Error installing conda environment

[rachel662]

Hi, I get an error when trying to install the conda environment - it says environment.yml file not found?

I have downloaded the zip file from this page and downloaded the example data, but then also when I run the 2nd cell in the pipeline it doesn’t recognise imcsegpipe as a module?

Thanks for your help Rachel

[nilseling]

Hi @rachel662 could you please explain how you are trying to install the conda environment?

[rachel662]

Hi there,

I used conda install imcsegpipe. I also tried via pip? Apologies if I’m using the wrong means to install it

Thanks for your help, Rachel

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On 17 Feb 2023, at 08:17, Nils Eling @.***> wrote:



Hi @rachel662https://github.com/rachel662 could you please explain how you are trying to install the conda environment?

— Reply to this email directly, view it on GitHubhttps://github.com/BodenmillerGroup/ImcSegmentationPipeline/issues/124#issuecomment-1434280836, or unsubscribehttps://github.com/notifications/unsubscribe-auth/APDCVFSHCH4HRVW7ESEFNELWX4XXZANCNFSM6AAAAAAU6X4EVE. You are receiving this because you were mentioned.Message ID: @.***>

[nilseling]

Please have a look at https://github.com/BodenmillerGroup/ImcSegmentationPipeline#usage. Step 3. shows the call conda env create -f environment.yml which allows you to build the right conda environment. The error "environment.yml file not found" means that you are not in the same directory as the environment.yml file.

[nilseling]

Closing now assuming this has been resolved

[Ewaoluwa1]

I tried to setup the environment using the environment.yml file through the web version of Anaconda (Anaconda3. 2023.07) but I encountered the following issue: CondaEnvException: Pip failed. Please, what could be wrong?

[nilseling]

It is hard to figure out what's going on. Could you please post the full output of the error here?

[Ewaoluwa1]

I changed the setup from Anaconda to Miniconda and it worked. Thank you