rueberger / division_detection Goto Github PK

Hi Rumberger

As of July 2020, I am no longer at Janelia and there are no plans to introduce support for training to this package. That being said, the training is relatively straightforward and should be easily reproducible by the experienced ML practitioner - I am happy to correspond via email.

#1 And could you please spend some time fixing the code?

Thank you!

Dear rueberger,

With great interest,
I have read your papers entitled
“In Toto Imaging and Reconstruction of Post-Implantation Mouse Development at the Single-Cell Level (2018)”.

I tried to use TGMM software.
But the module8 (Automated cell division detection) doesn’t work.

I installed docker and nvidia-docker as instructed
and executed the following command.

cd /home/ubuntu3/Software_Guide_Full/Division-Detection
make gpu_image

Then,
at Step 10/18 : RUN conda install -y -c ilastik pyklb,
the following message was displayed.

Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.

After this,

a message like Examining conflict for …... continued for a long time,
and the following message was displayed.

Found conflicts! Looking for incompatible packages. 
UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:
[…]
Your python: python=2.7

Finally,

I got the following error message:

The command '/bin/sh -c conda install -y -c ilastik pyklb' returned a non-zero code: 1
Makefile:14: recipe for target 'gpu_image' failed
make: *** [gpu_image] Error 1

See attached file A for full text of error.
A.txt

I can't understand why this happens.
I think the installation of docker and nvidia-docker was successful.
Because when I executed docker run hello-world,
the following message was displayed;

This message shows that your installation appears to be working correctly.

I would like to solve this problem by any means.

Would you tell me the solution?