Download

New! UTGB Shell installer using Java Web Start is available.

Release Notes

  • December 1st, 2011 UTGB Toolkit 1.5.8 released
    • Add CSEGTrack
    • Upgrade to snappy-java-1.0.4.1, picard-1.5.6, GWT2.4.0
  • July 6th, 2011 UTGB Toolkit 1.5.7 release
    • Migration to Tomcat 7.x
  • June 15th, 2011 UTGB Toolkit 1.5.6 released.
    • Fixes a corner-case bug when creating WIG database via utgb import.
  • April 28th, 2011 UTGB Toolkit 1.5.5 released.
    • Fixes a bug when compiling a new UTGB project
      • Do utgb upgrade in your project
    • Added utgb snappy command to compress/uncompress files
    • utgb deploy command now supports deployment to a remote Tomcat server
    • Maven-3.0.3 is embedded in UTGB. utgb maven can be used instead of installing mvn command.
  • March 24th, 2011 UTGB Toolkit 1.5.4 released.
    • Includes several bug fixes for version 1.5.1
    • Added utgb read-stat command for obtaining simple stats for BAM files
    • Added utgb draw-hist command for drawing histogram from the input data stream
    • Fixes installation problems in Windows
    • UTGB Installer now supports installation of the older versions.
  • March 22nd, 2011 UTGB Toolkit 1.5.1 released.
    • Improved the compilation and installation time by using ClassWorld launcher instead of packaging the all dependent libraries into one-jar file.
    • Update the utgb screenshot command to take the screenshot for multiple tracks
    • Upgraded to GWT2.1.0
    • utgb qseq2fastq now supports read names with suffixes for paired-end reads, e.g. /1, /2 etc.
    • Several minor bug fixes.
  • January 31st, 2011 UTGB Toolkit 1.5.0 released.
    • WIG database format update (You need to reconstruct wig databases using utgb import)
    • Added utgb snapshot command to create PNG images of tracks
    • Includes several minor bug fixes and dependent library upgrades.
  • December 2nd, 2010 UTGB Toolkit 1.4.10 released.
    • Improved the BAM drawing performance.
  • November 17th, 2010 UTGB Toolkit 1.4.8 released.
    • Fixed a bug in utgb import (bed file)
  • October 12th, 2010 UTGB Toolkit 1.4.7 released.
    • NOTICE! This release contains several major changes. (Documantation for these new features is yet to be done)
    • To upgrade your old UTGB project, do:
    • $ utgb upgrade

      in your project folder.

    • XML-based configuration files are changed to use Silk format, which is far easier to describe by hand.
    • Configuration switch via utgb -e (development|test|production) option.
    • Track view files are moved to (your project)/config/view folder. No restart of the serve is necessary to update the view. Use the address, http://localhost:8989/browser.html?view=sample if you create a new view file as config/view/sample.silk.
    • Support for BED/WIG/SAM/BAM formats in utgb import.
    • BAM file support in ReadTrack (paired-end read display, etc.)
    • -track
       -class: ReadTrack
       -property:
        -path: db/sample.bam

      (In this example, db/sample.bam and db/sample.bam.bai files must be exist to display the read data. You can create these files from SAM files via utgb import command.)

    • WIG file support in WigTrack:
    • -track
       -class: WigTrack
       -property:
        -path: db/sample.wig

      (First, you need to import your WIG files via utgb import command.)

    • Several utilties to manipulate Illumina's read data; e.g., utgb illumina2qseq, utgb qseq2fastq, utgb rename-fastq, etc.
    • Keyword database generator. (see also utgb keyword --help)
      • utgb keyword import (BED/SAM/BAM files)
    • (internal) Upgrading to GWT 2.0.4
  • December 10th, 2009 UTGB Shell 1.2.18 released
    • Some minor bug fixes
  • December 10th, 2009 UTGB Shell 1.2.16 released
    • Java Web Start based installer is available: http://utgenome.org/toolkit/utgb.jnlp
      • No need to manually download and unpack the archive. Just click the above link!
    • [Major] Upgraded to GWT 1.7
      • changed to use HostedMode of the Google Web Toolkit, when debugging the application in Eclipse
      • RPC (Remote Procedure Call) code for commnicating data between client and server-side codes snippet can be generated by utgb gwt command: RPCServiceXXX classes
    • [Major] Changed the configuration file format from XML to Silk, which is easier to edit the configuration.
    • Keyboard short cut for moving genome window is added
      • Left, Right keys for scrolling the genome window
      • Up, Down keys for zoom out/in the displayed position
    • URL of the genome browser becomes the Permalink, that is, you can copy and paste the URL to tell your friends what you see on the UTGB browser.
    • You can now switch the configuration file with -e [development, test, production] option in utgb server and utgb deploy commands.
    • The bundled SQLite JDBC now supports 32/64-bit Windows, Mac OS X, Linux.
      • Faster database query performance
    • Improved the drawing performance of intervals on genome window by using Priority Search Trees.

  • Aug 24th, 2009 UTGB Shell 1.2.5 released.
    • Fixed Issue 30: separate the class loaders of utgb-shell and web applications launched by the utgb-shell.
  • May 26th, 2009 UTGB Shell 1.2.3 released.
    • Included sample DAS and BED tracks to the default view.
  • May 26th, 2009 UTGB Shell 1.2.2 released.
    • BED and DAS format support
  • Feb 27th, 2009 UTGB Shell 1.2.1 released.
    • Fixed a packaging error, resulting in permission denied error when calling 'utgb compile' command.
    • Fixed a bug that the generated web application may use unstable-versions of utgb-core library.
    • Removed several warnings when compilng GWT applications.
    • Upgraeded to utgb-track-base 1.4.6 (uses GWT 1.5.3)
  • Jan 19th, 2009 UTGB Shell 1.2.0 released.