ngchm/ngchm-galaxy repository overview

This is an image of the Galaxy bioinformatics platform including the Next Generation Clustered Heat Map (NG-CHM) creation and visualization tools.

The NG-CHM Generator tool creates clustered heat maps with a wide range of options including several clustering techniques, different distance measures, the addition of annotation data as covariate bars and link outs for some defined data types.

After the heat map is created, the NG-CHM Heat Map Viewer provides a dynamic, interactive visualization of the heat map that enables exploration of the heat map data and configuration of the heat map appearance.

For a full description of NG-CHM Viewer capabilities see our documentation page: http://bioinformatics.mdanderson.org/main/NG-CHM-V2:Overview⁠.

Please see our videos on Running NG-CHM in a Docker Container and NG-CHM Heatmap Creation in Galaxy in our YouTube Tutorial Channel here: https://www.youtube.com/channel/UCADGir2q8IaI9cGQuzjSL9w⁠.

WARNING: You MUST register/login in Galaxy under the 'User' menu item to see the NG-CHM visualization option.

The Docker command used to create a Docker Container from the 'NG-CHM' Image:

docker run --name="NG-CHM" -d -p 8888:80 -p 7021:21 -e "GALAXY_CONFIG_ADMIN_USERS=[email protected]⁠" ngchm/ngchm-galaxy

Then in your browser (preferred Chome) enter: http://localhost:8888⁠

NOTE: The first time you enter Galaxy you MUST register (upper right within black bar: User -> Register), so that the NG-CHM tool visualization will be accessible. Any email address ([email protected]⁠), user name, and password will work. However, if you change the email in the Docker run command above ‘[email protected]⁠’ to an email address of your choosing, when you register (login) to Galaxy with this email you will have Galaxy Admin privileges. The galaxy display user name must be entirely lowercase.

The name of the Docker Container is ‘NG-CHM ‘. After the first time starting the NG-CHM container, use:

‘docker start NG-CHM’

to restart the Container that has your user login and Galaxy data/history.

If you remove the docker container or issue a new 'run' command to get updated software, you will lose data that you produced in Galaxy. For permanent data storage on your local machine, use the following ‘Docker run’ command. This will allow you to link an external folder on your computer to the NG-CHM container.

docker run --name="NG-CHM" -d -p 8888:80 -p 7021:21 -e "GALAXY_CONFIG_ADMIN_USERS=[email protected]⁠" -v /home/user/folderName/:/export/ ngchm/ngchm-galaxy

By including the additional “-v /pathFromRoot/folderName /:/export/” Container parameter, Docker will mount your machine’s folder /pathFromRoot/folderName/ into the Container’s /export/ directory, e.g “/home/Users/bobbrown/GalaxyDataFolder/:/export/” on the Mac.

Developed by MD Anderson Bioinformatics and Computational Biology Department and In Silico Solutions.