UCSC Xena Server

Work in progress.

Turn-key data server for functional genomics visualization.

View private genomic data on your laptop or institutional server, together with public data sets, without moving your data off-site, via UCSC cancer genomics web tools.

Installation

Download from https://genome-cancer.ucsc.edu/download/public/get-xena/index.html.

Usage

With installer

Double-click, or select from the application menu. This will start UCSC Xena, and present a UI for importing local data files.

Jar (server install)

Please use JRE 8.

$ java -jar cavm-0.10.0-standalone.jar [args]

If a display is available, the file import UI will be opened. Otherwise it will run headless. File imports are queued by running the jar again, with the -l (load) option.

Options

A full list of options can be displayed with

$ java -jar cavm-0.10.0-standalone.jar --help

Development

Run lein run to install dependencies and run the server. Make sure to have at least leiningen 2.4.1 available, otherwise the build process will fail. lein run -- --help will explain the additional options.

The server will prompt you to upload some sample data; there're some example files linked in the help file (click "Help" in the UCSC Xena Client interface and scroll down to "Installing a local Xena Hub to view your data from your laptop").

Acknowledgements

UCSC Xena uses the YourKit profiler.

YourKit supports open source projects with its full-featured Java Profiler. YourKit, LLC is the creator of YourKit Java Profiler and YourKit .NET Profiler, innovative and intelligent tools for profiling Java and .NET applications.

License

Copyright © 2015-2021 The Regents of the University of California

Distributed under the Apache License, version 2.0.