ImportError: No module named tensorflow , when installing scAlign about scalign HOT 5 CLOSED

It seems like you have the reticulate package installed, but you do not load it before specifying your conda environment. I would first try running library("reticulate") before use_condaenv("py36", required = T).

from scalign.

Hi, thanks for help. I am still getting the same problem, even after loading the reticulate library using library("reticulate")

from scalign.

Hi, sorry for the late reply.

I don't usually work with conda environments but what this sounds like is a LD_LIBRARY_PATH issue. Essentially, I think scAlign is trying to look at the system python packages and not the conda environment python packages (where Tensorflow is located).

Could you make sure that LD_LIBRARY_PATH contains the conda environment libs directory?

Here is a helpful stack overflow on the issue: https://stackoverflow.com/questions/46826497/conda-set-ld-library-path-for-env-only.

I'll try to recreate this scenario locally as well. Let me know if this works!

from scalign.

I have been thinking about this problem for a bit and I believe I might have made an incorrect assumption. Usually when I work with Conda environments I install R, Python, and RStudio directly to the Conda environment, activate the environment from the command line and then launch RStudio in the directory where I wish to do work:
(scAlign) tyler@t-i5-1050:~/scAlign$ rstudio
Is this the workflow you are using when trying to install scAlign?

from scalign.

Hi, thanks for looking into this! I had not been using a condo environment to install and run rstudio. I have tried it now, and everything works perfectly! Using this method, I did not have to set LD_LIBRARY_PATH

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