update README.md

README.md

 # transfertAnnot
 
 Tool used to tranfert annotation between different versions of assemblies.
+
+## Prerequist
+* Anaconda3
+Easy way to have a clean environment for Python 3.5 and other tools/lib (seqtk, snakemake numpy pandas).
+
+See instructions here: [http://docs.continuum.io/anaconda/install/linux/](http://docs.continuum.io/anaconda/install/linux/)
+
+* GMAP
+
+See here for installation: [http://research-pub.gene.com/gmap/](http://research-pub.gene.com/gmap/)
+
+## Create virtual environement fo the pipeline
+
+After anaconda is installed, we create an virtual environment with python3.5
+
+```console
+$ conda create --name iwgsc-tranfertAnnot.venv python=3.5 numpy pandas snakemake seqtk
+```
+
+Then we load the virtualenv we just created:
+
+```console
+conda activate iwgsc-tranfertAnnot.venv
+```
+
+## Installation
+
+```
+git clone git@forgemia.inra.fr:gdec-bioinfo/iwgsc/transfertannot.git
+```
+
+## Usage
+
+The pipeline consists in a Snakemake reciep and the input files are indicated in a config file [config.yml](config.yaml).
+
+For now, the pipeline requires:
+
+* Current reference
+   * GFF of annotation
+   * FASTA of reference sequence
+* New target reference sequence
+   * FASTA of reference sequence
+   * GMAP index 
+
+
+
+
+
+