granatumx/gbox-differentialexpression repository overview

⁠Prerequisites

You mainly need a working copy of Docker⁠. It is used exclusively to manage system configurations for running numerous tools across numerous platforms.

⁠Installation

• All docker images are at "https://hub.docker.com/u/granatumx⁠".
• All github repos are at "https://github.com/granatumx/⁠*".

First set up your scripts and aliases to make things easier. This command should pull the container if it does not exist locally which facilitates installing on a server.

source <( docker run --rm -it granatumx/scripts:1.0.0 gx.sh )

This command makes gx available. You can simply run gx to obtain a list of scripts available.

The GranatumX database should be running to install gboxes. The gbox sources do not need to be installed. A gbox has a gbox.tgz compressed tar file in the root directory which the installer copies out and uses to deposit the preferences on the database. Since these gboxes are in fact docker images, they will be pulled if they do not exist locally on the system. Convenience scripts are provided for installing specific gboxes.

$ gx run.sh                                         # Will start the database, taskrunner, and webapp
$ gx installGbox.sh granatumx/gbox-differentialexpression:1.0.0  # Install this gbox

# Now go to http://localhost:34567 and see this gbox installed when you add a step.

⁠Notes

The gbox has a set of parameters passed into it on the frontend. These are defined in the yamls/*.yaml file. This tool uses R functions for the granatum_sdk to set up the gbox.