Added trimmomatic installation

prepare_vm.sh

@@ -55,6 +55,23 @@ sudo chmod 777 /opt/fastqc-0.11.9/fastqc
 sudo ln -s /opt/fastqc-0.11.9/fastqc /usr/local/bin/fastqc-0.11.9
 sudo ln -s /usr/local/bin/fastqc-0.11.9 /usr/local/bin/fastqc
 rm -r ./FastQC
+cd ~
+
+
+echo "#### Installing Trimmomatic..."
+cd ~
+wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip
+unzip Trimmomatic-0.39.zip
+rm Trimmomatic-0.39.zip
+sudo cp -r Trimmomatic-0.39 /opt/
+rm -r Trimmomatic-0.39
+echo 'java -jar /opt/Trimmomatic-0.39/trimmomatic-0.39.jar $*' | sudo tee /usr/local/bin/trimmomatic-0.39
+sudo chmod 775 /usr/local/bin/trimmomatic-0.39
+sudo ln -s /usr/local/bin/trimmomatic-0.39 /usr/local/bin/trimmomatic
+
+
+
+
 
 echo "Installing R..."
 sudo apt -y install r-base