From dd5cb5366fa3c75d7404ededc80eb60546cdfb94 Mon Sep 17 00:00:00 2001
From: Kham Chaimae <khamchaimae@MacBook-Pro-de-Kham.local>
Date: Wed, 23 Oct 2024 10:52:34 +0200
Subject: [PATCH] commit Doc

---
 Doc/01install.md | 36 ++++++++++++++++++++++++++++++++++++
 Doc/02run.md     |  5 +++++
 2 files changed, 41 insertions(+)
 create mode 100644 Doc/01install.md
 create mode 100644 Doc/02run.md

diff --git a/Doc/01install.md b/Doc/01install.md
new file mode 100644
index 0000000..f16d02e
--- /dev/null
+++ b/Doc/01install.md
@@ -0,0 +1,36 @@
+#Install the 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/
+
+mkdir -p $HOME/micromamba
+
+#Add these lines to ~/.bashrc
+
+export PATH=$HOME/.local/bin:$PATH
+
+export MAMBA_ROOT_PREFIX=$HOME/micromamba
+
+eval "$(micromamba shell hook -s posix)"
+
+#Create a m2bsgreprod micromamba environment and install apptainer 1.3.2
+
+micromamba create --name m2bsgreprod python=3.12  -c conda-forge
+
+micromamba activate m2bsgreprod
+
+micromamba install conda-forge::apptainer=1.3.2
+
+#Build the apptainer image
+
+mkdir -p results/containers
+
+sudo /home/gonzalez/Software/micromamba/envs/m2bsgreprod/bin/apptainer  build results/containers/m2bsgreprod.sif   containers/m2bsgreprod.def
+
+
+
+
+
diff --git a/Doc/02run.md b/Doc/02run.md
new file mode 100644
index 0000000..86bb4f2
--- /dev/null
+++ b/Doc/02run.md
@@ -0,0 +1,5 @@
+#Execute the Rscripts
+
+micromamba activate m2bsgreprod
+
+apptainer exec results/containers/m2bsgreprod3.sif make -f workflows/makefile
\ No newline at end of file
-- 
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