icrsc/pisca-box repository overview

Institute of Cancer Research Scientific Software Group⁠
Please contact the scientific software team⁠ for support or information.

⁠Pisca-Box

Welcome to pisca-box. This application is a user-friendly interface to the pisca-beast plug-in for BEAST⁠ (Bayesian Evolutionary Anaylsis Sampling Trees). It has been created at the Institute of Cancer Research in collaboration with Arizona State University.

The pisca-beast plug-in adapts the BEAST MCMC calculations to apply to cancer evolution. The pisca-beast plug-in was created by Diego Mallo and is available on github⁠.

docker pull icrsc/pisca-box
docker run -p 8000:8501 icrsc/pisca-box

It is locally hosted on a port of your choice, in this case 8000. Open the app at http://localhost:8000/⁠

⁠Applications available in pisca-box

The BEAST eco-system includes command line utiltities and java gui applications, two of which are exposed here in pisca-box

• pisca-box is the main calculation engine, running the BEAST command-line utility with the PISCA java plug-in.
• beauti-box: beauti is the java gui application for creating xml files for the beast application. In beauti-box you can create pisca-specific xml files, with a helpful guide to the inputs.

⁠Further applications

pisca-run is also a containerised command line image⁠ that can be run locally or on an HPC cluster for heavier-duty use.