Installation of software

sudo apt-get update
sudo apt-get install gedit
sudo apt-get install git

#Install fastqc

sudo apt-get install fastqc

sudo apt-get install vcftools

#Download PGDSpider from here
cd /usr/local/
sudo cp ~/Downloads/PGDSpider_2.1.1.3.zip /usr/local/
sudo unzip PGDSpider_2.1.1.3.zip
sudo ln -s /usr/local/PGDSpider_2.1.1.3/PGDSpider2.sh /usr/local/bin/PGDSpider
sudo chmod 755 /usr/local/PGDSpider_2.1.1.3/PGDSpider2.sh
sudo gedit /usr/local/PGDSpider_2.1.1.3/PGDSpider2.sh
#Edit PGDSpider2.sh to read:

#!/bin/bash
java -Xmx4096m -Xms512m -jar /usr/local/PGDSpider_2.1.1.3/PGDSpider2.jar

#Install SplitsTree

#Download SplitsTree from here
cd /usr/local/
sudo cp ~/Downloads/splitstree4_unix_4_14_6.sh /usr/local/
sudo sh splitstree4_unix_4_14_6.sh

#Prepare prerequisites for Stacks

sudo apt-get install libdbd-mysql-perl
sudo apt-get install mysql-server mysql-client
sudo apt-get install php7.0 php-mysqlnd
sudo apt-get install libspreadsheet-writeexcel-perl
sudo apt-get install apache2
sudo apt-get install php libapache2-mod-php php-mcrypt php-mysql

#Install Stacks

#Download stacks-1.47.tar.gz from here to Downloads
#Please do not install other versions of stacks, including newer versions
sudo cp ~/Downloads/stacks-1.47.tar.gz /usr/local
cd /usr/local
sudo tar xfvz stacks-1.47.tar.gz
cd stacks-1.47/
sudo ./configure
sudo make -j 4
sudo make install

#Finish up preparing environment for Stacks

cd /usr/local/share/stacks/sql/
sudo cp mysql.cnf.dist mysql.cnf
sudo gedit mysql.cnf
#Edit user and password to reflect the values given in mysql
cd /etc/apache2/conf-available/
sudo gedit ./stacks.conf
#Edit stacks.conf to read:

<Directory "/usr/local/share/stacks/php">
    Order deny,allow
    Deny from all
    Allow from all
    Require all granted
</Directory>
Alias /stacks "/usr/local/share/stacks/php"

sudo ln -s /etc/apache2/conf-available/stacks.conf /etc/apache2/conf-enabled/stacks.conf
sudo cp /usr/local/share/stacks/php/constants.php.dist /usr/local/share/stacks/php/constants.php
sudo gedit /usr/local/share/stacks/php/constants.php
#Edit user and password to reflect the values given in mysql
sudo gedit /etc/apache2/apache2.conf
#Append "ServerName localhost" at the end of the apache2.conf
sudo apachectl restart

#Install admixture

#Download the Linux admixture binary from here to Downloads
sudo cp ~/Downloads/admixture_linux-x.x.x.tar.gz /usr/local/
cd /usr/local
sudo tar xfvz admixture_linux-x.x.x.tar.gz
sudo ln -s /usr/local/admixture_linux-x.x.x/admixture /usr/local/bin/
sudo apt-get autoremove