This is the primary Maven project for building the Cytoscape Desktop application. To report bugs in this or other Cytoscape Desktop sub-projects, please use the bug report form here. Cytoscape…
This is the primary Maven project for building the Cytoscape Desktop application.
To report bugs in this or other Cytoscape Desktop sub-projects, please use the bug report form here.
Cytoscape Core: Building Guide

Status:
- 4/2023 - Updated for 3.10.0 release
- 3/2025 - Updated for 3.10.3 release
Introduction
Cytoscape is a fairly complex application and its core distribution has multiple repositories for managing its code. This repository contains top-level pom file and utility script for building Cytoscape core distribution. Most App developers won't need to clone this repository. Keep reading below to learn about how to work with Cytoscape's source code.Target Audience
This document is a guide for developers who want to build the entire Cytoscape core distribution from scratch. If you are interested in building Cytoscape apps, you don't need to build Cytoscape from source. You can follow the guide here to learn more about Cytoscape app development:Requirements
You need the following tools to build latest development version of Cytoscape 3.10:- Computer with Windows, Mac, or Linux
- JDK 17
- Maven 3
- Git
- _cy.sh_ - Utility script for building Cytoscape core distribution (available in this repository).
Related repositories
All build scripts are moved to the following repository:Services
Note that some Cytoscape functions rely on code deployed as services available on web servers. Generally, such services are callable by Cytoscape or directly by non-Cytoscape clients (e.g., Python) in the larger bioinformatics community. Some services are provided by other organizations (e.g., PSICQUIC for importing public networks), while others are provided by Cytoscape developers (e.g., Diffusion) and are located in or rely on other GitHub repositories. Here is a list of known external repositories containing services called by Cytoscape and maintained by Cytoscape core developers:
Each repo contains information on how to build and deploy the service.Cytoscape 3 Core Directory Structure
Cytoscape source code is maintained in several GitHub repositories, and is organized into a main project and several sub-projects.The Core
── cytoscape
├── README.md
├── api
├── app-developer
├── cy.sh
├── gui-distribution
├── impl
├── parent
├── pom.xml
└── support
- parent - Contains several shared variables for building Cytoscape sub projects
- api - Public API bundles
- impl - Implementation bundles
- support - Misc. bundles for building core
- gui-distribution - Actual distribution created from core projects and core apps
- app-developer - API JAR file for app developers
Building Development Version of Cytoscape 3
Here is the step-by-step guide to build a development version of Cytoscape.tl;dr
git clone https://github.com/cytoscape/cytoscape.git
cd cytoscape
./cy.sh init
cd cytoscape
mvn -fae install -U -Dmaven.test.skip=true
./gui-distribution/assembly/target/cytoscape/cytoscape.sh
Eclipse Users - Eclipse Import Instructions
*NOTE: For first-time and new release builds, the build order matters and you may see an error involving event-api. The solution is to first build api/event-api, then build api, then build the entire package. Oh, and you can't skip tests for your first build; some poms depend on test outputs.*
*ANOTHER NOTE: If you see errors about "Could not transfer artifact" and "Blocked mirror for repositories," then you may be running a newer version of Maven that doesn't work for our repo at this time. Try Maven v3.6.0*
Branch Management
Cytoscape Core
For the core projects, development version always uses the branch named develop. Master branch is only for the final release. If you want to build the latest development version of Cytoscape, you should use develop branch for all sub-projects.
Core Apps branch management
Since core apps have their own release cycles, they have different branching scheme. Usually, features are developed in feature branches, and there is only one common branch called master. Head of the master branch is always the latest development version of the core app.
Step 1: Clone the Main Project
1. Install required tools: JDK, Maven, and Git. On some systems, these may be preinstalled - you can use those versions if they are relatively recent. Released versions of Cytoscape use
JDKs from Eclipse Adoptium.
2. Add JDK, Maven, and Git to your system PATH if necessary. On some platforms, this is done automatically on installation - try running mvn, git, or java at a command line to check this.
