Welcome to Magpie

MAGPIE is a web server application designed for collaborative work between scientists, especially in the field of bio- and life-sciences. It can be used within scientific groups, as well as in a larger scale on public servers. A demo server is available here.

Getting Started

Preinstalled Image

1. Install Virtualbox, following the description here.

2. Download the guest image from here and unzip the downloaded guest image to ~/VirtualBox VMs.

   $ mkdir ~/VirtualBox VMs
   $ unzip ~/Downloads/magpie-vbox-image.zip -d ~/VirtualBox VMs/
   

3. Add and configure the Virtualbox image by clicking on New. After, put in the name (Magpie), type (Linux), version (Ubuntu 64-bit), independent of the host machine. Set memory size to at least 4096 MB (depending on your system). Furthermore, set hard disk to use an existing virtual hard disk file and choose the .vdi file of the extracted guest image (~/VirtualBox VMs/Magpie-Image/Magpie.vdi). See here:

Click on Create.

4. Configure the number of CPUs used (Settings -> System -> Processor) to at least 2 and enabling PAE/NX by clicking on Enable PAE/NX. Set the attached network adapter (Settings -> Network -> Adapter 1) to Bridged Adapter.

5. Start the guest image

   Note: In case needed, the password is magpie.

6. Now you are able to connect by open up a browser (in host OR guest) and go to URL:

   magpie.local:3000
   

7. The administrative login is the following:

   Email: admin@admin.com
   Password: admin_password_17
   

8. Happy modelling ... :)

Manual Installation (tested under Ubuntu 18.04)

1. Install ruby and rails according to the official instructions. You can find the instructions for Ubuntu, Windows and Mac OSX here. There is no need to install MySQL or PostgreSQL.

2. Install necessary packages and gems:

   $ sudo apt-get install docker.io libmagic-dev redis-server libssl1.0-dev
   
   $ gem install foreman
   

3. stop redis-server and turn off start on boot-up

   $ sudo update-rc.d redis-server disable

   $ /etc/init.d/redis-server stop

4. Adding user to the docker group:

   $ sudo usermod -aG docker $(whoami)
   

   Afterwards you need to log off and log on.

5. Download the magpie project from github. If git is not installed you can either download it directly from here or install as follows:

   $ git clone https://github.com/christbald/magpie.git
   

6. Change into the magpie directory and install the bundles:

   $ cd magpie
   $ bundle install
   

7. Create the database with default entries and prepare the docker image:

   $ rails db:reset
   

8. Start the rails server:

   $ ./start_server.sh
   

9. Now you are able to connect by open up a browser and go to URL:

   localhost:3000
   

10. The administrative login is the following:

    Email: admin@admin.com
    Password: admin_password_17
    

11. Happy modelling ... :)