Lincoln D. Stein > GBrowse-2.53

GBrowse-2.53

This Release GBrowse-2.53  [Download] [Browse 10 Dec 2012
Latest Release GBrowse-2.54  [Download] [Browse 11 Dec 2012
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CPAN Testers FAIL (9)   [ View Reports ] [ Perl/Platform Version Matrix ]
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License The Perl 5 License (Artistic 1 & GPL 1)
Special Files
Build.PL
Changes
INSTALL
LICENSE
Makefile.PL
MANIFEST
META.json
README

Modules

Bio::DB::GFF::Aggregator::match_gap GFF3 match aggregator      
Bio::DB::GFF::Aggregator::reftranscript Bio::DB::GFF::Aggregator::reftranscript -- Aggregates references transcripts     0.10
Bio::DB::GFF::Aggregator::waba_alignment A WABA alignment     0.20
Bio::DB::GFF::Aggregator::wormbase_gene Wormbase gene aggregator     0.30
Bio::DB::SeqFeature::Store::Alias      
Bio::DB::SeqFeature::Store::Alias::Iterator      
Bio::DB::SeqFeature::Store::Alias::Segment      
Bio::DB::SeqFeature::Store::BedLoader      
Bio::DB::Tagger Simple object tagging system     1.00
Bio::DB::Tagger::Iterator      
Bio::DB::Tagger::Tag Authored tags      
Bio::DB::Tagger::mysql      
Bio::Graphics::Browser2     2.53
Bio::Graphics::Browser2::Action      
Bio::Graphics::Browser2::AdminTracks      
Bio::Graphics::Browser2::AuthorizedFeatureFile Add HTTP authorization features to FeatureFile      
Bio::Graphics::Browser2::CAlign Compiled helper for Bio::Graphics::Browser::Realign      
Bio::Graphics::Browser2::CachedTrack      
Bio::Graphics::Browser2::DataBase A simple cache for database handles      
Bio::Graphics::Browser2::DataLoader      
Bio::Graphics::Browser2::DataLoader::bam      
Bio::Graphics::Browser2::DataLoader::bed      
Bio::Graphics::Browser2::DataLoader::bigwig      
Bio::Graphics::Browser2::DataLoader::featurefile      
Bio::Graphics::Browser2::DataLoader::generic      
Bio::Graphics::Browser2::DataLoader::gff      
Bio::Graphics::Browser2::DataLoader::gff3      
Bio::Graphics::Browser2::DataLoader::sam      
Bio::Graphics::Browser2::DataLoader::wig2bigwig      
Bio::Graphics::Browser2::DataLoader::wiggle      
Bio::Graphics::Browser2::DataSource      
Bio::Graphics::Browser2::ExternalData      
Bio::Graphics::Browser2::GFFhelper Helps gbrowse plugins handle GFF      
Bio::Graphics::Browser2::I18n      
Bio::Graphics::Browser2::Markup Markup routines for sequences in text form      
Bio::Graphics::Browser2::MetaDB      
Bio::Graphics::Browser2::MetaSegment      
Bio::Graphics::Browser2::MetaSegment::Iterator      
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.     0.30
Bio::Graphics::Browser2::Plugin::AlignTwoSequences a plugin that executes NCBI's bl2seq on the current view     0.02
Bio::Graphics::Browser2::Plugin::Aligner Dump multiple alignments from GBrowse     0.23
Bio::Graphics::Browser2::Plugin::AttributeHiliter hilite features based on attributes     0.01
Bio::Graphics::Browser2::Plugin::AuthPlugin Base class for authentication plugins      
Bio::Graphics::Browser2::Plugin::BatchDumper     1
Bio::Graphics::Browser2::Plugin::Blat plugin to map sequences against the genome     0.01
Bio::Graphics::Browser2::Plugin::CMapDumper     0.80
Bio::Graphics::Browser2::Plugin::CreateBlastDB a plugin that creates a Blast-formatted database from a Bio::DB::GFF database     0.15
Bio::Graphics::Browser2::Plugin::FBTableDumper     0.80
Bio::Graphics::Browser2::Plugin::FastaDumper     0.30
Bio::Graphics::Browser2::Plugin::FilterTest     0.O1
Bio::Graphics::Browser2::Plugin::GeneFinder     0.2
Bio::Graphics::Browser2::Plugin::LDAPAuthenticate Authenticate user against an LDAP server      
Bio::Graphics::Browser2::Plugin::OligoFinder     0.15
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     1.00