If you need to add tools to the PATH, the steps you should follow vary by operating system. On Windows, this can be done in the Environment Variables dialog - open the file browser, right click on "Computer" or "This PC", select "Advanced system settings", then click "Environment Variables" - you should be able to edit the the PATH by selecting the PATH environment variable and clicking Edit. On Mac or Linux, you would need to edit the .profile, .bashrc or .zshrc file in your home directory to set environment variables, depending on the type of shell you are using. It may be helpful to add the following to .profile and set the PATH in .bashrc so that all shells will read the same values:
if [ -f ~/.bashrc ]; then
source ~/.bashrc
fi
Then, in .bashrc, add something like the following:
export PATH=/path/to/java/bin:/path/to/maven/bin:/path/to/git/bin:$PATH
Use the directories where binaries are located, as this will ensure that the command line knows where to find them.
3. Set the JAVA_HOME environment variable to the JDK 17 installation directory. This is only necessary if you have multiple versions of Java installed - if JDK 17 is the only one, Cytoscape will be able to automatically find it without the need for an environment variable. To do this, follow the same instructions as above, but for JAVA_HOME instead of PATH. On Windows, you may have to click the "Add..." button under System Variables if JAVA_HOME does not already exist. On Mac/Linux, you would add an additional line to .bashrc (or .profile if you set environment variables there) like the following.
export JAVA_HOME=/path/to/java
On Mac, you can use /usr/libexec/java_home -V
to show the paths of all installed JVMs.
4. MAVEN_HOME, and M2_HOME to your environment variables. On some platforms, this is done automatically on installation. These are environment variables that can be set using the same methods as JAVA_HOME and PATH, and should point to the Maven installation directory (example:
/path/to/Maven/apache-maven-3.6.3. Use the relevant echo command to test these (example: echo $MAVEN_HOME for Ubuntu/Mac or echo %MAVEN_HOME% on Windows).
5. If you are using Git for the first time, you need to set your name and e-mail address. To do this, use the following commands:
git config user.name "Your Name"
git config user.email [email protected]
Substitute your actual name and e-mail address in the commands.
6. Generate an ssh key and set it up on GitHub. To do this, you will first need to be added to the Cytoscape GitHub project by one of the core developers. Then, click the arrow in the top-right hand corner of any GitHub page and choose "Settings". Click "SSH and GPG keys", then follow the instructions on the linked guide to generate an SSH key on your particular operating system. Once you have generated an SSH key, return to the original "SSH and GPG keys" page and add the generated key using "New SSH key".
7. Clone this repository: git clone https://github.com/cytoscape/cytoscape.git
- Now you can see a new directory named cytoscape:
cytoscape <-- parent level directory
├── README.md
├── cy.sh
└── pom.xml
Shortcut
If you want to skip the following steps, you can use this command to clone and build all core projects and core apps:
./cy.sh init-all
Once finished, you can skip to Step 4.
Step 2: Clone the Sub Projects
1. _cd_ to the cloned main project directory: cd ./cytoscape
1. Execute the following command:
- Create new folder under current working directory: ./cy.sh init
1. Now you can see a new subdirectory (also) named cytoscape, which contains the sub projects:
cytoscape <-- parent level directory
├── README.md
├── cy.sh
├── cytoscape <-- subproject directory
│ ├── README.md
│ ├── api
│ ├── app-developer
│ ├── cy.sh
│ ├── gui-distribution
│ ├── impl
│ ├── parent
│ ├── pom.xml
│ └── support
└── pom.xml
Step 3: Building Cytoscape
1. Go into the cytoscape subproject directory cd ./cytoscape
1. Run Maven: mvn clean install -U
- Option: use mvn -fae clean install -U
(... see below)
1. Have a coffee break... It depends on your machine specification and internet connection speed, but will take 3-60 minutes. When you build Cytoscape for the first time, it will take a long time because maven downloads all dependencies from the remote server.
Step 4: Run the new build
Now you are ready to run the new
1. cd gui-distribution/assembly/target/cytoscape
1. Run development version of Cytoscape:
- Mac/Linux: ./cytoscape.sh
- Windows: ./cytoscape.bat
The option
-fae is short for "fail at end", which allows the build to continue even if unit tests fail. (Current unit tests
do fail during the first few compiles, but eventually pass.) When Maven
is done, you can find the application in gui-distribution/assembly/target/cytoscape`.
