Installation

Requirements

1. This workflow is intended only for GNU/Linux systems. Some of the rules invoke the GNU versions of commands like sed, grep, and sort, which may cause issues if you are on BSD systems like OpenBSD or macOS. The rules were not tested on BSD systems, so it might not be an issue, but I cannot say for certain. If using BSD systems, you may need to install the GNU versions of those commands and augment the rules to reflect those GNU commands. LepWrap will 100% not work on Windows (unless using it inside a WSL).

2. A conda installation

"Installing"

Because it's a Snakemake workflow, there is no "true" installation of LepWrap, which can be be considered good or bad depending on one's preferences. To get LepWrap, simply clone the git repository and begin using it as the working directory for your project. That's it!

git clone https://github.com/pdimens/LepWrap.git
cd LepWrap

Alternatively, you can manually download and unzip the release.

Then, you will need to create the pre-configured conda environment provided with the LepWrap repository:

conda env create -f conda_setup.yml -n lepwrap

The new environment will be called lepwrap and can be activated with

conda activate lepwrap

LepWrap comes with all the necessary scripts in the scripts folder, along with all the Lep-Map3 modules in the LM3 folder, a Snakefile with the target rule all, a rules folder, and all of it is configured to work out of the box (rather, out of that folder)!