Conda executable not found

[maartenpaul]

I would be happy to test your software to see how it can be used for segmentation and training on OMERO-stored image data.

I have tried to build your docker images using docker-compose.
I do run into an issue with building the seg-serve image.
The issue appears to occur from this line from the respective Dockerfile
https://github.com/hip-satomi/SegServe/blob/883b626a41fd696e0adf7bf944dad418a490f879/Dockerfile#L29

ERROR [seg-serve  9/14] RUN mlflow run https://github.com/hip-satomi/Cellpose-Executor.git -e info -v main
------      
 > [seg-serve  9/14] RUN mlflow run https://github.com/hip-satomi/Cellpose-Executor.git -e info -v main:
1.684 2024/12/16 09:09:55 INFO mlflow.projects.utils: === Fetching project from https://github.com/hip-satomi/Cellpose-Executor.git into /tmp/tmpvi_qruv4 ===
2.347 2024/12/16 09:09:56 ERROR mlflow.cli: === Could not find Conda executable at conda. Ensure Conda is installed as per the instructions at https://conda.io/projects/conda/en/latest/user-guide/install/index.html. You can also configure MLflow to look for a specific Conda executable by setting the MLFLOW_CONDA_HOME environment variable to the path of the Conda executable ===
------
failed to solve: process "/usr/local/bin/_dockerfile_shell.sh mlflow run https://github.com/hip-satomi/Cellpose-Executor.git -e info -v main" did not complete successfully: exit code: 1

Possibly something has changed in the dependencies of the Dockerfile? Do you maybe have a suggestion of a different branch of the repository that works?

Best, Maarten

[JojoDevel]

Hey Maarten,

thanks for making us aware of the issue. Seems to be an problem of using micromamba instead of conda for efficient environment management 🤔 I will investigate further