Adding documentation to install frangiPANe

README.rst

-frangiPANe was developed as a modular and interactive application to
-simplify the construction of a panreference using the map-then-assembly
-approach. It consists in a Jupyter Notebook application that centralizes
-code,documentation and interactive visualizations together
+README
+========
 
+.. image::      docs/source/_images/frangiPANe.png
+
+FrangiPANe is a tool designed to simplify the construction of a pan-reference using the map-then-assembly approach.
+It was previously developed as a modular and interactive application based on Jupyter Book.
+
+It has now been recoded and integrated into a Snakemake pipeline.
+
+
+How to install FrangiPANe ?
+-------------
+
+Requirement
+~~~~~~~~~~~~
+
+You have to install :
+
+* git (https://git-scm.com/)
+* singularity (https://...)
 
-How to use FrangiPANe ?
-=======================
 
 Clone the git repository
-------------------------
+~~~~~~~~~~~~
 
 ::
 
-   git clone ...
+   git clone https://forge.ird.fr/diade/frangipane.git
 
-Run FrangiPANe
---------------
+Install the frangiPANe python package
+~~~~~~~~~~~~
+
+::
+
+    cd PATH_2_FRANGIPANE_DIRECTORY
+    python3 -m pip install -U pip setuptools build
+    python3 -m pip install -e .
+
+
+Updating snakecdysis package (ref) using by frangiPANe
+
+::
+
+    python3 -m pip install snakecdysis@git+https://forge.ird.fr/phim/sravel/snakecdysis.git@main
+
+Install frangiPANe tool in a cluster mode
+~~~~~~~~~~~~
+
+::
+
+    frangiPANe install_cluster -s slurm -e singularity
+
+::
+
+    sh path2frangipane_directory/frangiPANe/frangiPANe-complete.sh
+
+
+Download singularity container
+~~~~~~~~~~~
 
 ::
 
-    snakemake -r -c1
+    wget ...
 
--  Download a dataset to test frangiPANe
+Checking if frangiPANe has been correctly installed
+~~~~~~~~~~~
 
 ::
 
-   wget https://itrop.ird.fr/frangiPANe/data_test.tar.gz
-   tar zxvf data_test.tar.gz
+    frangiPANe
+
+
+Run FrangiPANe
+--------------
+
+Download a dataset to test frangiPANe
+~~~~~~~~~~~
+
+::
+
+   frangiPANe test_install -d ../../data/
+
 
 Authors
 =======================