Installation

The following sections describe how to install the TallyNN analysis pipelines.

First clone the Github repo and activate the UMI-tools submodule:

git clone https://github.com/Acribbs/TallyNN.git
git submodule init
git submodule update

We recommend installing [miniconda](https://docs.conda.io/en/latest/miniconda.html), then creating a new environment and install mamba:

conda create -n tallynn
conda install mamba -c conda-forge

Next install the required software:

mamba env upate conda/environment/tallynn.yml

Then, at the moment, you will need to manually install the fork of umi tools. The fork is provided as a submodule within TallyNN. You can install it as follows:

git clone https://github.com/Acribbs/UMI-tools.git
git checkout AC-dualoligo
python setup.py install

To install tallynn code, navigate to the tallynn directory and run:

python setup.py develop