Platforms

MetaR can be installed on the following platforms:

  • Mac OS X El Capitan 10.11+
  • Windows 10+
  • any Linux distribution supporting Java 8 (check here for a complete list)

 

Install software required by MetaR

Users that install MetaR must follow step 1, 2, 3, 4, 5 described below.

STEPS FOR ALL USERS

Install Jetbrains MPS 3.4:
FOR MacOS USERS:

FOR WINDOWS USERS:

FOR LINUX USERS:

Install the Docker platform from
https://www.docker.com/products/docker#/
.

Depending on your machine’s system, follow the simple steps describe in the Mac (
https://docs.docker.com/docker-for-mac/
) or Windows (
http://docs.docker.com/docker-for-windows/
) tutorial to activate Docker on your system.

Install Kitematic Toolbox from https://www.docker.com/products/docker-toolbox.

Open Kitematic and search and create the ‘rocker-metar’ image:
install rocker-metar image

Install the MPS metaR plugin:

    • start the MPS application and open-up the plugin manager in MPS (menu MPS > Preferences… > Plugins)
    • select the “Browse Repositories…”, scroll the list of available plugins and install the plugin org.campagnelab.MetaR

Browse MPS repositories

  • restart the application to activate the plugin
Define the following Path Variable (menu MPS>Preferences…>Build, Execution, Deployment>Path Variables on Mac OS, menu MPS>Settings…>Build, Execution, Deployment>Path Variables on Windows/Linux)):

  • Name: org.campagnelab.metaR.results_dir
    Value: an arbitrary folder under /Users in Mac OS X or C:\Users in Windows where you want the results of MetaR analyses to be placed. (This directory can be empty the first time you start MetaR.)

Add results_dir var

Enable automatic reference re-resolution in the editor. For that, you need to enable the corresponding flag on the Editor page in the Project settings (menu MPS>Preferences…>Editor on Mac OS, menu MPS>Settings…>Editor on Windows/Linux) as shown: Enable broken references resolution

Troubleshooting

  • Were you able to install Kitematic? If no, please install the R language. Mac users also need to install XQuartz.
  • Having problems to download the rocker-metar image? Try one of the following tips.

 

Verify the installation

  1. Start the MPS application and open-up the plugin manager in MPS (menu MPS > Preferences… > Plugins). Check that the metaR plugin is listed, is not red and the checkbox next to the plugin name is checked.
  2. Make sure the required Path Variable is defined: Path variable.

Check out the Training Project

If you are unable to attend our training sessions, you can check out the sample project created during these sessions from our Git repository following these steps:

  • Start the MPS application, click on “Checkout from Version Control” in the right panel, then select “Git” from the drop down menu:
  • A form is shown requesting information about the repository. Insert the following value as Repository URL: git@bitbucket.org:campagnelaboratory/introtometar_tutorial.git. You can leave the default for the other values or change them as you prefer. Then click on the “Clone” button.
  • You can now open the project on your machine by clicking on the “Open Project” option (or from the MPS menu File > Open):Browse your local disk. The project is available in your HOME/MPSProjects/introtometar_tutorial folder.

This is how the project should look like when you open it: