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

The Easy Way™️

RECOMMENDED

Create an environment called lepwrap and install LepWrap into it in a single command.

conda create -n lepwrap -c bioconda lepwrap

Activate the environment with conda activate lepwrap

The Other Way

Step 1: Cloning LepWrap

Download a zip of this repository using the "Code" button on the top-right and unzip it on your machine or:

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

Step 2: Installing everything

Assuming you have anaconda or miniconda installed:

cd LepWrap
conda env create -f conda_setup.yml

This will create an environment called lepwrap that can be activated with:

conda activate lepwrap

Then, install all the software dependencies into the environment's path with

.misc/install.sh