Getting started on Windows

Use the following directions to quickly get started and run on Windows 10 the ExpressionMatrix2 software on a toy dataset distributed as part of the repository. These directions apply to release 0.4.0 or later, and assume that you choose to use release 0.4.0.

• The directions below use the Windows 10 Ubuntu application available on machines running Windows 10 with Fall Creators Update. There is no easy way to run on previous versions of Windows without using a virtualization tool such as VirtualBox or Docker.
• From the Microsoft Store, install the Windows 10 Ubuntu application.
• Enable the Windows Subsystem for Linux, as follows:
  • In Windows 10 search, type Settings to bring up the Settings dialog.
  • In Find a setting, type Windows features, then click on Turn Windows features on or off.
  • Scroll down to Windows Subsystem for Linux and check it to enable.
• In Windows 10 search, type Ubuntu to start the Ubuntu application. This creates an environment that can run Ubuntu applications.
• Use commands sudo apt-get install graphviz and sudo apt-get install python3 to install two necessary packages. This requires administrator privilege.
• Use command mkdir ExpressionMatrix2 to create a new directory in your Ubuntu home directory, then cd ExpressionMatrix2 to go to that directory.
• Use the following command to download the tar file for a release of the ExpressionMatrix2: wget https://github.com/chanzuckerberg/ExpressionMatrix2/releases/download/0.4.0/ExpressionMatrix2-0.4.0.tar
• At this point you can continue with the Getting Started directions for Ubuntu (for Python 3), beginning with Extract the files... here.

For convenience, the list below summarizes the commands to run. This assumes that the python3 and graphviz package are already installed.

mkdir ExpressionMatrix2
cd ExpressionMatrix2
wget https://github.com/chanzuckerberg/ExpressionMatrix2/releases/download/0.4.0/ExpressionMatrix2-0.4.0.tar
tar -xvf ExpressionMatrix2-0.4.0.tar
cd ExpressionMatrix2-0.4.0/tests/ToyTest1
export PYTHONPATH=~/ExpressionMatrix2/ExpressionMatrix2-0.4.0/build/Release-ubuntu16-nohdf5-python3
python3 run.py
python3 runServer.py