#!/bin/sh

#BTW - Bioinformatics Through Windows

#Update and upgrade Ubuntu
apt-get update -y
apt-get upgrade -y

#Install pip
apt-get install python3-pip -y

#create a qiime1 env
conda create -n qiime1 python=2.7 -y
conda activate qiime1
conda install -c conda-forge -c bioconda qiime=1.9.1 -y
conda install -c conda-forge libgfortran=3 -y

#Install R
apt-get install r-base -y

#Install Java
apt install default-jre -y

#graphical
apt-get install vim-gtk3 -y

#Download programs folder
wget https://github.com/vpylro/BioME/raw/master/bmp_win.tar.gz
tar -xvf bmp_win.tar.gz

#Install fastq-join
git clone https://github.com/brwnj/fastq-join
cd fastq-join
make
cd ..
cp fastq-join/fastq-join bmp_win/

#put programs folder in the PATH
echo "export PATH=$HOME/bmp_win:$PATH" >> $HOME/.bashrc

#put RDP in the PATH
echo "export RDP_JAR_PATH=$HOME/bmp_win/rdp_classifier_2.2/rdp_classifier-2.2.jar" >> $HOME/.bashrc

#update ".bashrc"
echo "export DISPLAY=:0" >> $HOME/.bashrc
source $HOME/.bashrc