install.phylo.day2.sh

#!/bin/bash

#Run this to :
#Download and install NCBI BLAST
#Install pip
#use pip to install Dendropy
#Download a reference genome
#download scripts from vinson's guthub
#download Biopython tools


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sudo chmod -R a+rX,u+w /var/cache/app-info/xapian/default
sudo apt-get install -y software-properties-common
sudo apt-add-repository universe
sudo apt-get -y update
sudo apt-get -y upgrade
sudo apt-get -y install default-jdk
#sudo apt-get -y install ncbi-blast+
sudo apt-get -y install python-pip
#sudo pip install -U dendropy
wget https://github.com/vinsondoyle/genbankProcessing/archive/master.zip
unzip master.zip
sudo cp genbankProcessing-master/*py /usr/local/bin
pip install biopython
#sudo apt-get install -y ncbi-blast+
#Install efetch (ncbi tools) by pasting install.efetch.txt into terminal
wget http://ormbunkar.se/aliview/downloads/linux/linux-version-1.22/aliview.install.run
chmod +x aliview.install.run
sudo ./aliview.install.run
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