Add README.md

README.md

+# 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