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. LepMak3r will 100% not work on Windows (unless using it inside a WSL).

2. A Snakemake installation (easiest with conda install -n env_name -c bioconda snakemake) where env_name is your target conda environment. This method obviously requires a conda installation.

3. An R installation. Once the workflow is complete, I will begin polishing it to include software targets for a conda environment, but until then you will need to take care of this yourself. The R package dplyr will be installed if it's not found.

"Installing"

Because it's a Snakemake workflow, there is no "true" installation of LepMak3r, which can be be considered good or bad depending on one's preferences. To get LepMak3r, 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/LepMak3r.git

Alternatively, you can manually download and unzip the release.

LepMak3r comes with all the necessary scripts in the scripts folder, along with all the LepMap3 modules in the LM3 folder, and the Snakefile is configured to work out of the box (rather, out of that folder).