Install GD perl module for bismark Mbiais plots

bismark_0.24.2.def

@@ -25,11 +25,30 @@ apt-get install -y --no-install-recommends \
     samtools \
     python2.7 \
     python2.7-dev \
-    perl \
     libtbb2
-    # hisat2
+
 ln -s /usr/bin/python2.7 /usr/bin/python
 
+# install perl and required librairies and tools
+apt-get install -y --no-upgrade --no-install-recommends \
+    perl \
+    build-essential \
+    cpanminus \
+    pkg-config \
+    libgd3 \
+    libgd-dev \
+    libpng16-16 \
+    libimage-png-libpng-perl \
+    libfont-freetype-perl
+
+# install GD for perl
+cpan -v
+cpanm -v
+cpan App::cpanminus
+cpanm ExtUtils::PkgConfig
+cpanm GD
+cpanm GD::Graph
+
 # get bismark code (no repo)
 wget -P /usr/bin/bismark --no-check-certificate https://github.com/FelixKrueger/Bismark/archive/refs/tags/v0.24.2.tar.gz
 tar -xvzf /usr/bin/bismark/v0.24.2.tar.gz -C /usr/bin/
@@ -38,6 +57,7 @@ rm -rf /usr/bin/bismark/
 # create mount directory for bowtie2 bind, to avoid problems
 mkdir /usr/bin/bowtie2
 
+
 %environment
 export PATH=${PATH}:/usr/bin/samtools/:/usr/bin/Bismark-0.24.2/:/usr/bin/bowtie2/:/usr/bin/python:/usr/bin/python2.7:/usr/lib/x86_64-linux-gnu/:/usr/lib/python2.7/
 export PYTHON=/usr/bin/python