Updating manual

README.rst

@@ -8,20 +8,22 @@ Previously developed as a modular and interactive application based on Jupyter B
 
 
 I - Installing FrangiPANe
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+#################
 
 Install the frangiPANe python package
-=======================
+=================
 
 Requirement
-----------------
+-----------------
+
 - `Git <https://git-scm.com/>`_
 
 - `Singularity <https://...>`_
 
 
 Clone the git repository
-"""""""""""""""""
+-----------------
+
 
 ::
 
@@ -40,11 +42,14 @@ Clone the git repository
 
         python3 -m pip install snakecdysis@git+https://forge.ird.fr/phim/sravel/snakecdysis.git@main
 
+
+
 Install frangiPANe tool
-=======================
+=================
+
 
 Choose only one mode
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+-----------------
 
 * in a cluster mode
 
@@ -59,14 +64,15 @@ Choose only one mode
     frangiPANe install_local
 
 Add the prompt complementation
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+-----------------
+
 ::
 
     sh path2frangipane_directory/frangiPANe/frangiPANe-complete.sh
 
 
 Download or build the singularity container in the container directory
-"""""""""""""""""
+-----------------
 
 ::
 
@@ -76,7 +82,7 @@ Download or build the singularity container in the container directory
     singularity build frangiPANe.sif frangiPANe.def
 
 Checking if frangiPANe has been correctly installed
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+"""""""""""""""""
 
 ::
 
@@ -121,7 +127,8 @@ Checking if frangiPANe has been correctly installed
 
 
 II - Downloading a dataset to test frangiPANe
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+#################
+
 
 ::
 
@@ -129,18 +136,18 @@ II - Downloading a dataset to test frangiPANe
 
 
 III - Run FrangiPANe
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+#################
+
 
-local mode
-=======================
+**local mode**
 
 ::
 
     frangiPANe -e
     frangiPANe run_local -c frangiPANe/install_files/config.yaml --threads 2
 
-Cluster mode
-=======================
+**cluster mode**
+
 ::
     module load python/3.8.12
 
@@ -169,7 +176,7 @@ Cluster mode
 
 
 IV - Outputs
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+#################
 
 ::
 
@@ -198,14 +205,14 @@ IV - Outputs
 
 
 Authors
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+#################
 
 * For version 2.0: *Sebastien Ravel and Christine Tranchant-Dubreuil (2024).*
 
 * For version 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
@@ -216,6 +223,6 @@ Licence
 -  Copyright 2024
 
 Reference
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+#################
 
 .. [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..