Installation

GenIE-Sys can be installed in a few different methods as below.

Docker installation

Docker is a software that provides the ability to package and run an application in an isolated environment called a container. Install the Docker and run it before start the following steps. Open the terminal and use following commands.

Docker installation can be tested or run in several ways.

1.) Run using Play with Docker The quickest way to test the GenIE-Sys, it takes only a few minutes

2.) Run with already built in Docker image The fastest way to run the GenIE-Sys locally or your own server

docker run --rm -i -t -p "80:80" -p "3308:3306" -v ${PWD}/genie:/app -v ${PWD}/mysql:/var/lib/mysql -e MYSQL_ADMIN_PASS="mypass" --name geniesys irusri/docker4geniesys

3.) Build image locally using Dockerfile and run This is quite slow since you have to build the image locally

git clone https://github.com/irusri/docker4geniesys.git  
cd docker4geniesys  
docker-compose up

👍 Now you can access the GenIE-Sys on http://localhost/geniesys/ URL.

You can access MySQL database using mysql -u admin -pmypass -h localhost -P 3308 or using phpMyAdmin. As you may noticed here admin is the default MySQL username and mypass is the default password. You can change that in docker-compose.yml file.

If you are running on a production environment, we recommend changing the password for MySQL user.

Install with Apache webserver

When you use standalone web server installation with MAMP, you have to make sure to install and configure all required software and packages that are necessary for different plugins. Required packages listed here.

MAMP is a solution stack composed of Apache, MySQL and PHP used together to develop and run dynamic web sites on computers.

Start page of the MAMP software

Installing MAMP is just a matter of downloading the app from the MAMP website and running the installer. It will install a MAMP app in your Applications folder.

MAMP basic settings panel

By starting the MAMP app you are also starting your Apache and MySQL server. You should now be able to reach your local server at http://localhost:8888.

By default, MAMP uses port 8888 for Apache and port 8889 for MySQL. It is convenient to change the MySQL and Apache ports to 3306 and 80 respectively to use default MySQL and Apache ports.

MAMP advanced settings

Download GenIE-Sys

Copy GenIE-Sys to MAMP Webserver

You will find the source of GenIE-Sys in your download folder. So you just need to Copy GenIE-Sys folder into the corresponding ~/Applications/MAMP/htdocs/ folder.

That is basically what you need to do in order to install GenIE-Sys on your Mac’s local server. You should now be able to access it at: http://localhost:[port number]/geniesys in your browser. Now you can see the essential website up and running. However to configure it correctly please update the configuration file as described in the next section.

All good, next we need to customise our new website and load our genome into the database.