Commit 89a7a45f authored by Gonzalo S Nido's avatar Gonzalo S Nido
Browse files

Update prepare_vm.sh with installation of FastQC

parent 7ef42c14
......@@ -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
......
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