conda package conflicts

[abraham-abin13]

Hi,
I am looking forward to trying you approach to my dataset. I am setting up the conda env for step 2 but running into several version and package conflicts. It seems the primary issue is stemming from the magic package. I am installing it from bioconda, then I have numpy and scipy conflicts.

Do you happen to have an updated enviornment with more recent packages that are compatible with each other?

In the meantime, I am going to keep troubleshooting and try a combination of pip and conda installs. I will update here if I find a successful set up.

Thanks - Abin

[abraham-abin13]

I seem to have found this specific conda env to work for all the scripts:

name: bio_env
channels:

• conda-forge
• bioconda
• defaults
  dependencies:
• python=3.12.2
• anndata=0.10.8
• matplotlib=3.8.4
• numpy=1.26.4
• pandas=2.2.1
• scanpy=1.10.1
• cobra=0.29.0
• swiglpk=5.0.10
• scipy=1.12.0
• python-libsbml>=5.19
• pip
• pip:
  • --ignore-installed
  • magic-impute==3.0.0