Ubuntu_22_setup.bash

#!/bin/bash

#setting up in a fresh Ubuntu install. Tested on Ubuntu 22.04.3 LTS

#create and move into the External_tools directory
mkdir External_tools
cd External_tools

#install tRNAscan-SE
echo "installing tRNAscan"
sudo apt-get -y update
sudo apt-get -y upgrade
sudo apt-get -y install gcc make perl automake zlib1g-dev hmmer python3 python3-dev python3-pip build-essential python3-tk g++ zlib1g libjpeg-dev
wget http://eddylab.org/infernal/infernal-1.1.2.tar.gz
tar -zxvf infernal-1.1.2.tar.gz
cd infernal-1.1.2
./configure
make
make check
sudo make install
cd ..

wget http://trna.ucsc.edu/software/trnascan-se-2.0.0.tar.gz
tar -zxvf trnascan-se-2.0.0.tar.gz
cd tRNAscan-SE-2.0
./configure
make
sudo make install
sudo chmod 755 /usr/local/lib/tRNAscan-SE/tRNAscanSE/
cd ..
echo "tRNAscan-SE tRNAscan-SE" > ../external_tools.txt

#installing bedtools
wget https://github.com/arq5x/bedtools2/releases/download/v2.27.1/bedtools-2.27.1.tar.gz
tar -zxvf bedtools-2.27.1.tar.gz
cd bedtools2
make
sudo cp ./bin/* /usr/local/bin/
cd ..
echo "bedtools bedtools" >> ../external_tools.txt

#install barrnap-0.9
echo "installing barrnap"
wget https://github.com/tseemann/barrnap/archive/0.9.tar.gz
tar -zxvf 0.9.tar.gz
echo "barrnap $PWD/barrnap-0.9/bin/barrnap" >> ../external_tools.txt

#installing Prodigal
echo "installing prodigal"
git clone https://github.com/hyattpd/Prodigal
cd Prodigal
sudo make install
cd ..
echo "prodigal prodigal" >> ../external_tools.txt

#install python packages
echo "install python packages"
sudo pip3 install numpy scipy matplotlib biopython bcbio-gff tqdm scikit-learn matplotlib matplotlib-venn

#move external_tools.txt
cp ../external_tools.txt ../feature_calculation/external_tools.txt
cp ../external_tools.txt ../prediction/external_tools.txt

echo "finished"