Installation

Install Galaxy

To install Galaxy:

git clone https://github.com/galaxyproject/galaxy.git
cd galaxy
./run.sh

This command will clone the Galaxy Github repository, install all needed dependencies in a python virtual environment, and start up a local galaxy server. Navigate to http://localhost:8080 to access the server from your browser.

Install the MCMICRO Tools

Each of the MCMICRO modules can be installed as a galaxy tool from the Main Galaxy Toolshed.

• Basic Illumination
• ASHLAR
• Coreograph
• UnMicst
• S3Segmenter
• quantification
• naivestates

Upload the MCMICRO Galaxy workflow

Two workflows are currently available for running MCMICRO in Galaxy.

• MCMICRO Tissue Microarray Workflow
• MCMICRO Whole Slide Tissue Workflow

To upload a workflow, naviate to the Workflow page, click Upload, select the workflow file (.ga), and Import workflow.

Need Help?

For more help installing galaxy, try the Get Galaxy docs. Interested in running Galaxy with Docker? Check out Galaxy Docker Image and Tutorials.