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2.09 Mon May 24 18:45:48 PDT 2010
* To turn off caching of the config file (which is causing deparse errors for some
callbacks) set the environment variable GBROWSE_NOCACHE to a true value
(like "1" or "yes"). This must be done in the Apache config.
* Fixed various bugs in the processing of SAM and BAM files.
* BAM parser now creates BigWig indexes if library is available.
* Fixed "no overloaded magic in Bio::DAS::Segment" error.
* Made Menus and tabbed section labels larger (if you don't like,
edit htdocs/css/dropdown/default-theme.css).
* Moved track table into its own tabbed section.
* TrackFinder plugin now hilights the matches in the track table.
* New "subtrack table" and "subtrack select" options allow you to create nice
sortable tables of potential subtracks. The old "select" option is still
supported, but deprecated.
* Added "kewl" blinds down effect when changing tabs.
* Greatly improved track configuration.
* From E.O. Stinson: added fixes for embedding GBrowse in other web pages.
* From E.O. Stinson: Added support for regex-style datasources that let you define
one data source that will pass different options to a script-based config depending
on the URL.
* From E.O. Stinson: Added a move_to_name function for navigating to a region in one step
via a URL call.
2.08 Thu May 20 22:46:13 EDT 2010
* Added the ability to control the toggle state of each category and subcategory at
startup time by using the "category state" and "category default state" options
(see the GBROWSE2 HOWTO at http://gmod.org/wiki/GBrowse_2.0_HOWTO#Appearance_Settings)
* Fixed searches on Bio::DB::GFF databases so that exact searches work again.
* Fixed the busy spinner so that it doesn't stick in "on" state when region is empty
and user turns on tracks.
2.07 Mon May 17 10:27:56 EDT 2010
` * Tracked down the "let Lincoln know bug is not fixed" bug, and found a real solution.
This was happening when user presses "back" button on browser after an unsuccessful
search. This still triggers a log message until we know the bug is really and truly
fixed.
* BAM track download now works properly under both FastCGI and mod_perl. mod_perl
download requires Bio-SamTools 1.19.
* Requires Bio::Graphics version 2.09, which addresses a bug in which subroutines
defined in init_code could not be referenced within callbacks.
2.06 Thu May 13 17:10:59 EDT 2010
* Fixed dangling references to GFFPrinter.pm module, which was renamed TrackDumper.pm
* Requires Bio::Graphics version 2.08, in order to fix the init_code option, which stopped
working when config file caching was introduced in Bio::Graphics 2.07.
2.05 * Implemented a new caching scheme for communicating with renderfarm slaves.
This will improve performance, but requires Bio::Graphics version 1.05.
* Experimental local rendering code -- each track is rendered in a separate process.
* Reverted to older versions of prototype and scriptaculous due to Google
Chrome incompatibilities.
* Preferred way to separate labels is now to use the "l" option and separate
labels with "%1E", as in "l=mdc-1%1Esma-23%1Eunknown genes"
* Work around race conditions in the 05.deferredrendering regression tests.
May still fail if system is under lots of load during test.
* Fixed bug in change_track_order javascript that prevented track order change from
"sticking" when track labels contained underscores.
* Download icons now selectively download GFF3, SAM or WIG data.
* Early support for a "show_summary" option in [TRACK DEFAULTS] and [TRACK] stanzas. If this
is present and set to a length in bases, then when the user tries to display a region
larger than the length the track will display feature density instead. For this to
work, the database adaptor must support a feature_summary() method. This is being actively
worked on in bioperl, but is not currently available.
2.04 * Can set the subtracks to be displayed by default using the new "select default" option.
* New syntax for select option:
select = type ;
dpy-27 'dpy-27 chip' =101;
htz-1 'htz-1 chip' =102;
pol2 'polymerase II' =103;
sdc-3 'sdc-3 chip' =104;
Everything following the = sign is an optional comment (modencode uses it for the submission ID).
The old syntax for this still works.
* Added a TrackFinder plugin which will limit tracks according to their key,
citation, or "keywords" option, based on keyword matches the user types in.
* Prevent gbrowse_img zombie processes from accumulating under FastCGI.
