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

.. _OpenBEL Navigator: https://github.com/OpenBEL/kam-nav .. _Model Builder: https://github.com/Selventa/model-builder .. _apps: https://github.com/Selventa/sdp-cytoscape3/tree/experimental/apps .. _launcher: https://github.com/Selventa/sdp-cytoscape3/tree/experimental/launcher .. _resources: https://github.com/Selventa/sdp-cytoscape3/tree/experimental/resources .. _scripts: https://github.com/Selventa/sdp-cytoscape3/tree/experimental/scripts .. _tools: https://github.com/Selventa/sdp-cytoscape3/tree/experimental/tools .. _env.sh: https://github.com/Selventa/sdp-cytoscape3/tree/experimental/env.sh .. _go.sh: https://github.com/Selventa/sdp-cytoscape3/tree/experimental/scripts/go.sh .. _build: https://github.com/Selventa/sdp-cytoscape3/tree/experimental/scripts/build.sh .. _test: https://github.com/Selventa/sdp-cytoscape3/tree/experimental/scripts/test.sh .. _deploy: https://github.com/Selventa/sdp-cytoscape3/tree/experimental/scripts/deploy.sh .. _undeploy: https://github.com/Selventa/sdp-cytoscape3/tree/experimental/scripts/undeploy.sh .. _loop-deploy: https://github.com/Selventa/sdp-cytoscape3/tree/experimental/scripts/loop-deploy.sh .. _package: https://github.com/Selventa/sdp-cytoscape3/tree/experimental/scripts/package.sh .. _start: https://github.com/Selventa/sdp-cytoscape3/tree/experimental/scripts/start.sh .. _stop: https://github.com/Selventa/sdp-cytoscape3/tree/experimental/scripts/stop.sh