diff --git a/README.rst b/README.rst
index 0e40035393d4d7196ba7bc248ee36125a29b71ef..3af8e845bd92d62dc4fb5e520ac0fc4eb6cb56f7 100644
--- a/README.rst
+++ b/README.rst
@@ -3,33 +3,32 @@ README
.. image:: docs/source/_images/frangiPANe.png
+FrangiPANe
+=========
+
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 ?
+I - Installing FrangiPANe
-------------
-Requirement
-~~~~~~~~~~~~
+**Requirement**
-You have to install :
+- [Git](https://git-scm.com/)
+- [Singularity](https://...)
-* git (https://git-scm.com/)
-* singularity (https://...)
+**Clone the git repository**
-Clone the git repository
-~~~~~~~~~~~~
::
git clone https://forge.ird.fr/diade/frangipane.git
-Install the frangiPANe python package
-~~~~~~~~~~~~
+**Install the frangiPANe python package**
::
@@ -38,52 +37,241 @@ Install the frangiPANe python package
python3 -m pip install -e .
-Updating snakecdysis package (ref) using by frangiPANe
+**Updating snakecdysis package (ref) using by frangiPANe if necessary**
-::
+```bash
+python3 -m pip install snakecdysis@git+https://forge.ird.fr/phim/sravel/snakecdysis.git@main
- python3 -m pip install snakecdysis@git+https://forge.ird.fr/phim/sravel/snakecdysis.git@main
+**Install frangiPANe tool**
-Install frangiPANe tool in a cluster mode
-~~~~~~~~~~~~
+Choose only one mode
+
+* in a cluster mode
::
frangiPANe install_cluster -s slurm -e singularity
+* or in local mode
+
+::
+
+ frangiPANe install_local
+
+**add the prompt complementation**
+
::
sh path2frangipane_directory/frangiPANe/frangiPANe-complete.sh
-Download singularity container
+Download or build the singularity container in the container directory
~~~~~~~~~~~
::
- wget ...
+ # Download the container
+ wget https://itrop.ird.fr/frangiPANe/frangiPANe.sif
+ # OR build the container
+ singularity build frangiPANe.sif frangiPANe.def
+
+**Checking if frangiPANe has been correctly installed**
+
+
+::
+
+ frangiPANe
+
+II - Downloading a dataset to test frangiPANe
+-------------README
+========
+
+.. image:: docs/source/_images/frangiPANe.png
+
+FrangiPANe
+=========
+
+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.
+
+
+I - How to install FrangiPANe ?
+-------------
+
+**Requirement**
+
+- [Git](https://git-scm.com/)
+- [Singularity](https://...)
+
+
+**Clone the git repository**
+
+
+::
+
+ git clone https://forge.ird.fr/diade/frangipane.git
+
+**Install the frangiPANe python package**
+
+::
+
+ cd PATH_2_FRANGIPANE_DIRECTORY
+ python3 -m pip install -U pip setuptools build
+ python3 -m pip install -e .
+
+**Install frangiPANe tool**
+
+Choose only one mode
+
+* in a cluster mode
+
+::
+
+ frangiPANe install_cluster -s slurm -e singularity
+
+* or in local mode
+
+::
+
+ frangiPANe install_local
+
+**add the prompt complementation**
+
+::
+
+ sh path2frangipane_directory/frangiPANe/frangiPANe-complete.sh
+
-Checking if frangiPANe has been correctly installed
+Download or build the singularity container in the container directory
~~~~~~~~~~~
+::
+
+ # Download the container
+ wget https://itrop.ird.fr/frangiPANe/frangiPANe.sif
+ # OR build the container
+ singularity build frangiPANe.sif frangiPANe.def
+
+**Checking if frangiPANe has been correctly installed**
+
+
::
frangiPANe
+II - Download a dataset to test frangiPANe
+-------------
+
+::
+
+ frangiPANe test_install -d path_to_directory_that_contains_data
+
-Run FrangiPANe
+III - Run FrangiPANe
--------------
-Download a dataset to test frangiPANe
-~~~~~~~~~~~
+**local mode**
+
+::
+
+ frangiPANe -e
+ frangiPANe run_local -c frangiPANe/install_files/config.yaml --threads 2
+
+**cluster mode**
+
+::
+
+ frangiPANe run_cluster -c /scratch/tranchant/data_test_config.RN.yaml #--cluster-config
+/scratch/tranchant/frangipane/frangiPANe/install_files/cluster_config_ITROP.yaml
+
+::
+
+ #!/bin/bash
+
+ #SBATCH -J frangiPANe
+ #SBATCH -o frangiPANe."%j".out
+ #SBATCH -e frangiPANe."%j".err
+
+ #SBATCH --mail-user christine.tranchant@ird.fr
+ #SBATCH --mail-type=ALL
+
+ #SBATCH -p normal
+ #SBATCH -w node1
+ #SBATCH -c 1 # number of nodes
+
+ module load python/3.8.12
+ module load singularity/4.0.1
+ frangiPANe run_cluster -c /scratch/tranchant/data_test_config.RN.yaml
+
+Authors
+--------------
+
+For version 2.0:
+Sebastien Ravel and Christine Tranchant-Dubreuil (2024).
+
+Previous versions
+
+0.1: Christine Tranchant-Dubreuil and al. (2023). FrangiPANe, a tool for creating a panreference using left behind reads. NAR Genom Bioinform. doi: 10.1093/nargab/lqad013.
+
+Licence
+--------------
+
+- Licencied under CeCill-C
+ (http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html) and
+ GPLv3
+
+- Intellectual property belongs to IRD/UMR DIADE.
+
+- Written by Sebastien Ravel and Christine Tranchant-Dubreuil
+
+- Copyright 2024
+
+
+::
+
+ frangiPANe test_install -d path_to_directory_that_contains_data
+
+
+III - Run FrangiPANe
+--------------
+
+**local mode**
+
+::
+
+ frangiPANe -e
+ frangiPANe run_local -c frangiPANe/install_files/config.yaml --threads 2
+
+**cluster mode**
::
- frangiPANe test_install -d ../../data/
+ frangiPANe run_cluster -c /scratch/tranchant/data_test_config.RN.yaml #--cluster-config
+/scratch/tranchant/frangipane/frangiPANe/install_files/cluster_config_ITROP.yaml
+::
+
+ #!/bin/bash
+
+ #SBATCH -J frangiPANe
+ #SBATCH -o frangiPANe."%j".out
+ #SBATCH -e frangiPANe."%j".err
+
+ #SBATCH --mail-user christine.tranchant@ird.fr
+ #SBATCH --mail-type=ALL
+
+ #SBATCH -p normal
+ #SBATCH -w node1
+ #SBATCH -c 1 # number of nodes
+
+ module load python/3.8.12
+ module load singularity/4.0.1
+ frangiPANe run_cluster -c /scratch/tranchant/data_test_config.RN.yaml
Authors
-=======================
+--------------
For version 2.0:
Sebastien Ravel and Christine Tranchant-Dubreuil (2024).
@@ -93,7 +281,7 @@ Previous versions
0.1: Christine Tranchant-Dubreuil and al. (2023). FrangiPANe, a tool for creating a panreference using left behind reads. NAR Genom Bioinform. doi: 10.1093/nargab/lqad013.
Licence
-=======
+--------------
- Licencied under CeCill-C
(http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html) and