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Hello,

Thank you for developing PySCENIC. I am having difficulty running the very first step. I have done the following:

I processed my data with Seurat and now have transferred to Scanpy and made a loom file to load in PySCENIC with no issues.

When I try to run the !pyscenic grn ... command, I get the following error:
/bin/sh: 1: pyscenic: not found

Alternatively, I copied the code for arboreto_with_multiprocessing.py and using nano, saved it as a .py file. When I try to execute it in terminal:

arboreto_with_multiprocessing.py
/path/loom.loom
/path/hs_hgnc_tfs.txt
--method grnboost2
--output adj.tsv
--num_workers 20
--seed 777

I get an error that reads: "arboreto_with_multiprocessing.py: command not found".

I checked and I am using all updated packages (anndata 0.7.4, scanpy 1.6.0, dask 1.0.0).

I have run one data set of ~7K cells in R already but it took over 3 weeks running. I am hoping the Python version can save time. I am new to python so any help will be much appreciated.

Thanks,

Hi @s849 ,

pyscenic: not found sounds like your environment isn't active, or you haven't properly installed pyscenic. You only need the ! if you're running from a jupyter notebook cell, otherwise it's just pyscenic grn . To run the script you can use the leading ./ like ./arboreto_with_multiprocessing.py , or if you haven't set execute permissions on the script, just python arboreto_with_multiprocessing.py .

Thanks! I was able to get it to work. I now have another naive question;

What goes here: {f_db_names}

Is this a path to the feather files or specific names?