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GBrowse-2.29
River stage zero No dependents
++

Changes for version 2.29

  • Updated mod_fcgid "FcgidInitialEnv" directive to current recommended name.
  • You can now narrow the search to features with a desired primary tag using the syntax "desired_tag:feature_name"
  • You can exclude a list of primary tags from search results in the database definition stanza using the syntax:
    • foo:database
      • exclude types = type1 type2 type3
  • The appearance of the track selection table has been updated to be less "busy".
  • Uploaded track names assigned automatically (e.g. "upload_6842") can now be edited by shift-clicking on the track name.
  • You can now select the format for track data generated by clicking on the "disk" icon in the track title bar.
  • Fixed unwanted behavior in which searches that returned multiple features would open up all tracks corresponding to those features even if user did not select them.
  • Fixed "permission denied" error opening cgisess.db when installing on a fresh system.

Documentation

auto_install_databases.pl
Download and install GFF data sets
ucsc_genes2gff.pl
Convert UCSC Genome Browser-format gene files into GFF files suitable for loading into gbrowse
bp_load_gff.pl
Load a Bio::DB::GFF database from GFF files.
gbrowse_clean.pl
Clean up sessions and other temporary gbrowse2 files
gbrowse_netinstall.pl
gbrowse_netinstall.pl
gtf2gff3
load_genbank.pl
Load a Bio::DB::GFF database from GENBANK files.
make_das_conf.pl
Create GBrowse config files from DAS sources
process_gadfly.pl
Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser
ncbi_2_gff.pl
Massage NCBI chromosome annotation into GFF-format suitable for Bio::DB::GFF
process_sgd.pl
Massage SGD annotation flat files into a version suitable for the Generic Genome Browser
ucsc_genes2gff.pl
Convert UCSC Genome Browser-format gene files into GFF files suitable for loading into gbrowse
wiggle2gff3.pl
axt2phy.pl
convert AXT pairwise alignment files to GFF, Fasta and wig files
ace2gff.pl
convert a phrap produced, ace file into a gff formatted file
blast2gff.pl
Convert a BLAST result file into a GFF file
import_ncbi_mv_hs.pl
make gff files from NCBI Map Viewer data files.
contrib::install_macosx::README
pod::BIOSQL_ADAPTER_HOWTO
pod::CONFIGURE_HOWTO
pod::CONTROLLER
pod::DAS_HOWTO
pod::FAQ
pod::GBROWSE_IMG
pod::GENBANK_HOWTO
pod::INSTALL.MacOSX
pod::INSTALL
pod::MAKE_IMAGES_HOWTO
pod::ORACLE_AND_POSTGRESQL
Bio::Graphics::Browser::Plugin
Base class for gbrowse plugins.
pod::README-berkeley-gadfly
pod::README-chado
pod::README-gff-files
pod::README-lucegene

