Installation problems in 2026

[kthorner]

Hi everyone, I'm sharing notes to hopefully help others (and perhaps get the attention of the developers). I had to modify things just to get it installed and run the initial pycisTopic steps. Will update if necessary.

After downloading scenicplus, I followed the advice in these two issues:
#586
#617

This addresses the problems I had with the python version, setuptools, and pybedtools. My final script looked something like this:

conda create --name scenic python=3.11.11 -y

source activate scenic

pip install --upgrade pip

pip install --upgrade setuptools wheel

conda install -c bioconda pybedtools -y

cd scenicplus

pip install . --no-deps

pip install -r requirements.txt --no-deps

[kthorner]

Downstream of this, QC was also not working due to connection issues with ensembl/biomart. I had success using biomaRt (in R) to create the TSS bed file.