Note that if you want to test the new build with a clean slate, we recommend to remove the entire ~/CytoscapeConfiguration directory.
Step 5: Continue with Eclipse project steps
If you are developing in Eclipse, continue to set up with these steps. You can also configure Eclipse to debug Cytoscape.----
New from 3.10.0: Core Apps
___Core Apps___ are Cytoscape Apps that are included with the Cytoscape distribution. They are located in their own separate GitHub repositories. Cytoscape depends on the latest version of each core app deployed to the Nexus repository, so you don't need to build core apps to build Cytoscape core.As of Cytoscape 3.10.0 (March 2023), Cytoscape core distribution comes with the following core apps:
https://github.com/cytoscape/cytoscape-gui-distribution/blob/develop/assembly/pom.xml#L447
Optional Projects
This repository contains sample code for app developers and it will not be included in the core distribution. You don't have to build this repository if you just want to build the Cytoscape Core distribution. ----Building Core Apps
All of the core apps are maintained in their own repository and if you want to try the latest version of the core app, you need to build them separately.Step 1: Checking out core apps
Assuming you are in the subproject directory of Cytoscape project (not the parent level), then./cy.sh apps will check out every core app into the apps subdirectory. Each is hosted in its own GitHub repository, and changes can be committed directly to each directory. All of the core apps are hosted under this org account:
Step 2: Building Core Apps
All of core apps are independent to each other and there is no dependency among those. To build the apps, you can just _cd_ to the app's directory and run:mvn clean install -U
to build the latest version. You can also use the following command from top-level directory to build all core apps:
./cy.sh build-apps
This command simply runs mvn clean install for each core app directory.
Step 3: Install the new build
To test changes, install the JAR from the Cytoscape menu at Apps > App Store > Install Apps from File, or copy to the~/CytoscapeConfiguration/3/apps/installed directory.
----
Adding a new Core App
If you need to add an new core apps, you need to follow these steps:Step 1: Update directory structure
All of the Cytoscape core apps should respect the following conventions for consistency. 1. Organize the directory - The top level directory should contain only the minimal set of files..
├── .gitignore
├── README.md
├── pom.xml
└── src
├── main
└── test
- Create proper _.gitignore_ file
- Add _README.md_ to briefly describe the app
- Make sure _src_ contains only main and test sub directories
1. Use standard group and package name
- _org.cytoscape_ should be used as the group ID
- Package name also needs to be updated to follow the standard, like: org.cytoscape.YOUR_APP_NAME
Step 2: Update pom.xml
1. Use standard name and IDorg.cytoscape
my-app
3.5.0
bundle
My APP
1. Add all required plugin instructions
- The core app should work as an independent repository. This means you should not depends on any parent pom file.
- All instructions, including compiler arguments and parameters for BND plugin should be provided
- Make sure you have proper information for the following sections:
- repositories ( You can just copy these from an existing pom, like CyREST: https://github.com/cytoscape/cyREST/blob/3e1ef7fcf867dbcd80749618c4134173e02688e9/pom.xml#L35)
- distributionManagement ( You can just copy these from an existing pom, like CyREST: https://github.com/cytoscape/cyREST/blob/3e1ef7fcf867dbcd80749618c4134173e02688e9/pom.xml#L35)
- scm
- build
1. Update version number
- Use standard versioning convention. For example, if your app is introduced for Cytoscape 3.5.0, set your app's version to 3.5.0. DO NOT USE _-SNAPSHOT_ SUFFIX.
Step 3: Add proper set of unit tests
If you don't have test suite, you should add it. This is important to detect errors caused by future changes.Step 4: Test the new build locally
Once you finish all of the changes above, build it locally. If everything looks OK, install it to Cytoscape and test the app.Step 5: Move your repository to the Cytoscape org account
Mov…
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Java ★ 0 9mo agoExplain → -
old-cytoscapeweb-redirected
This hosts a landing page that directs old cytoscapeweb users to cytoscape.js and the new cytoscape web projects
CSS ★ 0 1y agoExplain → -
cytoscapeweb-website ▣
Cytoscape Web's Website and documentation
HTML ★ 0 1y agoExplain → -
analyzer
Stripped down version of Network Analyzer core app
Java ★ 0 2y agoExplain → -
cy-session-cleaner
This Cytoscape 3 app cleans up sessions that have become too large
★ 0 2y agoExplain → -
cyjs-export-full ⑂
Template for full export option in Cytoscape 3.2.0.
