From 2f8d6036a75d4ca4854423c38a82c0f7ec4f0a75 Mon Sep 17 00:00:00 2001
From: BIOPZ-Gypas Foivos <foivos.gypas@unibas.ch>
Date: Fri, 1 Feb 2019 09:21:39 +0100
Subject: [PATCH] Add README.md

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+# Riboseq pipeline
+
+## Requirements
+
+* wget
+* git
+* singularity
+
+## Features
+
+Pipeline for Ribo-Seq data. It consists of two snakemake workflows:
+* prepare_annotation: Prepares the annotation files
+* process_data: Processes the Ribo-Seq data
+
+## Installation
+
+The recommended way is to create a virtual environment via conda and install the snakemake dependenies.
+**In order to run the workflows you need to run it in a system where singularity is available.**
+
+### Step 1: Download miniconda 3 installation file (if not already installed)
+
+
+for Linux:
+```
+wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+```
+
+### Step 2: Install miniconda 3
+
+Make sure that you run the 'bash' shell and execute:
+
+for Linux:
+```
+bash Miniconda3-latest-Linux-x86_64.sh
+```
+
+### Step 3: Create a new conda environment
+
+Create a new conda environment
+```
+conda create --name riboseq_pipeline --channel bioconda --channel conda-forge snakemake=4.8.1
+```
+
+Activate the virtual environment
+```
+conda activate riboseq_pipeline
+```
+
+You can deactivate later the virtual environment as
+```
+conda deactivate
+```
+
+Check if snakemake was installed properly
+```
+snakemake --help
+```
+
+### Step 4: Clone the repository
+```
+git clone ssh://git@git.scicore.unibas.ch:2222/AnnotationPipelines/riboseq_pipeline.git
+```
+
+## Configure pipeline
+
+ToDo
-- 
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