Modules

b64_encoded_gif_renderer.pm
a renderer (HTML) for b64_encoded_gif type MOBY Objects
b64_encoded_jpeg_renderer.pm
a renderer (HTML) for b64_encoded_jpeg type MOBY Objects
text_formatted_renderer.pm
a renderer (HTML) for text-formatted type MOBY Objects
text_html_renderer.pm
a renderer (HTML) for text_html type MOBY Objects
text_plain_renderer.pm
a renderer (HTML) for text_plain type MOBY Objects
text_xml_renderer.pm
a renderer (HTML) for text_xml type MOBY Objects
Bio::Graphics::Browser2::Plugin::AlignTwoSequences
a plugin that executes NCBI's bl2seq on the current view
Bio::Graphics::Browser2::Plugin::Aligner
Dump multiple alignments from GBrowse
Bio::Graphics::Browser2::Plugin::AttributeHiliter
hilite features based on attributes
Bio::Graphics::Browser2::Plugin::Blat
plugin to map sequences against the genome
Bio::Graphics::Browser2::Plugin::CreateBlastDB
a plugin that creates a Blast-formatted database from a Bio::DB::GFF database
Bio::Graphics::Browser2::Plugin::PamAuthenticate
Authenticate user via Pluggable Authentication Modules
Bio::Graphics::Browser2::Plugin::PrimerDesigner
a plugin to design PCR primers with primer3
Bio::Graphics::Browser2::Plugin::ProteinDumper
A plugin for dumping translated protein sequences in various formats
Bio::Graphics::Browser2::Plugin::RestrictionAnnotator
Generate a restriction map track in GBrowse
Bio::Graphics::Browser2::Plugin::SequenceDumper
A plugin for dumping sequences in various formats
Bio::Graphics::Browser2::Plugin::SimpleTrackFinder
Limit list of tracks to those that match a name pattern
Bio::Graphics::Browser2::Plugin::SourceTrackFinder
Limit list of tracks to those that contain arbitrary fields
Bio::Graphics::Browser2::Plugin::Spectrogram
Bio::Graphics::Browser2::Plugin::TrackFinder
Limit list of tracks to those that mention keywords
contrib/Coverage/plugin/Coverage.pm
DAS::GUS
DAS-style accession to a gus database
DAS::GUS::Segment
DAS-style access to a GUS database
DAS::GUS::Segment::Feature
DAS::Util
A simple XML sql parser
contrib/install_macosx/BuildConfig.pm
install_util/GBrowseInstall.pm
Bio::DB::GFF::Aggregator::match_gap
GFF3 match aggregator
Bio::DB::GFF::Aggregator::reftranscript
Bio::DB::GFF::Aggregator::waba_alignment
A WABA alignment
Bio::DB::GFF::Aggregator::wormbase_gene
Wormbase gene aggregator
Bio::DB::Tagger
Simple object tagging system
Bio::DB::Tagger::Tag
Authored tags
Bio::Graphics::Browser2::AuthorizedFeatureFile
Add HTTP authorization features to FeatureFile
Bio::Graphics::Browser2::CAlign
Compiled helper for Bio::Graphics::Browser::Realign
Bio::Graphics::Browser2::DataBase
A simple cache for database handles
Bio::Graphics::Browser2::GFFhelper
Helps gbrowse plugins handle GFF
Bio::Graphics::Browser2::Markup
Markup routines for sequences in text form
Bio::Graphics::Browser2::OptionPick
Pick options
Bio::Graphics::Browser2::PadAlignment
Insert pads into a multiple alignment
Bio::Graphics::Browser2::Plugin
Base class for gbrowse plugins.
Bio::Graphics::Browser2::Plugin::AuthPlugin
Base class for authentication plugins
Bio::Graphics::Browser2::PluginSet
A set of plugins
Bio::Graphics::Browser2::Realign
Perl extension for Smith-Waterman alignments
Bio::Graphics::Browser2::RegionSearch
Search through multiple databases for feature matches.
Bio::Graphics::Browser2::RemoteSet
A set of plugins
Bio::Graphics::Browser2::Util
Exported utilities
CGI::Toggle
Utility methods for collapsible sections
Bio::Graphics::Browser::CAlign
Compiled helper for Bio::Graphics::Browser::Realign

