more detailed logs ? How can I debug this ?

Thanks

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Debugging launching using the public Binder system is limited because you cannot get those logs. However, I believe your issue in this case is fairly straightforward and you don’t need to start pursuing local efforts to get things working.

The issue seems to be you are using a custom dockerfile that hasn’t been edited to be compatible with Binder. See here and follow the guides linked there if you absolutely want to continue using a Dockerfile.

I’d advise against that route though for two reasons: 1) Dockerfiles are only meant to be used in complex cases as they are harder make work and keep working with Binder; & 2) since you seem to want this repo to work with a number of different avenues it will be easier to distinguish the binder route. So I’d suggest you make a binder directory in the root of your repo and make a requirements.txt file, see here, where you list the pip installable packages you seem to be installing with your Dockerfile. (See here for information about that binder folder.) For the other steps in your Dockerfile, you would do them in a postBuild file, see here.

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I had some C++ dependencies which needed to be compiled, so I had to use Dockerfile.
In the end it was a problem with user configuration (more precisely UID).

Thanks for all the informative links !