CSS ★ 0 2y agoExplain → -
cytoscape.js-npm-autotweet
Automatically tweets new releases for your npm packages to your twitter account
JavaScript ★ 0 3y agoExplain → -
mapSourceAndTarget
No description.
Java ★ 0 3y agoExplain → -
welcome ▣
Core App: Welcome Screen
Java ★ 0 4y agoExplain → -
command-dialog ▣
Core App: Command Dialog
Java ★ 0 4y agoExplain → -
opencl-layout
Core App: OpenCL Layout
Java ★ 0 3y agoExplain → -
webservice-psicquic-client
Core App: PSICQUIC Client
Java ★ 0 4y agoExplain → -
app-manager-rework
No description.
HTML ★ 0 3y agoExplain → -
opencl-cycl
No description.
Java ★ 0 3y agoExplain → -
ndex-enrichment-rest-model
No description.
Java ★ 0 2y agoExplain → -
datasource-biogrid
Core App: BioGrid Data Source
Java ★ 0 4y agoExplain → -
cytoscape-support
Cytoscape 3 support bundles.
Java ★ 0 8mo agoExplain → -
cytoscape-parent
Cytoscape 3.x parent pom file.
★ 0 3mo agoExplain → -
communitydetection-rest-server
Community Detection REST Service
Java ★ 0 2y agoExplain → -
cyannotation-cx2js
Renders Cytoscape Desktop annotations from CX files via cytoscape.js-canvas
JavaScript ★ 0 3y agoExplain → -
gsoc2021-enrichment-tool
code repo for GSoC 2021 Enrichment Tool project
Java ★ 0 5y agoExplain → -
core-apps-meta
Meta app for all core apps
Java ★ 0 5y agoExplain → -
seurat-wrappers ⑂
Community-provided extensions to Seurat
R ★ 0 5y agoExplain → -
communitydetection-rest-model
No description.
Java ★ 0 2y agoExplain → -
PathwayStudioImporter ⑂
Cytoscape Importer app for Pathway Studio files
Java ★ 0 5y agoExplain → -
cx2js-example
No description.
JavaScript ★ 0 6y agoExplain → -
webservice-biomart-client
Core App: BioMart Client
Java ★ 0 4y agoExplain → -
psi-mi
Core App: PSI-MI support
Java ★ 0 4y agoExplain → -
json
Core App: JSON support
Java ★ 0 1y agoExplain → -
cytoscape-perf ⑂
Cytoscape performance benchmarks and scripts
Java ★ 0 6y agoExplain → -
network-analyzer
Core App: Network Analyzer
Java ★ 0 4y agoExplain → -
enhancer
Control panel to create the string needed by enhancedGraphics
Java ★ 0 7y agoExplain → -
cy-end-to-end-tests-python ⑂
End to end tests for Cytoscape in Python
Python ★ 0 7y agoExplain → -
cytoscapeconsortium
Web site for CytoscapeConsortium.org
CSS ★ 0 8y agoExplain → -
cytoscape.js-fisheye
Fisheye view functionality for Cytoscape.js
JavaScript ★ 0 8y agoExplain → -
prefs
Unit test of the interface for 3.7 Preferences
Java ★ 0 8y agoExplain → -
cyjs-extension-testbed
For all your ES6 pre-compiled cytoscape extension testing needs
JavaScript ★ 0 7y agoExplain → -
cxio_examples
Examples on how to create new aspects.
Java ★ 0 10y agoExplain → -
cytoscape-tests
Repository for testing materials and procedures for Cytoscape Core and Core Apps
★ 0 10y agoExplain → -
homebrew-science ⑂
Scientific formulae for the Homebrew package manager
Ruby ★ 0 11y agoExplain → -
code.cytoscape.org
Static content for code.cytoscape.org
★ 0 12y agoExplain →
No repos match these filters.