adding first doc installation part into README

README.md

@@ -4,21 +4,17 @@
 [![SnakemakeVersions](https://img.shields.io/badge/snakemake-≥5.10.0-brightgreen.svg?style=flat)](https://snakemake.readthedocs.io)
 [![Singularity](https://img.shields.io/badge/singularity-≥3.3.0-7E4C74.svg)](https://sylabs.io/docs/)
 
-![](docs/source/_images/RNAja.png)
-
-About RNAja
-===============
+## About RNAja
 
-RNAja is a pipeline written in snakemake, allowing to analyse RNAseq data, perform differential expression analysis on it and output a report in Rmarkdown.
-The output are compatible with the database diffexDB https://bioinfo-web.mpl.ird.fr/cgi-bin2/microarray/public/diffexdb.cgi.
+RNAja is a pipeline written in snakemake, allowing to analyse RNAseq data, perform differential expression analysis using several mappers and counters. RNAja is the only pipeline able to compare method effects over DE genes.    
 
-**Homepage:**
+![](docs/source/_images/RNAja.png)
 
-## Authors
+### Authors
 
-- Aurore Comte (IRD)
+* Aurore Comte (IRD), Christine Tranchant (IRD), Julie Orjuela (IRD)
 
-Some parts of RNAja code and documentation were inspired or came from the pipelines below.
+Some parts of RNAja code and documentation were inspired or came from the pipelines below. 
 
 - Culebront (Julie Orjuela *et al.*) https://github.com/SouthGreenPlatform/culebrONT
 
@@ -26,20 +22,103 @@ Some parts of RNAja code and documentation were inspired or came from the pipeli
 
 - BulkRNA (Camille Cohen) https://github.com/CamilleCohen/ProjetTuteur-_BulkRNA
 
-Thanks and acknowledgements
-==========================
+RNAja uses SnakEcdysis package https://snakecdysis.readthedocs.io/en/latest/package.html to perform installation and execution in local and cluster mode developed by Sébastien Ravel (CIRAD).
+
+
+## 1. Install dependencies and clone RNAja
+
+Check dependencies for iKISS : Python >= 3.10.12 and Snakemake >= 7.32.4
+
+Here, you can install RNAja from the gitlab source code such as :  
+
+``` bash
+    git clone git@forge.ird.fr:phim/rnaja-pipeline.git
+    cd rnaja-pipeline
+    python3 -m pip install .
+```
+
+Don't forget to export RNAja into the $PATH environment path by  
+``` bash
+    export PATH=/home/$USER/.local/bin/:$PATH`
+``` 
+
+### 1.1 Installing in local mode 
+
+```bash
+   RNAja install_local --help
+   RNAja install_local
+```
+
+### 1.2 Installing in cluster mode
+
+Install RNAja in cluster mode using **singularity** container from rnaja_utilities https://itrop.ird.fr/RNAja_utilities/
+
+```bash
+   RNAja install_cluster --help
+   RNAja install_cluster --scheduler slurm --env singularity
+```
+
+Please run command line 'RNAja edit_cluster_config' before the first run of RNAja see https://forge.ird.fr/phim/rnaja-pipeline/README.md and configure by default threads and memory resources.
+
+## 2. Running a datatest
+
+Running test with a datatest from RNAja_utilities in a repertory TEST
+
+```bash
+   RNAja test_install --help
+   RNAja test_install -d TEST
+```
+
+### 2.1 Running your data in LOCAL mode
+
+launching suggested command line done by RNAja, in LOCAL mode: 
+
+```bash
+   RNAja run_local --help
+   RNAja run_local -t 8 -c TEST/data_test_config.yaml --singularity-args "--bind $HOME"
+```
+
+In local mode, it's possible to allocate threads to some rules using `--set-threads` snakemake argument such as
+
+```
+    RNAja run_local -t 8 -c TEST/data_test_config.yaml --set-threads hisat2_index=4 hisat2_map_paired=2 
+```
+
+### 2.2 Running your data in CLUSTER mode
+
+Now you can launch suggested command line done by RNAja in `cluster` mode BUT before  you need to configurate cluster parameters running command line 'RNAja edit_cluster_config' before the first run and modify threads, ram, node and computer resources.
+RNAja does a copy of `cluster_config.yaml` file into your home `"/home/$USER/.config/rnaja_pipeline/cluster_config.yaml"`
+
+```bash
+   RNAja run_cluster --help 
+   RNAja edit_cluster_config
+```
+
+If singularity was selected in installation of RNAja, it could be needed to give argument `--singularity-args \"--bind $HOME\"` to Snakemake, by using :
+
+```bash
+   RNAja run_cluster --help
+   RNAja run_cluster -c TEST/data_test_config.yaml --singularity-args "--bind $HOME"
+   
+   # here a example adapted to @IFB HPC
+   #RNAja run_cluster -c TEST/data_test_config.yaml --singularity-args "--bind /shared:/shared"
+   
+   #you can also use snakemake parameters as 
+   #RNAja run_cluster -c TEST/data_test_config.yaml --singularity-args "--bind $HOME" --rerun-incomplete --nolock
+```
+
+**Important Note** : In i-Trop cluster, run RNAja using ONLY a node, data has to be in "/scratch" of chosen node. Use `nodelist : nodeX` parameter inside of `cluster_config.yaml`̀ file.
+
+-----------------------
+## Acknowledgements
 
 Thanks to Ndomassi Tando (i-Trop IRD) by administration support.
 
-The authors acknowledge the IRD i-Trop HPC <https://bioinfo.ird.fr/> (South Green Platform <http://www.southgreen.fr>) at IRD
-Montpellier for providing HPC resources that have contributed to this work.
+The authors acknowledge the IRD i-Trop HPC <https://bioinfo.ird.fr/> (South Green Platform <http://www.southgreen.fr>) at IRD Montpellier for providing HPC resources that have contributed to this work.
 
 Thanks to Alexis Dereeper for his help and the development of diffexDB <https://bioinfo-web.mpl.ird.fr/cgi-bin2/microarray/public/diffexdb.cgi>.
 
-License
-=======
+## License
 
 Licenced under MIT https://opensource.org/license/mit/.
-
 Intellectual property belongs to IRD and authors.
-