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cellgeni / sceasy

A package to help convert different single-cell data formats to each other
GNU General Public License v3.0
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Default conda installation instructions for searat -> h5ad convert not working #30

Closed inodb closed 3 years ago

inodb commented 3 years ago

On OSX it took a bit of trial & error to get the environment of sceasy working.

I used mamba over conda because it is faster, but should result in the same env: 

 mamba create -n sceasy r-sceasy python=3

Some deps were not installed properly, so had to reinstall openblas and r-stringi:

 conda install anndata==0.6.19 -c bioconda
 mamba install -c conda-forge openblas
 mamba remove r-stringi
 mamba install r-stringi r-sceasy

Then there is some funkiness with anndata not working with the scipy env:

 pip install scipy==1.2.1

After that things worked fine. Maybe adding some of these notes to the README could be helpful. That being said: compared to most bioinf tools this was pretty easy to install, so kudos 👏

nh3 commented 3 years ago

Many thanks for your suggestion! Readme updated.