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BodenmillerGroup / ImcSegmentationPipeline

A pixel classification based multiplexed image segmentation pipeline
https://bodenmillergroup.github.io/ImcSegmentationPipeline/
MIT License
83 stars 35 forks source link

Conda doesnt install imctools in Mac #4

Closed Rcasan closed 3 years ago

Rcasan commented 5 years ago

Using the environment file found in setup conda does not install imctools when run in mac (without giving any warning).

The workaround was to install it manually by opening a console from the imctools environment and running:

pip install git+https://github.com/BodenmillerGroup/imctools.git@develop-test

votti commented 5 years ago

A second person was also affected by this. Does anybody know why this problem occurs in Mac?

glynnelson commented 5 years ago

I used the Anaconda GUI installer on Mac, and neither imctools or conda-imctools are listed as part of the install. @Rcasan - you say to install fromt he imctools environment- how do you know where this is if it hasn't installed it? I looked in Anaconda environment and it isn't listed (because it isn't installed presumably).

votti commented 5 years ago

Hi, I think following the guide and installing this environment file _(https://github.com/BodenmillerGroup/ImcSegmentationPipeline/blob/development/setup/conda_imctools.yml) should produce an imctools conda environment. It just does however not install the imctools python package in MacOS. (I will definitely change the environement name in the future to prevent these kind of missunderstandings.)

To get the imctools python package installed into the imctools environment: 1) open Anaconda Navigator 2) go the 'Environmentssection 3) you should have there animctoolsenvironment listed 4) click on theplaysign triangle and chooseOpen Terminal 5) In the terminal typeconda activate imctools 6) Type & Run:pip install imctools -> This will install theimctoolspython package into theimctools` conda environment.

glynnelson commented 5 years ago

That seems to have worked, thanks Votti. I should have followed this line from the imc_preprocessing notebook:

To install the imctools envrionment: -> Install conda: https://www.anaconda.com/download/#linux -> The conda environment file is found in ImcSegmentationPipeline/Setup/conda_imctools.yml -> On a conda console type: conda env create -f PATHTO/conda_imctools.yml

whereas I was trying to use the GUI after installing Anaconda but failing. Once I had done this, I have it working. Oh, and in answer to my own question, the 'imctools environment' was just the path for the file conda_imctools.yml. Now I need to get some datafiles!

votti commented 4 years ago

This is still - sometimes - an issue in Mac :/ Does anybody have an idea how to force anaconda in MacOS to install pip dependencies?