Add R installation in picard singularity image

picard_3.0.0.def

@@ -2,42 +2,50 @@ BootStrap: docker
 From: centos:8
 
 %help
-This is a singularity container packing picard tools v3.0.0 and java 17.
-Author : yannis.duffourd@u-bourgogne.fr
+This is a singularity container packing picard tools v3.0.0 and java 17. An R installation (4.3.3) is also provided as it is required by some picard tools. 
+Author : yannis.duffourd@u-bourgogne.fr, valentin.vautrot@u-bourgogne.fr
 
 This singularity recipe is open source and free. Please redistribute it as well.
 No warranty is provided.
 
-%setup
-mkdir ${SINGULARITY_ROOTFS}/data
-
-%files
-
 %post
 sed -i 's/mirrorlist/#mirrorlist/g' /etc/yum.repos.d/CentOS-*
 sed -i 's|#baseurl=http://mirror.centos.org|baseurl=http://vault.centos.org|g' /etc/yum.repos.d/CentOS-*
 
-yum update -y
-yum install -y epel-release wget
+dnf update -y --exclude=filesystem
+dnf install -y epel-release wget
+dnf --enablerepo=powertools install -y openblas-devel
+
+# # install R with (old) java included
+# dnf install -y R-4.3.3-1.el8.x86_64
+# dnf remove -y java-1.8.0-openjdk java-1.8.0-openjdk-devel java-1.8.0-openjdk-headless
+
+# # install R
+dnf install -y R-core-4.3.3-1.el8.x86_64
 
-# install java
-yum install -y java-17-openjdk java-17-openjdk-devel
+# # install java
+dnf install -y java-17-openjdk java-17-openjdk-devel
 
-# install picard
+# # install picard
 mkdir /opt/picard_3.0.0
 wget -O /opt/picard_3.0.0/picard.jar https://github.com/broadinstitute/picard/releases/download/3.0.0/picard.jar 
 
-# cleanup
+# cleanup       
 
 %labels
 Maintainer Yannis Duffourd
 Updater Yannis Duffourd <yannis.duffourd@u-bourgogne.fr>
-ContainerVersion v1.0
+ContainerVersion v1.1
 PicardTools 3.0.0 (Broad institute)
+R version 4.3.3
+Java version 17.0.1
 
 %environment
     export JAVA_HOME=$(dirname $(dirname $(readlink $(readlink $(which java)))))
     export PATH=$PATH:$JAVA_HOME/bin
 
 %runscript
-echo "OK"
+echo "java version : "
+java -version
+echo "R version : "
+R --version
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