Institute of Cancer Research Scientific Software Group
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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.
This PISCA-BOX repo is containerised and available on docker hub Using the commands below you can pull it from docker and run it as a locally hosted web application.
If you don't have docker, there are instructions on how to install it here
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/
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.
pisca-run is also a containerised command line image that can be run locally or on an HPC cluster for heavier-duty use.