Changes for version 2.20
- 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.
Documentation
Download and install GFF data sets
Convert UCSC Genome Browser-format gene files into GFF files suitable for loading into gbrowse
Load a Bio::DB::GFF database from GFF files.
Clean up sessions and other temporary gbrowse2 files
Load a Bio::DB::GFF database from GENBANK files.
Create GBrowse config files from DAS sources
Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
Massage NCBI chromosome annotation into GFF-format suitable for Bio::DB::GFF
Massage SGD annotation flat files into a version suitable for the Generic Genome Browser
Massage WormBase GFF files into a version suitable for the Generic Genome Browser
Convert UCSC Genome Browser-format gene files into GFF files suitable for loading into gbrowse
convert AXT pairwise alignment files to GFF, Fasta and wig files
convert a phrap produced, ace file into a gff formatted file
Convert a BLAST result file into a GFF file
make gff files from NCBI Map Viewer data files.
Base class for gbrowse plugins.
Modules
a renderer (HTML) for b64_encoded_gif type MOBY Objects
a renderer (HTML) for b64_encoded_jpeg type MOBY Objects
a renderer (HTML) for text-formatted type MOBY Objects
a renderer (HTML) for text_html type MOBY Objects
a renderer (HTML) for text_plain type MOBY Objects
a renderer (HTML) for text_xml type MOBY Objects
a plugin that executes NCBI's bl2seq on the current view
Dump multiple alignments from GBrowse
hilite features based on attributes
plugin to map sequences against the genome
a plugin that creates a Blast-formatted database from a Bio::DB::GFF database
Authenticate user via Pluggable Authentication Modules
a plugin to design PCR primers with primer3
A plugin for dumping translated protein sequences in various formats
Generate a restriction map track in GBrowse
A plugin for dumping sequences in various formats
Limit list of tracks to those that match a name pattern
Limit list of tracks to those that contain arbitrary fields
Limit list of tracks to those that mention keywords
DAS-style accession to a gus database
DAS-style access to a GUS database
A simple XML sql parser
GFF3 match aggregator
A WABA alignment
Wormbase gene aggregator
Simple object tagging system
Authored tags
Add HTTP authorization features to FeatureFile
Compiled helper for Bio::Graphics::Browser::Realign
A simple cache for database handles
Helps gbrowse plugins handle GFF
Markup routines for sequences in text form
Pick options
Insert pads into a multiple alignment
Base class for gbrowse plugins.
Base class for authentication plugins
A set of plugins
Perl extension for Smith-Waterman alignments
Search through multiple databases for feature matches.
A set of plugins
Exported utilities
Utility methods for collapsible sections
Compiled helper for Bio::Graphics::Browser::Realign
Provides
in lib/Bio/DB/SeqFeature/Store/BedLoader.pm
in lib/Bio/DB/Tagger.pm
in lib/Bio/DB/Tagger/mysql.pm
in lib/Bio/Graphics/Browser2.pm
in lib/Bio/Graphics/Browser2/Action.pm
in lib/Bio/Graphics/Browser2/UserTracks.pm
in lib/Bio/Graphics/Browser2/CachedTrack.pm
in lib/Bio/Graphics/Browser2/DataLoader.pm
in lib/Bio/Graphics/Browser2/DataLoader/bam.pm
in lib/Bio/Graphics/Browser2/DataLoader/bed.pm
in lib/Bio/Graphics/Browser2/DataLoader/bigwig.pm
in lib/Bio/Graphics/Browser2/DataLoader/featurefile.pm
in lib/Bio/Graphics/Browser2/DataLoader/generic.pm
in lib/Bio/Graphics/Browser2/DataLoader/gff.pm
in lib/Bio/Graphics/Browser2/DataLoader/gff3.pm
in lib/Bio/Graphics/Browser2/DataLoader/sam.pm
in lib/Bio/Graphics/Browser2/DataLoader/wiggle.pm
in lib/Bio/Graphics/Browser2/DataSource.pm
in lib/Bio/Graphics/Browser2/ExternalData.pm
in lib/Bio/Graphics/Browser2/I18n.pm
in lib/Bio/Graphics/Browser2/RegionSearch.pm
in lib/Bio/Graphics/Browser2/RegionSearch.pm
in lib/Bio/Graphics/Browser2/RegionSearch.pm
in lib/Bio/Graphics/Browser2/Region.pm
in lib/Bio/Graphics/Browser2/Render.pm
in lib/Bio/Graphics/Browser2/Render/HTML.pm
in lib/Bio/Graphics/Browser2/Render/Login.pm
in lib/Bio/Graphics/Browser2/Render/Slave.pm
in lib/Bio/Graphics/Browser2/Render/Slave/Status.pm
in lib/Bio/Graphics/Browser2/RenderPanels.pm
in lib/Bio/Graphics/Browser2/Session.pm
in lib/Bio/Graphics/Browser2/Shellwords.pm
in lib/Bio/Graphics/Browser2/SubtrackTable.pm
in lib/Bio/Graphics/Browser2/TrackDumper.pm
in lib/Bio/Graphics/Browser2/UserTracks.pm
in lib/Bio/Graphics/Browser2/UserDB.pm
in lib/Bio/Graphics/Browser2/UserTracks.pm
in lib/Bio/Graphics/Browser2/UserTracks/Database.pm
in lib/Bio/Graphics/Browser2/UserTracks/Filesystem.pm
in lib/Bio/Graphics/GBrowseFeature.pm
in lib/Bio/Graphics/Karyotype.pm
in lib/Bio/Graphics/Browser2/DataLoader/wiggle.pm
in lib/Bio/Graphics/Browser2/GFFhelper.pm
in lib/Bio/Graphics/Browser2/DataBase.pm
in lib/Legacy/DB/SyntenyBlock.pm
in lib/Legacy/DB/SyntenyIO.pm
in lib/Legacy/Graphics/Browser.pm
in lib/Legacy/Graphics/Browser/I18n.pm
in lib/Legacy/Graphics/Browser/PageSettings.pm
in lib/Legacy/Graphics/Browser/Synteny.pm
in lib/Legacy/Graphics/Browser/Util.pm
in lib/Legacy/Graphics/Browser.pm
in lib/Bio/Graphics/Browser2/DataLoader/featurefile.pm