* Generate correct Galaxy callback URL and inhibit menu item when Galaxy not configured.
* OligoFinder plugin now works with gbrowse2.
* Updated js libraries to prototype 1.6.1 and scriptaculous 1.8.3.
2.03 * GBrowse_details: display of aligned sequences improved.
* Can now paste remote BAM URLs into "import a track" field.
* Private (authenticated) sessions never expire.
* Fixed bug that led to a keyword search always returning multiple hits
* Added a scalebar on top of the details ruler.
* Fixed bug in installation paths of example databases (rbuels)
* Bugfix to support for subroutines in user-defined 'head' configuration options (rbuels)
* Bug fix to avoid hitting database each time the client checks on the status of a render request.
* Bug fix to treat timed-out cache operations the same as timed-out render operations.
* Bug fix to interrupt long system operations, like MySQL queries.
2.02 * Sheldon McKay rolled gbrowse_syn back into gbrowse2
* Fixed bug in parsing of configuration lines from cut-and-paste uploads
* Added ability to look at current session's user and upload IDs.
* Track dumper now accepts option to dump all chromosomes; however only works with
local databases.
* Fixed display of hard-clipped sequences in gbrowse_details.
* Added a spinner that displays when tracks are updating.
* Fixed appearance of subtrack selector.
2.01 * Fixed "multiple segment" exception in gbrowse_detail.
* gbrowse_details now draws alignments correctly when both reference and target
report "-" strand. This happens in samtools.
* Fixed default location of users sqlite database; it now lives in /var/www/gbrowse2/databases
* Fixed SMTP configuration for login script so that unencrypted connections to gateway now
work.
2.00 * The "admin" user can upload public tracks. Use gbrowse_set_admin_passwd.pl to
initialize the account.
* If session arguments not specified in GBrowse.conf, software will pick the fastest
version.
* Brought tutorial into synch with new features and syntax.
* "Build demo" now works correctly.
* Install registration feature activated.
1.9990 * Re-added the ability to group tracks into NxM tables.
* Fixed bug in which database ID was not filled in on the clickable imagemap when
multiple features are shown.
* Implemented the Finder plugin interface.
* Balloon popups now work when gbrowse_img is embedded (from Xiaoqi Shi's patch).
* Fixed track sharing client functionality.
1.9984 * gbrowse_img now shows karyotype display when multiple regions are selected.
* Fixed install paths and verified that you can install into home directory.
1.9983 * Not released.
1.9982 * Undid some of the damage left by the upload code cleanup.
* Can now upload gzipped and bzipp2ed files for all file types.
* SAM and BAM file uploading supported, provided Bio::DB::BAM library is installed
and there is a suitable FASTA file for the reference genome in one of the tracks.
1.9981 * The old-style upload code has been removed.
1.998 * WARNING: WIG FILE UPLOADING NOT WORKING.
* New tabbed layout for browser, uploads & preferences.
* Background uploading working well; will now resume automatically if window is closed and reopened.
* Editing of uploaded files and config files now working properly.
1.9971 * Fixed bugs that were preventing name searches from working across BAM databases.
* Fixed incorrect character sets returned from asynchronous calls.
* Implemented asynchronous upload of files.
1.997 * Fixed bad bug in cookie handling that allowed cookies from one session to overwrite
another when mod_perl or fastcgi in use.
* Started working on redesign of data uploading and sharing.
1.996 * Add "feature_limit" option to keep very populous tracks under control.
* Attempt to fix problem of FastCGI processes hanging around even after apache restarted.
* Installer will no longer overwrite locally-modified configuration files.
* Will now cache piped files and freshen cache at an interval set by "expire data sources".
1.995 * Install to an alternate location (e.g. home directory) by using --install_base argument when
calling perl Build.PL.
* Don't overwrite user's configuration files when doing an upgrade install!
1.994 * Fixed another bug in the cache expiration code that was causing session information
to expire at end of user's browser session.
* Added abiity to tag tracks by their "track source" and "data source" and to turn them
on and off using this information.
* Added a track filtering ability via plugins.
* Fixed FastCGI support so that changes to GBROWSE_CONF are recognized each time
the FastCGI server runs. This allows you to change GBROWSE_CONF on a per-directory
basis using <Location> and SetEnv.
