sdp-cytoscape3

A distribution of cytoscape3 apps for model building with the SDP. The cytoscape distribution is opened via Java Web Start using the launcher code. The launcher starts cytoscape separately from the Java Web Start process.

It includes the following apps:

• OpenBEL Navigator: Explore knowledge networks
• Model Builder: Build biological networks with supporting data from knowledge networks.

project structure

This project provides tools and scripts necessary to build and test within a self-contained cytoscape installation.

• Cytoscape apps are contained within the apps directory. Each app uses a similar project structure that allows rapid development, integration and deployment.
• The cytoscape launch code run via Java Web Start is contained within launcher directory.
• Build resources are contained within the resources directory.
• The build environment's scripts are contained within the scripts directory.
• The build environment tools are contained within the tools directory.

The build environment config is defined in env.sh. It provides a bash repl that allows the developer to run different steps of the build. This is defined in go.sh.

development commands

Use the go.sh script to run build commands during development. Some important options are:

• build
  • builds the apps/distribution
• test
  • builds and test the apps/distribution
• deploy
  • deploy apps to tools/cytoscape
• undeploy
  • undeploy apps from tools/cytoscape
• loop-deploy
  • build and deploy apps to tools/cytoscape
• package
  • package the sdp-cytoscape distribution
• start
  • start cytoscape in tools/cytoscape
• stop
  • stop cytoscape in tools/cytoscape

environment customisation

Scripts and tools are driven by environment variables in env.sh. Environment variables can be overriden in an env.sh.custom file that you must create (this file is ignored by git).

You might want to do the following:

• build a different set of apps
  • set the DEV_APPS_DIR environment variable to your directory contains apps
• use a different cytoscape installation to deploy apps into
  • set the DEV_CY3_DIR environment variable to your cytoscape directory
• set the log file for tools/cytoscape
  • set the DEV_CY3_LOG_FILE environment variable to the log file path