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snap-stanford / mars

Discovering novel cell types across heterogenous single-cell experiments
MIT License
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requirements.txt #14

Closed elenichri closed 3 years ago

elenichri commented 3 years ago

Hello. I wanted to try MARS for my project. I created a new environment via conda, which I called mars. Then I installed requirements.txt via conda again while read requirement; do conda install --yes $requirement; done < requirements.txt 2>error.log

Then, when I ran the cellbench.ipynb, I got a lot of errors from the very beginning, while loading the required libraries. Looking at the error.log that I created above, I see that many libraries could not be found. For example, annoy==1.16.0. Doing conda search annoy, I see that there is no package called just annoy, but python-annoy instead. I am wondering if the requirements.txt file is outdated...? And which python version is MARS built on? I have python 3.8 in my system. I actually rarely use python, I am an R user, so I may miss something here.

Thank you very much!

elenichri commented 3 years ago

I managed to work around the above. However, new incompatibilities have risen (see my new issue: MARS code problems)