From 30f8b1ab1109301f6dbdc0bcca0127fe0323e4f4 Mon Sep 17 00:00:00 2001
From: christine <christine.tranchant@ird.fr>
Date: Sat, 6 Jan 2024 12:30:47 +0100
Subject: [PATCH] Updating manual
---
README.rst | 23 ++++++++++++-----------
1 file changed, 12 insertions(+), 11 deletions(-)
diff --git a/README.rst b/README.rst
index 11c2e1d..87a1cbb 100644
--- a/README.rst
+++ b/README.rst
@@ -41,7 +41,7 @@ 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
"""""""""""""""""
@@ -76,7 +76,7 @@ Download or build the singularity container in the container directory
singularity build frangiPANe.sif frangiPANe.def
Checking if frangiPANe has been correctly installed
-"""""""""""""""""
+=======================
::
@@ -121,7 +121,7 @@ Checking if frangiPANe has been correctly installed
II - Downloading a dataset to test frangiPANe
-=======================
+####################
::
@@ -129,17 +129,18 @@ II - Downloading a dataset to test frangiPANe
III - Run FrangiPANe
-=======================
+####################
-**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
@@ -168,7 +169,7 @@ III - Run FrangiPANe
IV - Outputs
-=======================
+####################
::
@@ -197,14 +198,14 @@ IV - Outputs
Authors
-=======================
+####################
* 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
@@ -215,6 +216,6 @@ Licence
- Copyright 2024
Reference
-=======================
+####################
.. [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..
--
GitLab