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install_ubuntu_debian.sh
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install_ubuntu_debian.sh
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#!/usr/bin/env bash
echo
echo "Burrows-Wheeler Aligner, SAMTools and VarScan are required for the NGS pipeline of MutaNET. Do you wish to install them on your system?"
echo
read -p "Type y for yes or n for no." -n 1
echo
echo
if [[ $REPLY =~ ^[Yy]$ ]]
then
sudo apt-get install -y bwa
echo
sudo apt-get install -y samtools
echo
sudo apt-get install -y varscan
echo
sudo apt-get install -y default-jre
fi
echo
echo "Python 3 is required if you want to run MutaNET from source code. It is NOT required when using the executable. Do you wish to install Python 3 and the required Python 3 packages (numpy, matplotlib, scipy, fpdf, pyyaml) on your system?"
echo
echo
read -p "Type y for yes or n for no." -n 1
echo
echo
if [[ $REPLY =~ ^[Yy]$ ]]
then
sudo apt-get install -y python3
echo
sudo apt-get install -y python3-tk
echo
sudo apt-get install -y python3-pip
echo
pip3 install --upgrade pip --user
echo
pip3 install numpy --user
echo
pip3 install matplotlib --user
echo
pip3 install scipy --user
echo
pip3 install fpdf --user
echo
pip3 install pyyaml --user
echo
fi