From 2041d1fb641088b3bc12bc0366b011c727f271d2 Mon Sep 17 00:00:00 2001 From: coolneng Date: Sat, 13 Nov 2021 17:59:32 +0100 Subject: [PATCH] Update README --- README.org | 57 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) diff --git a/README.org b/README.org index e69de29..ba63727 100644 --- a/README.org +++ b/README.org @@ -0,0 +1,57 @@ +* Adapter parser + +This tool parses fastqc reports to extract the adapter sequences, from the *Overrepresented sequences*, and then outputs them to a text file. + +** Technologies + +- Pandas + +** Installation + +This project uses [Nix](https://nixos.org/) to ensure reproducible +builds. + +1. Install Nix (compatible with MacOS, Linux and + [WSL](https://docs.microsoft.com/en-us/windows/wsl/about)): + +#+begin_src bash +curl -L https://nixos.org/nix/install | sh +#+end_src + +2. Clone the repository: + +#+begin_src bash +git clone https://git.coolneng.duckdns.org/coolneng/adapter-parser +#+end_src + +3. Change the working directory to the project: + +#+begin_src bash +cd adapter-parser +#+end_src + +4. Enter the nix-shell: + +#+begin_src bash +nix-shell +#+end_src + +After running these commands, you will find yourself in a shell that +contains all the needed dependencies. + +** Usage + +#+begin_src bash +python src/parser.py -h +#+end_src + +#+RESULTS: +: +: \[\] usage: parser.py [-h] input output +: +: positional arguments: +: input directory containing the fastqc reports +: output file where to export the sequences +: +: optional arguments: +: -h, --help show this help message and exit