1.993 * Fixed bug in the cache expiration code that caused cache time to be set
abnormally low and prevented cached data from being cached.
1.992 * Added the gbrowse_clean.pl script for cleaning up stale temp files
* Normalized expiration and caching arguments.
1.991 * Added a variety of different session locking mechanisms after I discovered.
that flock doesn't always work across NFS-mounted file systems.
1.990 * Fixed bug in which the hilighting of features got "stuck" on beige.
* Fixed bug in which changing the chromosome of a region but leaving
the coordinates the same caused redisplay of the previous region.
1.989 * Another attempted fix of Galaxy problems. The galaxy_incoming option was not handled correctly.
* Fix track dumping/sharing so that uploaded files are dumped/shared correctly.
1.988 * Fix handling of DBI databases so that various intermittent SQL errors ("server went away")
no longer occur.
* Fixed Galaxy support to return correct MIME type. This
should correct problems people have had with track data not
loading into Galaxy.
* fixed bug that was causing remote tracks that didn't happen
to contain any features in current view to remain greyed out
1.90 * server farm rearchitecture introduced
* big cleanup of defunct files; migrating to Module::Build
1.67 * Templates now the norm, use gbrowse_not to get the "no templates" version.
* The das script now works (more or less) with Bio::DB::SeqFeature::Store adaptor. Not tested
with chado adaptor.
1.66 * The popup zoom menu will never show a region larger than the overview.
* Fixed collapsible sections so that they store their state in transient named cookies
rather than in a single bit vector.
1.65 * Improved support for negative and fractional coordinates, such as those used
in some genetic maps.
1.64 * Revamped state handling to use CGI::Session instead of cookies
* Added Russian and Polish language translations
* Fixed chado adaptor bug for older chado databases with both
SO and SOFA loaded
* Fixed bug to allow multple 'add' parameters
* Added an option to turn on and off the background grid.
* Fixed extraneous redirect when calling gbrowse_img.
1.63
* Added a new "region" panel which is intermediate in size between the overview
and the detail panels. Thanks to Barry Healy for coding this. Use the new
"region segment" configuration option to turn this feature on.
* Added ability to open and close sections with a JavaScript toggle.
* Added ability to group tracks logically.
* Added the "initial landmark" configuration option to bring up a
default region the first time user visits the web page.
* Added the "quicklink plugins" option to add selected plugins to
the links list underneath the instructions.
* Added compatibility with mod_perl version 2 (via ModPerl::Registry)
* Added the ability to highlight multiple features using URL arguments.
* Added the ability to highlight multiple sequence regions using URL arguments.
* Added the ability to turn off the autosearch feature which restores the previous
region when the user revisits the browser.
* Added sections on grouping tracks by category, defining
region panels, and loading Berkeleydb databases to tutorial.
* Added a "hide" option to use when semantic zooming should turn a track
off altogether.
* Added README-lucegene.pod, describing the Lucegene GFF adaptor
* The link option in the config file can now be used to override the built-in linking
rules from DAS sources.
* Moved plugins menu to a more prominent position.
* Uploaded features can now be placed in details panel, overview panel, or both panels.
* init_code subroutines and anonymous callbacks are now placed in the same package so that
one can refer to the other.
* The feature name search now no longer does a wildcard PREFIX search (*foo*), which was killing
performance. It still does a wildcard SUFFIX search (foo*).
* You can now use the parameters "enable" and "disable" to
selectively open or close a set of tracks without blowing
away the settings for all the other tracks the way "label" does.
* gbrowse_img now takes a "highlight" parameter that will highlight the indicated
named feature(s) in yellow.
* gbrowse_details will now evaluate URL options expressed as anonymous subroutines (contributed
by Cyril Pommier).
* gbrowse_details now accepts a general formatting rule syntax
that allows the formatting of each tag value to be precisely
controlled.
* Changed mainform submission method from POST to GET when MSIE detected,
in order to defeat evil "cache has expired" message. This hack is
under the control of the "msie hack" option, and is false by default.
1.62 Mon Apr 5 09:43:25 EDT 2004
* Added request timeout option for very long requests.
