From 0cf734a0ed6b42f1e77f44f2227246a3218fcbea Mon Sep 17 00:00:00 2001
From: christine <christine.tranchant@ird.fr>
Date: Sat, 6 Jan 2024 12:36:18 +0100
Subject: [PATCH] Updating manual
---
README.rst | 45 ++++++++++++++++++++++++++-------------------
1 file changed, 26 insertions(+), 19 deletions(-)
diff --git a/README.rst b/README.rst
index 87a1cbb..234eba3 100644
--- a/README.rst
+++ b/README.rst
@@ -8,20 +8,22 @@ Previously developed as a modular and interactive application based on Jupyter B
I - Installing FrangiPANe
-####################
+#################
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
-"""""""""""""""""
+-----------------
* in a cluster mode
@@ -59,14 +64,15 @@ Choose only one mode
frangiPANe install_local
Add the prompt complementation
-"""""""""""""""""
+-----------------
+
::
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
-=======================
+"""""""""""""""""
::
@@ -121,7 +127,8 @@ Checking if frangiPANe has been correctly installed
II - Downloading a dataset to test frangiPANe
-####################
+#################
+
::
@@ -129,18 +136,18 @@ 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
@@ -169,7 +176,7 @@ Cluster mode
IV - Outputs
-####################
+#################
::
@@ -198,14 +205,14 @@ 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
@@ -216,6 +223,6 @@ 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..
--
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