Generic Model Organism Database Project Files

GBROWSE README

The Generic Genome Browser (GBrowse) is a simple but highly
configurable web-based genome browser.  It is a component of the
Generic Model Organism Systems Database project (GMOD).

Recent Changes:

Version 2.23 (bugfix release)
   * Added an "example_scripts" directory that contains a perl scripts that show how to manipulate
     sessions, upload custom tracks, and get basic information about services. This directory accompanies
     new REST API documentation located at http://gmod.oicr.on.ca/wiki/GBrowse2_REST_API.
   * Fixed missing "registration" link in login dialog. This occurred when openid was unavailable.
   * Fixed popup dialogs in the "Help" menu so that they appear again.
   * Fixed file upload status display to prevent upload details section from disappearing when
     uploading very small files.
   * Tinkered with session settings to minimize session lock timeouts.
   * Removed some dangling warnings in the track sharing module.
   * Made SQLite the default user account database.
   * Fixed default SQLite user account database to be created in /var/www/gbrowse2/databases rather
     than in / (root) directory.

Version 2.22 (bugfix release)
   * Fixed gbrowse_img to reactivate documented ability to list multiple tracks with t=track1+track2+track3
   * Fixed startup to avoid Javascript crashing on autocomplete initiation when user accounts turned off. This
     had caused the "eurl" param (used to import external data tracks via URL) to fail.

Version 2.21 (bugfix release)
   * Fix all references to File::Path 'remove_tree" to "rm_tree" in order to work
   with older versions of File::Path.
   * Fixed display bug in Safari (popup balloons not working after zooming into a track).
   * Fixed Internet Explorer crash when uploading new files.
   * Fixed 'eurl=url' remote feature addition.
   * Added basic ipad functionality.
   * Newly-added uploaded tracks appear on the top now.

Changes: Version 2.20 (feature release)
    * User uploads can be run in the usual file-based mode or with a new database-driven system that
      supports sharing files between users based on public, group, casual (with a sharing link)
      and private permissions.
    * Added the ability to load wider details images. Detail tracks can then be dragged left and right
      without having to load more data from the server. To enable, add a property to the conf file
      called "details multiplier" and give it a value greater than 1 (3 is recommended).
    * Overview and scale tracks now show markers for both the currently viewed segment and the entire segment
      that is loaded.  The loaded segment colours can be set with the settings "loaded_segment_fill" and 
      "loaded_segment_outline"
    * Currently viewed position markers are now drawn with javascript with opacity set to 0.5 (this was 
      necessary so that position markers can move as the user drags tracks). Therefore the markers will 
      show up as a lighter colour than before, so settings 'hilite fill' and 'hilite outline' may need to
      be updated
    * Internationalization has been updated so that almost all strings in GBrowse can now be translated,
      including strings in javascript.
    * Subtrack labels now float on top of the underlying image data so that they show even when
      scrolling around.
    * Added a ruler option, which shows a draggable vertical ruler floating over the details tracks which helps 
      users to line things up.
    * Track configuration dialog handles the vista plot in addition to regular and quantitative
      tracks.
    * Added a simple authentication plugin framework that allows you to authenticate against external
      authentication systems.
    * Added the PamAuthenticator plugin, which will authenticate against any Pluggable Authentication
      Module compatible data source (e.g. Unix, NIS, LDAP, Kerberbos, AD).
    * The ability to register new accounts can be disabled by setting "user accounts registration=0"
      in GBrowse.conf.
    * Support for Open ID can be disabled by setting "user accounts openid=0"
      in GBrowse.conf.
    * Fixed bug that caused regions with identical start and end coordinates but different chromosomes to be
      inappropriately cached to the same location.
    * Fixed bug in which tracks with a "remote feature" did not display correctly the very first time they
      are added to the session.