Merge branch 'master' of https://git.app.uib.no/gni042/wgbs-pipeline

prepare_vm.sh

@@ -44,6 +44,18 @@ sudo ln -s /opt/Bismark-0.22.3/bismark2bedGraph /usr/local/bin/bismark2bedGraph-
 sudo ln -s /opt/Bismark-0.22.3/bismark /usr/local/bin/bismark-0.22.3
 sudo ln -s /opt/Bismark-0.22.3/bam2nuc /usr/local/bin/bam2nuc-0.22.3
 
+echo "#### Installing FastQC"
+cd ~
+wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip
+unzip fastqc_v0.11.9.zip 
+rm fastqc_v0.11.9.zip 
+sudo mkdir /opt/fastqc-0.11.9
+sudo cp -r FastQC/* /opt/fastqc-0.11.9/
+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
+
 echo "Installing R..."
 sudo apt -y install r-base
 sudo apt -y install libcurl4-openssl-dev libxml2-dev