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