* Added additional padding to prevent scales of xyplot glyph from being
cut off.
* Added ability to search within external annotation files for uploaded
features. You will need to CVS update bioperl-live to get this feature.
* Fixed problem of external annotation files disappearing.
* Fixed the problem of three-frame translation glyph showing wrong
translation. HOWEVER, for the [x]flip feature to work properly,
you will need to CVS update bioperl-live.
* Fixed the problem of segments shrinking by 1 bp when the starting
segment length was an odd number.
* Fixed problem of gbrowse_img consuming all available memory
when displaying 3d party features in absolute coordinates.
* Fixed problem of only one feature being found during wildcard search
and identically-named matches are on different reference sequences.
* Fixed problem of track settings disappearing when "update image" is
pressed when the track checkboxes are hidden.
* Fixed cross-site scripting bug (security hole) reported by Toshiaki
Katayama.
* Added a pairwise_plot glyph for showing linkage disequilibrium,
paired blast scores, and other pairwise feature data.
* Use can now turn on and off the overview tracks.
* Fixed chado adaptor to properly render the gbrowse_details page.
* Patch from Eric Just to eliminate unecessary URL arguments.
* Fixes from Jack Chen to get colors in multiple alignments "just right."
* Several fixes, improvements to the chado adaptor.
* added code to the chado adaptor to allow it to generate
URLs to corresponding cmap features
1.61 Wed Mar 17 21:59:16 EST 2004
* Moved the BioSQL adaptor to 'experimental'. It is not guaranteed
to work.
* Really fixed the landmark problem (the 1.60 release was premature)
* Quashed warnings from the GeneFinder plugin
* Suppress warnings generated by coderefs in the link and window_target
options. See make_map() to turn this back on - it might not be the
greatest idea to turn off warnings
1.60 Tue Mar 16 16:36:45 EST 2004
* Fixed problem of some landmarks not being recognized using
the Class:Name syntax.
1.59 Mon Feb 16 13:56:46 EST 2004
* Fixed security hole related to track level security
* Fixed functioning related to arbitrary (non-base) units
* Fixed a bug that caused hanging when fetching reference sequences
* Updated BioSQL adaptor
* Updated ImportFeatures.pm and ExportFeatures.pm to better support
GFF3 and fascilitate Apollo import and export
* Added support for 3rd party DAS anotations
* Added a MOBY server
* Added a proof-of-concept filter module
* added allele_tower glyph
1.58 Wed Dec 31 10:49:20 EST 2003
* Fixed memory leak when used with mod_perl
* Fixed bug with link URL when the same feature type occurred in more
than one track
* Added SVG "Publication quality image" option; as a result, GD 2.07
is the minimum version of GD required.
* Added the ability to modify html display via callbacks utilizing
segment and page setting objects.
* Fixed alignment problems in gbrowse_details
* Fixed several items with the chado/gmod adaptor
* Added documentation for installing on MacOSX
* Added a simple MOBY browser (see CONFIGURE_HOWTO for configuring it).
* Fixed a long pathname bug with the Windows PPM install.
1.57 Sat Oct 4 21:59:19 EDT 2003
* Fixed formatting errors in gbrowse_details alignments.
* Fixed bug in generation of interspersed HTML that prevented one from
providing a code reference for the html1 option.
* New idiogram glyph for putting images of Giemsa-stained chromosomes
in the overview.
* Added Icelandic translation
* Updated French translation
* GET syntax for invoking gbrowse now changed from
http://localhost/cgi-bin/gbrowse?source=yeast
to
http://localhost/cgi-bin/gbrowse/yeast
This will allow restriction by data sources using Apache's standard
authentication/authorization techniques.
* Default time for cookie expiration reduced to 7 days. This will avoid
issues arising from previous change.
* Added mechanisms to restrict individual tracks by username and
password
or by host, domain, or IP address.
* Fixed ppm install utility script
* Updated documentation to reflect the new GET syntax
* Fixed sequence alignments in gbrowse_details when there are minus
strand sequences.
1.55
* Removed hard coded paths in install scripts
* Auto-open tracks that contain matches to the search term. This avoids
nasty behavior in which someone searches for "collagen" and never sees
what it was that matched.