Provides

Bio::DB::SeqFeature::Store::BedLoader
in lib/Bio/DB/SeqFeature/Store/BedLoader.pm
Bio::DB::Tagger::Iterator
in lib/Bio/DB/Tagger.pm
Bio::DB::Tagger::mysql
in lib/Bio/DB/Tagger/mysql.pm
Bio::Graphics::Browser2
in lib/Bio/Graphics/Browser2.pm
Bio::Graphics::Browser2::Action
in lib/Bio/Graphics/Browser2/Action.pm
Bio::Graphics::Browser2::AdminTracks
in lib/Bio/Graphics/Browser2/UserTracks.pm
Bio::Graphics::Browser2::CachedTrack
in lib/Bio/Graphics/Browser2/CachedTrack.pm
Bio::Graphics::Browser2::DataLoader
in lib/Bio/Graphics/Browser2/DataLoader.pm
Bio::Graphics::Browser2::DataLoader::bam
in lib/Bio/Graphics/Browser2/DataLoader/bam.pm
Bio::Graphics::Browser2::DataLoader::bed
in lib/Bio/Graphics/Browser2/DataLoader/bed.pm
Bio::Graphics::Browser2::DataLoader::bigwig
in lib/Bio/Graphics/Browser2/DataLoader/bigwig.pm
Bio::Graphics::Browser2::DataLoader::featurefile
in lib/Bio/Graphics/Browser2/DataLoader/featurefile.pm
Bio::Graphics::Browser2::DataLoader::generic
in lib/Bio/Graphics/Browser2/DataLoader/generic.pm
Bio::Graphics::Browser2::DataLoader::gff
in lib/Bio/Graphics/Browser2/DataLoader/gff.pm
Bio::Graphics::Browser2::DataLoader::gff3
in lib/Bio/Graphics/Browser2/DataLoader/gff3.pm
Bio::Graphics::Browser2::DataLoader::sam
in lib/Bio/Graphics/Browser2/DataLoader/sam.pm
Bio::Graphics::Browser2::DataLoader::wiggle
in lib/Bio/Graphics/Browser2/DataLoader/wiggle.pm
Bio::Graphics::Browser2::DataSource
in lib/Bio/Graphics/Browser2/DataSource.pm
Bio::Graphics::Browser2::ExternalData
in lib/Bio/Graphics/Browser2/ExternalData.pm
Bio::Graphics::Browser2::I18n
in lib/Bio/Graphics/Browser2/I18n.pm
Bio::Graphics::Browser2::MetaDB
in lib/Bio/Graphics/Browser2/RegionSearch.pm
Bio::Graphics::Browser2::MetaSegment
in lib/Bio/Graphics/Browser2/RegionSearch.pm
Bio::Graphics::Browser2::MetaSegment::Iterator
in lib/Bio/Graphics/Browser2/RegionSearch.pm
Bio::Graphics::Browser2::Region
in lib/Bio/Graphics/Browser2/Region.pm
Bio::Graphics::Browser2::Render
in lib/Bio/Graphics/Browser2/Render.pm
Bio::Graphics::Browser2::Render::HTML
in lib/Bio/Graphics/Browser2/Render/HTML.pm
Bio::Graphics::Browser2::Render::Login
in lib/Bio/Graphics/Browser2/Render/Login.pm
Bio::Graphics::Browser2::Render::Slave
in lib/Bio/Graphics/Browser2/Render/Slave.pm
Bio::Graphics::Browser2::Render::Slave::Status
in lib/Bio/Graphics/Browser2/Render/Slave/Status.pm
Bio::Graphics::Browser2::RenderPanels
in lib/Bio/Graphics/Browser2/RenderPanels.pm
Bio::Graphics::Browser2::Session
in lib/Bio/Graphics/Browser2/Session.pm
Bio::Graphics::Browser2::Shellwords
in lib/Bio/Graphics/Browser2/Shellwords.pm
Bio::Graphics::Browser2::SubtrackTable
in lib/Bio/Graphics/Browser2/SubtrackTable.pm
Bio::Graphics::Browser2::TrackDumper
in lib/Bio/Graphics/Browser2/TrackDumper.pm
Bio::Graphics::Browser2::UserConf
in lib/Bio/Graphics/Browser2/UserTracks.pm
Bio::Graphics::Browser2::UserDB
in lib/Bio/Graphics/Browser2/UserDB.pm
Bio::Graphics::Browser2::UserTracks
in lib/Bio/Graphics/Browser2/UserTracks.pm
Bio::Graphics::Browser2::UserTracks::Database
in lib/Bio/Graphics/Browser2/UserTracks/Database.pm
Bio::Graphics::Browser2::UserTracks::Filesystem
in lib/Bio/Graphics/Browser2/UserTracks/Filesystem.pm
Bio::Graphics::GBrowseFeature
in lib/Bio/Graphics/GBrowseFeature.pm
Bio::Graphics::Karyotype
in lib/Bio/Graphics/Karyotype.pm
Bio::Graphics::Wiggle::Loader::Nosample
in lib/Bio/Graphics/Browser2/DataLoader/wiggle.pm
FakeHomol
in lib/Bio/Graphics/Browser2/GFFhelper.pm
LRUCache
in lib/Bio/Graphics/Browser2/DataBase.pm
Legacy::DB::SyntenyBlock
in lib/Legacy/DB/SyntenyBlock.pm
Legacy::DB::SyntenyIO
in lib/Legacy/DB/SyntenyIO.pm
Legacy::Graphics::Browser
in lib/Legacy/Graphics/Browser.pm
Legacy::Graphics::Browser::I18n
in lib/Legacy/Graphics/Browser/I18n.pm
Legacy::Graphics::Browser::PageSettings
in lib/Legacy/Graphics/Browser/PageSettings.pm
Legacy::Graphics::Browser::Synteny
in lib/Legacy/Graphics/Browser/Synteny.pm
Legacy::Graphics::Browser::Util
in lib/Legacy/Graphics/Browser/Util.pm
Legacy::Graphics::BrowserConfig
in lib/Legacy/Graphics/Browser.pm
MyFeatureFileLoader
in lib/Bio/Graphics/Browser2/DataLoader/featurefile.pm

Other files