From a400c6a07191851ffecea5e04354e4e9db3c6adb Mon Sep 17 00:00:00 2001
From: SOLER Fiona <s23014817@V-PJ-47-029.salsa.univ-amu.fr>
Date: Mon, 28 Oct 2024 15:08:23 +0100
Subject: [PATCH] containers
---
results/containers/m2bsgreprod.def | 38 ++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)
create mode 100644 results/containers/m2bsgreprod.def
diff --git a/results/containers/m2bsgreprod.def b/results/containers/m2bsgreprod.def
new file mode 100644
index 0000000..cd2c834
--- /dev/null
+++ b/results/containers/m2bsgreprod.def
@@ -0,0 +1,38 @@
+Bootstrap: docker
+From: rocker/rstudio:4.1.3
+
+%post
+ # Update the system and install necessary libraries for building R packages
+ apt-get update && \
+ apt-get install -y \
+ libcurl4-openssl-dev \
+ libssl-dev \
+ libssh2-1-dev \
+ libxml2-dev \
+ libxt-dev \
+ libgit2-dev \
+ zlib1g-dev \
+ && apt-get clean \
+ && rm -rf /var/lib/apt/lists/*
+
+ # Install necessary R packages
+ R -e "install.packages(c('devtools', 'plyr', 'BiocManager'), repos='https://cran.biotools.fr')"
+
+ # Install Bioconductor packages
+ R -e "BiocManager::install(c('snpStats', 'SNPRelate'))"
+
+ # Install GenABEL.data from the CRAN archive
+ R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/GenABEL.data/GenABEL.data_1.0.0.tar.gz', repos=NULL, type='source')"
+
+ # Install the archived GenABEL package from the CRAN archive
+R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/GenABEL/GenABEL_1.8-0.tar.gz', repos=NULL, type='source')"
+
+R -e 'install.packages("genetics")'
+
+R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/LDheatmap/LDheatmap_1.0-6.tar.gz', repos=NULL, type='source')"
+
+
+%environment
+ # Set R library paths if necessary
+ export R_LIBS_USER=/usr/local/lib/R/site-library
+
--
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