To realize data-driven reproducible cytometry analysis and accelerate the adoption of computational analysis methods by both translational and clinical researchers, we have developed a web-based computational infrastructure – FlowGate – to improve the accessibility and usability of the cutting-edge data analytical approaches to cytometry data processing and analysis.
In the grails_webapp folder you can find the source code for FlowGate’s front-end GUI. Installation instrucutions can be found in below. Also the docker images can be found at: https://hub.docker.com/r/jcvifg/flowgate
runing the webapp directly or via docker image (terminal commands in italics)
install grails 3.2.9 (follow instructions at visit http://www.grails.org/download.html and install version 3.2.9) documentation can be found at: http://docs.grails.org/3.2.9/guide/index.html check grails version by typing
grails -v (Terminal/Console[ix/ux] or Cmd[Wdos])
expected output | Grails Version: 3.2.9 | Groovy Version: .... | JVM Version: .....
clone repository (assuming git installed)
git clone https://github.com/JCVenterInstitute/Flowgate_GUI.git
change into cloned directory
cd Flowgate_GUI
unzip "grails-spring-security-ui.zip" into ~/.m2/repository/org/grails/plugins !do not fallback to version 3.0.2 (compile 'org.grails.plugins:spring-security-ui:3.0.2') !do not update to 3.1.2 (compile 'org.grails.plugins:spring-security-ui:3.1.2') which is for grails 3.3.x (https://grails-plugins.github.io/grails-spring-security-ui/latest/) 3.1.0-BUILD SNAPSHOT is needed for docker image creation and also needed for web-archive creation (war-file)
change into subfolder grails_webapp
cd grails_webapp
run application directly by executing the command:
grails run
expected output Grails application running at http://localhost:8585/flowgate in environment: .... and locate your internet browser to: http://localhost:8585/ after the app started when finished initialization
the app can be closed using the ctrl + c key combination
to create a docker image: (you must be located in the grails_webapp folder) execute command: ./gradlew assemble buildImage
Key Developers: Mehmet Kuscuoglu (JCVI), Peter Acs (Stanford), and David Nadeau (UCSD/SDSC)
DAFi algorithm can be found at: https://github.com/JCVenterInstitute/DAFi-gating
Contact: Yu "Max" Qian, Ph.D., mqian@jcvi.org or qianyu.cs@gmail.com, J. Craig Venter Institute
Funding: NIH/NIAID U01TR001801