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morris-lab / CellOracle

This is the alpha version of the CellOracle package
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Installation issue on Mac book pro/ VS Code #181

Open jw235 opened 9 months ago

jw235 commented 9 months ago

Hey there, I pip installed cell oracle on my vs code 3.8.18 environment on an apple m2 silicon and I am not able to import cell oracle in my Jupyter notebook cell. Did anyone experience the same issue ? Thanks in advance.

momur commented 7 months ago

Hello,

I attempted installing celloracle on my local pc (Mac, M1) but it didnt work for so many reasons. I was only able to manage installing it on HPC servers.

hope that helps

DrNamwob commented 3 months ago

Were you able to get it working? I have an Apple M1 and finally got things working after quite a struggle. I can help if you're still working through this.

momur commented 3 months ago

No, I couldn't make it work on my pc. I installed it on servers, working on there. But I would love to hear if you have tips to share?

DrNamwob commented 3 months ago

Sure, I can try to help. There were several issues, but the main ones included installing velocyto, gimmemotifs, and then celloracle itself.

I had to use a different compiler to install velocyto -- G++. For gimmemotifs, I installed it from source, but had to go in and modify one of the files because it wasn't formatted properly. I also installed celloracle from source and had to change the requirements.txt file to not include gimmemotifs (because I already installed it directly). There were several subissues along the way, but those were relatively easy to fix, like installing the specific versions of various packages. I hope this helps!

If you have any specific issues, please feel free to reach out via email. I see that you're also a PhD student/candidate. bowmand8@msu.edu