PUMA: Panoptic segmentation of nUclei and tissue in MelanomA Banner

🚀 PUMA Challenge Docker Submission Question

🚀 PUMA Challenge Docker Submission Question ¶

By: aia_wt on March 7, 2025, 8:43 a.m.

Hi everyone! How should the Dockerfile be written correctly?

Currently, the Dockerfile ends with the following lines:

RUN chmod +x ./inference.sh 

# entrypoint to run
ENTRYPOINT ["./inference.sh"]

# default arguments, can be overridden
CMD ["--input", "/input/images/melanoma-wsi", "--output", "/output", "--cp", "/checkpoint", "--tta", "4", "--inf_workers", "4", "--pp_tiling", "10", "--pp_workers", "4"]

Should I run test_run.sh at the end automatically? If yes, how should I modify the Dockerfile to execute test_run.sh after inference.sh finishes without affecting the current functionality?

Any help or suggestions would be greatly appreciated! 🙏 Thank you in advance!

Re: 🚀 PUMA Challenge Docker Submission Question ¶

By: mschuiveling on March 7, 2025, 11:56 a.m.

Hi aia_wt,

I asked the person who helped me to create the docker container to help with the problem. This was her response:

Hi,

Thanks for your question! If you want to execute test_run.sh after inference.sh finishes without affecting the current functionality, you can use a wrapper script.

1. Create entrypoint.sh
bash
(# ! /bin /bash)

# Run inference.sh 
./inference.sh 

# Run test_run.sh after inference.sh completes
./test_run.sh


2. Modify the Dockerfile 
dockerfile
# Make the entrypoint script executable
RUN chmod +x ./entrypoint.sh

# Set the new entrypoint to the wrapper script
ENTRYPOINT ["./entrypoint.sh"]

# Default arguments, can still be overridden
CMD ["--input", "/input/images/melanoma-wsi", "--output", "/output", "--cp", "/checkpoint", "--tta", "4", "--inf_workers", "4", "--pp_tiling", "10", "--pp_workers", "4"]

Hope this helps!