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theislab / chemCPA

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.
https://arxiv.org/abs/2204.13545
MIT License
88 stars 23 forks source link

Creating chemCPA environemnt #105

Closed v-mahughes closed 1 year ago

v-mahughes commented 1 year ago

I am having issues setting up the chemCPA environment. I cloned the repo onto my machine and executed the command: 'conda env create -f environment.yml.' I get the following error:

Solving environment: failed

ResolvePackageNotFound:

So I removed moses and RDKit from the .yml file. I then run 'conda env create -f environment.yml.' again, with the intention to install MOSES / Rdkit manually after it is done running via these instructions found on the MOSES github repo:

'The simplest way to install MOSES (models and metrics) is to install RDKit: conda install -yq -c rdkit rdkit and then install MOSES (molsets) from pip (pip install molsets). If you want to use LatentGAN, you should also install additional dependencies using bash install_latentgan_dependencies.sh.

If you are using Ubuntu, you should also install sudo apt-get install libxrender1 libxext6 for RDKit.'

However, it gets stuck on 'Solving Environment.' Please let me know how I should proceed!

tuln128 commented 1 year ago

Hi, I think the simplest way is to adjust the content of the environment.yml file. Instead of removing moses from the file, you'd better move that line below the line containing pip: , like this:

(Do not work) dependencies:

---> (Should work) - pip:

Hope it helps,

siboehm commented 1 year ago

Sorry for responding so late to this issue, I must've completely missed it when you posted it. Both moses and sfaira aren't part of the environment.yml anymore, so this original issue should be resolved. If anyone else is having issues setting up this environment on Linux / Mac then I'm happy to help, just open a new issue.