* Support for highlighting the matched feature in yellow. Highlighted
feature is persistent across sessions (may annoy people - consider
a selectable option)
* Support for a "highlight" plugin class which will highlight features
based on matching attributes or other queries.
1.54 Thu Aug 28 12:08:15 EDT 2003
* Really fixed the security hole that was only partially fixed in 1.53.
* Fixed the config file associated with the tutorial.
* Fixed the install scripts so that they work on Windows.
* Added a patch to allow GBrowse to dump GenBank and EMBL formatted
files while using BioPerl 1.2.2.
* Modified GFFDumper to dump GFF from multiple sources, not just
what is in the primary data source. This functionality is still
experimental and not fully tested.
* Added more complete documentation for using GBrowse with GenBank
formated files
1.53 Thu Aug 21 14:40:54 EDT 2003
* Security hole that allowed the display of /etc/passwd and other
files fixed
* Documentation reworked as pod and which is converted to html on
install. That documentation is then available at
http://localhost/gbrowse
* Added an extensive tutorial, also available at http://localhost/gbrowse
* Added tools for making it easier to create a PPM package for Windows
* Added a 'nascent' synteny browser.
* Added gbrowse_details, a CGI that gives skeletal details on each feature
* Added an optional 'flip mode' to flip the orientation of the display
* Added a multiple alignment plugin
* Added a GeneFinder plugin
* Added support for the chado database schema
* Added support for the PostgreSQL database server
* Added a script for converting UCSC genome data to GFF3
* Added a script for loading Genbank/EMBL files to a GFF database
1.51 Thu Mar 6 13:40:09 EST 2003
* Number of search results returned by keyword search now configurable.
* Made it possible for same feature to belong to multiple tracks.
* Fixed HTML title so that Perl memory location of segment object won't
sometimes appear.
* Added new link to gbrowse_img, so that people can embed images of a region
in other HTML pages.
* Added option to hide the whole banner for those who prefer a minimal interface.
1.50 Thu Feb 27 09:05:37 EST 2003
* Added Dutch language support.
* Added missing POXIX.pm file that was causing bizarre behavior for some browsers.
* Fixed bug in label() subroutine that was causing crashes for some config files.
* Added human GFF processor to installed scripts.
* Fixed bug in htdocs_install.pl that created tmp directory with wrong permissions,
resulting in permission failures the first time gbrowse run.
1.49 Thu Feb 13 17:25:20 EST 2003
* Version 1.48 was missing some .pl files needed to successfully install.
1.48 Sun Feb 9 12:55:48 EST 2003
* Added ability to group related features with dotted lines.
* Added ability to pop up a new window when following links.
* Preliminary Chado database support.
* Added information on optimizing performance at SQL layer
(see INSTALL).
* Internationalization support: added Korean, Spanish, Chinese.
* Flybase/Gadfly conversion script now works on Release 3 data format.
1.47 Tue Oct 8 14:44:44 EDT 2002
* Bug fix release.
* Fixed source sorting so that lowest alphabetically-sorted
configuration file is accepted by default. Otherwise,
the default is BioSQL, which is not installed on most
machines and causes an internal server error.
* Fixed the plugins so that they are not turned on by default.
* Changed the default empty track style from "suppress" to "key."
* Better error reporting.
* Changed passwd=>pass in all the sample config files.
1.46 Sun Oct 6 18:25:05 EDT 2002
* Major feature release.
* Internationalization support: French, Italian, Japanese, English.
* Some features need BioPerl 1.1; see patch file
* Flexible support for semantic zooming.
* Histograms in the overview and detailed views.
* Multiple labeled features in overview.
* Preliminary Oracle and BioSQL support.
* Revamped and simplified stylesheet.
* Hooks for adding HTML to display.
* Track labels can now be between tracks.
1.45 Sun Jul 7 17:32:08 EDT 2002
* Major feature release.
* Added conversion script for human genome annotations from NCBI.
* New CDS/reading frame glyph.
* New 3-frame translation glyph.
* FASTA dumper now dumps out decorated FASTA files.
* Sequence dumper supports output in GenBank, EMBL, GAME, BSML and other
formats (thanks to magic of Bio::SeqIO).
