* 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