📦 Installation

📦 Installation#

Clone the repository#

Depending on whether you have set up SSH or HTTPS with PAT, you can clone the repository.

SSH:

git clone git@github.com:HCA-integration/scAtlasTb.git

HTTPS:

git clone https://github.com/HCA-integration/scAtlasTb.git

Requirements#

  • Linux (preferred) or MacOS (not rigorously tested, some bioconda dependencies might not work out-of-the-box)

  • Conda, e.g., via miniforge (recommended) or miniconda

The modules are tested and developed using task-specific conda environments, which should be quick to set up when using libmamba.

📝 Note If you use conda version 22.11 or above, make sure you set the conda solver to libmamba for significantly faster installation. For newer versions or if you are using mamba directly, libmamba should already be the default.

Install dependencies#

All the conda environments used by the toolbox are under envs/*.yaml. You will at least require the snakemake environment.

conda env create -f envs/snakemake.yaml

You can install the other environments as needed, for different parts of the workflow (modules, rules).