installation issue?

[jychoi0616]

Hi the cryoCARE team,

I recently installed the v.0.2. and encountered to two issues.

The first one is I cannot call the built in python-scripts even after doing conda activate cryocare_11. So I had to copy all the python script to each directory that I wanted to run. I did install using miniconda & pip install cryoCARE described in read.me. Is there another step I have to do for proper installation?

Also, the predict_config.json file included in the v.0.2. release folder seemed to not compatible with v.0.2 yet (Or I must have done something wrong). When I run the cryoCARE_predict with the provided predict_config.json, I get this following error:

"Your config is not in the format that cryoCARE >=0.2 requires. Fallback to cryoCARE 0.1 format. Invalid config format."

For your reference, the .json file I used was: { "path": "cryocare_model", "even": "TS_04_EVN_volume_b6_wbp/tomogram.mrc", "odd": "TS_04_ODD_volume_b6_wbp/tomogram.mrc", "n_tiles": [1, 1, 1], "output": "cryocare_model/denoised", "overwrite": false }

Best wishes, Joy

[EuanPyle]

Hi Joy, for the "Your config is not in the format that cryoCARE >=0.2 requires. Fallback to cryoCARE 0.1 format. Invalid config format." message, it is probably because "path" is set to cryocare_model. "path" needs to point to the tar.gz file created by the training step. To double check this is correct, in the directory you are entering the cryoCARE_predict.py command, try: ls [whatever the path you enter in the json file is] If it says 'no such file' or similar then the path is incorrect.

Regarding the install, did you have the earlier version of cryoCARE working? Maybe create a fresh environment (just re-do the install but call it 'cryocare_11_b' or something). if you did.

[jychoi0616]

Hi Euan,

Thanks for the quick reply! The path I wrote was the correct path including the tar.gz file. I actually found it worked when I specify the tar.gz file name (not just path itself). Thanks!

The earlier versions of cryoCARE used to work to call the built-in python script, but actually I found it doesn't do anymore either. I tried creating a fresh environment and re-installing, but it still didn't call the built-in python script. Do you know where the python script should be located in order to be called? I could manually locate the scripts to the directory?

Thank you, Joy

[EuanPyle]

If installed correctly, you really shouldn't need to move the scripts. One thing you could try is making sure the scripts (where they were installed) are on your PATH via: export PATH="path/to/the/scripts:$PATH" Note this will only work on a bash shell. If using tcsh or csh try: set path = ( path/to/the/scripts $path )

[jychoi0616]

Hi Euan,

Thank you for reply. The export PATH still didn't help (I restarted the terminal after changing the bashrc). I now have a feeling that this might be an issue specific to my workstation (rather than cryoCARE).

Thanks for helping, Joy