From 4f0936718b89f37399744332113ae313890112c3 Mon Sep 17 00:00:00 2001
From: coolneng <akasroua@gmail.com>
Date: Mon, 3 May 2021 23:27:19 +0200
Subject: [PATCH] Add installation instruction to README

---
 README.org | 42 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/README.org b/README.org
index 0d167ac..9eba96e 100644
--- a/README.org
+++ b/README.org
@@ -1,3 +1,45 @@
 * locigenesis
 
 locigenesis is a tool that generates an immune repertoire and runs it through a sequence reader simulation tool, to generate sequencing errors.
+
+** Installation
+
+This project uses [[https://nixos.org/][Nix]] to ensure reproducible builds.
+
+*** Using Nix
+
+1. Install Nix (compatible with MacOS and Linux):
+
+#+begin_src shell
+curl -L https://nixos.org/nix/install | sh
+#+end_src
+
+1. Clone the repository:
+
+#+begin_src shell
+git clone https://git.coolneng.duckdns.org/coolneng/locigenesis
+#+end_src
+
+3. Change the working directory to the project:
+
+#+begin_src shell
+cd locigenesis
+#+end_src
+
+4. Enter the nix-shell:
+
+#+begin_src shell
+nix-shell
+#+end_src
+
+After running these commands, you will find yourself in a shell that contains all the needed dependencies.
+*** Without Nix
+
+The following dependencies need to be installed:
+
+- R
+- [[https://github.com/GreiffLab/immuneSIM/][immuneSIM]]
+- [[https://github.com/tidyverse/stringr][stringr]]
+- Java Development Kit (JDK)
+
+** Usage