scnic v1-dev tutorial walk through

[madiapgar]

I need some help reviewing the SCNIC tutorial I wrote for lab meeting next week! The full tutorial can be found here.

Important

The installation instructions on the tutorial WILL NOT WORK since they assume that SCNIC's bioconda build has been updated (it hasn't)

Installing the development version of SCNIC:

1. clone the dev_MA_2026 branch of the SCNIC github repo

git clone -b dev_MA_2026 --single-branch https://github.com/lozuponelab/SCNIC.git

2. install the SCNIC development conda environment (when SCNIC's bioconda build is updated, this won't be necessary)

## move into the SCNIC directory you just cloned
cd SCNIC/

## create environment based on included dev_env.yml file - this installs all of SCNIC's dependencies 
## M chip mac users need to specify rosetta 
CONDA_SUBDIR=osx-64 conda env create -f dev_env.yml

3. use pip to install SCNIC v1-dev and verify installation

## make sure you're still within the SCNIC directory!
## this is what actually installs SCNIC for you
pip install -e .

## verify install
scnic --help