added cloning and virtual environment procedure

README.md

@@ -17,12 +17,24 @@ This pipeline analyses the raw RNA-seq data and produce a file containing normal
 - `data/`: a folder containing samples.txt (sample descriptions) and subsetted paired-end fastq files used to test locally the pipeline. Generated using [Seqtk](https://github.com/lh3/seqtk):
 `seqtk sample -s100 {inputfile(can be gzipped)} 250000 > {output(always gunzipped)}`
 This folder should contain the `fastq` of the paired-end RNA-seq data, you want to run.
-- `envs/`: a folder containing the environments needed for the conda package manager. If run with the `--use-conda` command, Snakemake will install the necessary softwares and packages using the conda environment files. 
+- `envs/`: a folder containing the environments needed for the conda package manager. If run with the `--use-conda` command, Snakemake will install the necessary softwares and packages using the conda environment files.
 - `samples.tsv`:  a file containing information about the names, the paths and the conditions of the samples used as input for the pipeline. **This file has to be adapted to your sample names before running the pipeline**.
 
 
 # Usage
 
+## Download or clone the Github repository
+You will need a local copy of the `Snakemake_hisat-DESeq` on your machine. You can either:
+- use git in the shell: `git clone git@github.com:KoesGroup/Snakemake_hisat-DESeq.git`
+- click on "Clone or download" and select `download`
+
+## Installing and activating a virtual environment
+First, you need to create an environment where `Snakemake` and the python `pandas`package will be installed. To do that, we will use the conda package manager.   
+1. Create a virtual environment named `rnaseq` using the `global_env.yaml` file with the following command: `conda env create --name rnaseq --file envs/global_env.yaml`
+    Then, activate this virtual environment with source activate chipseq
+
+The Snakefile will then take care of installing and loading the packages and softwares required by each step of the pipeline.
+
 ## Configuration file
 Make sure you have changed the parameters in the `config.yaml` file that specifies where to find the sample data file, the genomic and transcriptomic reference fasta files to use and the parameters for certains rules etc.  
 This file is used so the `Snakefile` does not need to be changed when locations or parameters need to be changed.