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tbepler / topaz

Pipeline for particle picking in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Also featuring micrograph and tomogram denoising with DNNs.
GNU General Public License v3.0
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Topaz commands not running. #45

Closed ACheong97 closed 4 years ago

ACheong97 commented 4 years ago

I installed the topaz environment with Python 3.6. When I try to enter a command, I get the following:

topaz --help 'topaz' is not recognized as an internal or external command, operable program or batch file. I checked my paths and I am sure I am running on 3.6 so I am not sure what is going on. Any help would be nice!

tbepler commented 4 years ago

Did you install topaz following the anaconda instructions here? If so, you probably need to activate your conda environment before running topaz:

source activate topaz
topaz --help
ACheong97 commented 4 years ago

Yes, I activated my environment but with "conda activate topaz" since my Anaconda version is later than 4.4, but it still does not work.

tbepler commented 4 years ago

What is the output of 'conda list' inside your topaz environment?

ACheong97 commented 4 years ago

image Looks something like this.

tbepler commented 4 years ago

It looks like topaz is not installed in your environment. Try running the topaz install commands again with the environment activated.

ACheong97 commented 4 years ago

I installed topaz and when I use conda list, I can see topaz is now installed in the environment. I ran topaz --help and got: Program 'topaz' failed to run: No application is associated with the specified file for this operation

tbepler commented 4 years ago

I suspect this is an issue with conda on windows, but unfortunately I don't have a windows machine on hand to investigate. Apparently conda may not play nicely with powershell (https://stackoverflow.com/a/54811138, see also https://github.com/conda/conda/issues/626#issuecomment-480365662). Do other programs work from within the environment? E.g. will jupyter notebook launch?

ACheong97 commented 4 years ago

Notebook works fine. The same issue persists after adding the path to the topaz environment and after installing PSCondaEnvs from the 1st link.

tbepler commented 4 years ago

Have you tried installing topaz from source?

ACheong97 commented 4 years ago

I was able to successfully run topaz denoise --help after executing "pip install ." I am pretty sure it works now. Thanks for the help.

tbepler commented 4 years ago

Great, sorry the conda install was such a problem. I'll need to find a windows computer to look into this further.

TimYi commented 2 years ago

I find another approach to get it work on windows:

  1. find topaz executable file: C:\Users\$USER\Anaconda3\envs\topaz\Scripts\topaz.py
  2. rename it to topaz.bat
  3. change it's content to: python -m topaz.main %*