From 6f38a4a62148d8d13be51b59e33c3535bd50c71e Mon Sep 17 00:00:00 2001
From: KHAM Chaimae <k24022051@V-PP-47-L-145.salsa.univ-amu.fr>
Date: Fri, 8 Nov 2024 16:07:32 +0100
Subject: [PATCH] Ajout d'explications au niveau des scripts

---
 Doc/01install.md | 12 +++++++++---
 Doc/02run.md     |  8 ++++++--
 2 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/Doc/01install.md b/Doc/01install.md
index f16d02e..b8822ac 100644
--- a/Doc/01install.md
+++ b/Doc/01install.md
@@ -1,14 +1,18 @@
 #Install the micromamba
 
+#Download and extract micromamba:
+
 curl -L https://micromamba.snakepit.net/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
 
 mkdir -p $HOME/.local/bin
 
 mv bin/micromamba $HOME/.local/bin/
 
+#Create the root directory for micromamba:
+
 mkdir -p $HOME/micromamba
 
-#Add these lines to ~/.bashrc
+#Add the following lines to your ~/.bashrc to configure the environment:
 
 export PATH=$HOME/.local/bin:$PATH
 
@@ -16,15 +20,17 @@ export MAMBA_ROOT_PREFIX=$HOME/micromamba
 
 eval "$(micromamba shell hook -s posix)"
 
-#Create a m2bsgreprod micromamba environment and install apptainer 1.3.2
+#Create a new micromamba environment named m2bsgreprod with Python 3.12:
 
 micromamba create --name m2bsgreprod python=3.12  -c conda-forge
 
 micromamba activate m2bsgreprod
 
+#Install Apptainer 1.3.2:
+
 micromamba install conda-forge::apptainer=1.3.2
 
-#Build the apptainer image
+#Create the output directory and build the apptainer image:
 
 mkdir -p results/containers
 
diff --git a/Doc/02run.md b/Doc/02run.md
index 86bb4f2..f9b405c 100644
--- a/Doc/02run.md
+++ b/Doc/02run.md
@@ -1,5 +1,9 @@
-#Execute the Rscripts
+#Execution guide
+
+#Activate the Environment
 
 micromamba activate m2bsgreprod
 
-apptainer exec results/containers/m2bsgreprod3.sif make -f workflows/makefile
\ No newline at end of file
+#Use Apptainer to execute the make command inside the container and run the Makefile:
+
+apptainer exec results/containers/m2bsgreprod3.sif make -f workflows/makefile
-- 
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