Installation

You can obtain the code for the pipeline from https://github.com/Vicky-Hunt-Lab/HuntLab-smallRNA. To download, click the code button and copy the URL. You can then download it to a computer with git installed on it by opening the command line and running:

$ git clone https://github.com/Vicky-Hunt-Lab/HuntLab-smallRNA.git

It is recommended to use mamba to install this pipeline. To perform the installation, ensure mamba is installed on the machine, navigate to the directory containing the code and environment.yml file, then run:

$ mamba env create -f environment.yml

This will create a conda environment called huntlab-smallrna. This can then be activated each time you want to use the software with the command:

$ mamba activate huntlab-smallrna

By default, this provides the hlsmallrna executable. This provides all of the tasks listed in this documentation, each one can be run by typing hlsmallrna followed by the name and options for the task.