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These operations were last performed on Ubuntu 20.04 LTS

Instances of a gEAR Portal are most often run within a cloud instance, where you can choose your own operating system and resources. On Google Cloud for a starter instance I chose an e2-standard-2 (2 vCPUs and 48GB RAM) with 300GB of solid state disk space. You'll definitely want to increase the CPU as you gain more simultaneous users and RAM depending on your dataset sizes. Once you create and start the instance:

$ sudo apt update
$ sudo apt upgrade

Reboot if there are kernel updates (or just to be safe if you don't know.)

$ cd && mkdir git
$ sudo apt install git
$ git clone https://github.com/jorvis/gEAR.git

MYSQL

$ sudo apt install mysql-server

Follow instructions in our setup.mysql.md document

R

sudo apt install r-base

Python

Follow instructions in setup.python.md document

APACHE

$ sudo apt install apache2 apache2-dev

Follow instructions in setup.apache.md document

gEAR portal

$ cd ~/git
$ git clone https://github.com/jorvis/gEAR.git
$ cd /var
$ sudo rm -rf www && sudo ln -s ~/git/gEAR/www

Data transfer

If moving to a new instance and you need to transfer data you need

to shift the contents of the following directories:

$HOME/git/gEAR/www/datasets $HOME/git/gEAR/www/analyses

Permissions

Permissions need to be writeable for your apache user.

$ cd /var/www
$ chmod 777 datasets analyses/* uploads/files/