* Full set of restriction enzymes in restriction enzyme annotator plugin.
* Support for named external feature tracks in popup menu.
* External feature tracks are now highlighted in selection list.
* Fixed uploaded files so that they are persistent.
* Minor aesthetic improvements.
* REQUIRES: BioPerl 1.02.
* STILL PENDING: Internationalization/localization fixes
1.44 Mon May 6 19:14:45 EDT 2002
* Bug fix that caused keyword searches to fail on case mismatch.
* Number of matches now printed at top of multiple-match page.
1.43 Mon May 6 14:38:40 EDT 2002
* Bug fix to correct a server error that occurred when multiple
features match a search term.
* Added very preliminary support for using GBrowse as a
front end for GenBank and EMBL databases.
1.42 Sun May 5 11:35:22 EDT 2002
* Fixed a bad url in the help generated by gbrowse_img.
1.41 Sat May 4 16:19:20 EDT 2002
* Added gbrowse_img script; this allows local and remote HTML pages
to inline the images generated by gbrowse.
1.40 Fri Apr 12 20:49:50 EDT 2002
* Minor documentation fixes.
* Patch file now fixes a host of small display problems in bioperl 1.0
1.39 Fri Apr 12 00:18:10 EDT 2002
* Fixed problems compiling and installing on Solaris systems.
* Added the wormbase_gene aggregator. Useful for the c. elegans gff file.
* If you pick up the latest bioperl-live (or apply extras/bioperl-1.0.patch)
there are fixes in Bio::Graphics that prevent genes from disappearing
when zoomed all the way into an intron.
1.38 Mon Apr 8 21:16:12 EDT 2002
* Previous version would crash on vanilla Bioperl 1.0 installations.
This problem has been fixed, but at the cost of disabling wildcard
searches. To get wildcard searches, upgrade to Bioperl 1.01 using
CVS or the patch file in extras/bioperl-1.0.patch.
* Fixed aesthetic problems with a phantom "plugin:Restriction Sites"
entry appearing on the key even when restriction sites are turned
off.
* Fixed intermittent "Couldn't open database" errors.
* Fixed intermittent scrambling of user settings.
1.37 Sun Mar 31 16:10:11 EST 2002
* Plugin architecture completed see README-PLUGINS
* Sample plugins provided:
Restriction site annotator
Find regions by searching for oligos
GFF dumper
FASTA dumper
1.36 Sat Mar 23 23:28:10 EST 2002
* Completely reworked the way that track options are stored.
* Allow multiple files to be uploaded.
* Added online help documentation.
* Preparation for plug-in architecture.
1.35 Tue Mar 5 23:32:14 EST 2002
* Fixed mkpath bug in Browser.pm (wouldn't run without mods)
* Fixed typos in sample .conf files.
1.34 Tue Feb 19 14:22:31 EST 2002
* Fixed JavaScript code so that the popup zoom menu works correctly with konqueror
and old Netscape.
* Robustified in the face of server timeout errors.
1.33 Mon Feb 18 17:41:28 EST 2002
* Made the zoom/scroll navigation bar more intuitive (in my opinion)
* Zoom levels more configurable
* Cleaned up the GIF buttons (install will overwrite the old ones)
* Added GC and DNA content glyph to example config file
1.32 (intermediate version, do not use)
1.31 Thu Jan 24 15:44:40 EST 2002
* Fixed GFF and FASTA dumping problems.
* Version number is now printed at bottom of page.
1.30 Thu Jan 24 12:01:52 EST 2002
* Clarified the method for installing in non-standard locations
and gave an example for RedHat.
1.20 Mon Jan 21 17:43:06 EST 2002
* Fixed a bug that appeared with newer versions of Bio::DB::GFF
in which features with multiple locations showed up with the
same location repeated.
1.01 Fri Jan 11 13:12:36 EST 2002 Lincoln Stein <lstein@cshl.org>
* Better error reporting for when a database can't be opened
for whatever reason.
1.00 2002-01-02 Lincoln Stein <lstein@cshl.org>
* Made GGB a project separate from Bio::Graphics
* Wrote lots of documentation!