icrsc/pisca-run repository overview

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

⁠Pisca-Run

Welcome to pisca-run. This application is a containerised command line interface to the pisca 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.

To communicate with the container's file system a drive must be mounted. In this case the drive is /your/xml/dir, but should be the folder where your xml input file is. The folder with the xml file is also used as the working directory, so the output files will be written to this folder. The container maps your folder to the fixed folder /project/xml so this should be unchanged.

To pull from either docker or singularity:

docker pull icrsc/pisca-run
singularity pull docker://icrsc/pisca-run

Docker and singularity use different inputs for the drive mapping -v and -B respectively.

The docker command is

docker run -v /your/xml/dir:/mnt icrsc/pisca-run your.xml

The singularity command is:

singularity run -B /your/xml/dir:/mnt docker://icrsc/pisca-run your.xml

⁠Further applications

pisca-box is user friendly web interface⁠ that can be run on the localhost and can be used for lighter use of pisca and for tutorials and help.