diff --git a/README.md b/README.md index aefab73..d9f7188 100644 --- a/README.md +++ b/README.md @@ -12,16 +12,21 @@ LepMak3r is a reusable pipeline to use the linkage map software [Lep-Map3](https ### How to install You will need a `Snakemake` installation, along with cloning this repository locally. -#### 1. Installing snakemake + +#### 1. Cloning LepMak3r +Download a zip of this repository using the "Code" button on the top-right and unzip it on your machine or: +```bash +git clone https://github.com/pdimens/LepMak3r.git +``` + +#### 2. Installing other dependencies Assuming you have `anaconda` or `miniconda` installed: ```bash -conda create -n environment_name -c bioconda snakemake +conda create -f conda_LepMak3r.yml ``` -where `environment_name` is whatever name you want to call the the snakemake conda environment. -#### 2. Cloning LepMak3r -Download a zip of this repository using the "Code" button on the top-right and unzip it on your machine or: +This will create an environment called `lepmak3r` that can be activated with: ```bash -git clone https://github.com/pdimens/LepMak3r.git +conda activate lepmak3r ``` ### How to run