Remove maxATAC interpretation for independent development

MiraldiLab / maxATAC

Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks

Apache License 2.0

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Remove maxATAC interpretation for independent development #59

Closed tacazares closed 2 years ago

tacazares commented 3 years ago

We have compatibility and package issues with the interpretation code as referenced in #58. There are some shap + numpy based conflicts that are causing a lot of our installs to fail. We want to make the interpretation code into its own repository or a branch of the maxATAC codebase. We will start to work a version of maxATAC that does not depend on the interpretation function.

FaizRizvi commented 2 years ago

With this latest fix I was able to install maxatac both locally as well as as on BMI. I believe @tacazares has installed this on OSC without a problem.

Notes: This version of maxATAC was very easy to install for me. I ran:

conda create -n maxatac_IS59 python=3.9 conda activate maxatac_IS59 #Creating and activating the conda env

pip3 install -e .

#For local install I had to conda deactivate and reactivate the env #Now just run maxatac

maxatac

tacazares commented 2 years ago

One note on installation, I had issues with installing pysam on my local machine. The fix was to first update all of your c compilers and xcode utils. I used the package manager brew to do this.

I used brew update and brew upgrade to update these packages.