Bio::Graphics::Browser2::Plugin::RandomGene     0.3
Bio::Graphics::Browser2::Plugin::RestrictionAnnotator Generate a restriction map track in GBrowse     0.25
Bio::Graphics::Browser2::Plugin::SequenceDumper A plugin for dumping sequences in various formats     0.14
Bio::Graphics::Browser2::Plugin::SimpleTrackFinder Limit list of tracks to those that match a name pattern     0.25
Bio::Graphics::Browser2::Plugin::SinWave     0.1
Bio::Graphics::Browser2::Plugin::SourceTrackFinder Limit list of tracks to those that contain arbitrary fields     0.25
Bio::Graphics::Browser2::Plugin::Spectrogram     1.1
Bio::Graphics::Browser2::Plugin::Submitter     0.1
Bio::Graphics::Browser2::Plugin::TestAuthenticator      
Bio::Graphics::Browser2::Plugin::TestFinder      
Bio::Graphics::Browser2::Plugin::TrackDumper     1.00
Bio::Graphics::Browser2::Plugin::TrackFinder Limit list of tracks to those that mention keywords     0.25
Bio::Graphics::Browser2::Plugin::test     0.10
Bio::Graphics::Browser2::PluginSet A set of plugins      
Bio::Graphics::Browser2::Realign Perl extension for Smith-Waterman alignments      
Bio::Graphics::Browser2::Region      
Bio::Graphics::Browser2::RegionSearch Search through multiple databases for feature matches.      
Bio::Graphics::Browser2::RemoteSet A set of plugins      
Bio::Graphics::Browser2::Render      
Bio::Graphics::Browser2::Render::HTML      
Bio::Graphics::Browser2::Render::HTML::TrackListing      
Bio::Graphics::Browser2::Render::HTML::TrackListing::Categories      
Bio::Graphics::Browser2::Render::Login      
Bio::Graphics::Browser2::Render::Slave      
Bio::Graphics::Browser2::Render::Slave::Status      
Bio::Graphics::Browser2::Render::SnapshotManager      
Bio::Graphics::Browser2::Render::TrackConfig      
Bio::Graphics::Browser2::RenderPanels      
Bio::Graphics::Browser2::SendMail      
Bio::Graphics::Browser2::Session      
Bio::Graphics::Browser2::Shellwords      
Bio::Graphics::Browser2::SubtrackTable      
Bio::Graphics::Browser2::TrackDumper      
Bio::Graphics::Browser2::TrackDumper::RichSeqMaker      
Bio::Graphics::Browser2::UserConf      
Bio::Graphics::Browser2::UserDB     0.5
Bio::Graphics::Browser2::UserTracks      
Bio::Graphics::Browser2::UserTracks::Database      
Bio::Graphics::Browser2::UserTracks::Filesystem      
Bio::Graphics::Browser2::Util Exported utilities      
Bio::Graphics::Browser::CAlign Compiled helper for Bio::Graphics::Browser::Realign      
Bio::Graphics::GBrowseFeature      
Bio::Graphics::Karyotype      
Bio::Graphics::Wiggle::Loader::Nosample      
CGI::Toggle Utility methods for collapsible sections      
FakeHomol      
GBrowseGuessDirectories      
GBrowseInstall      
InstallUtil      
LRUCache      
Legacy::DB::SyntenyBlock      
Legacy::DB::SyntenyIO      
Legacy::Graphics::Browser     1.17
Legacy::Graphics::Browser::I18n     1.01
Legacy::Graphics::Browser::PageSettings      
Legacy::Graphics::Browser::Synteny     0.01
Legacy::Graphics::Browser::Util      
Legacy::Graphics::BrowserConfig      
MobyServices::GbrowseServices      
MobyServices::b64_encoded_gif_renderer a renderer (HTML) for b64_encoded_gif type MOBY Objects      
MobyServices::b64_encoded_jpeg_renderer a renderer (HTML) for b64_encoded_jpeg type MOBY Objects      
MobyServices::text_formatted_renderer a renderer (HTML) for text-formatted type MOBY Objects      
MobyServices::text_html_renderer a renderer (HTML) for text_html type MOBY Objects      
MobyServices::text_plain_renderer a renderer (HTML) for text_plain type MOBY Objects      
MobyServices::text_xml_renderer a renderer (HTML) for text_xml type MOBY Objects      
MyFeatureFileLoader      

Documentation

Bio::Graphics::Browser::Plugin Base class for gbrowse plugins.  
auto_install_databases.pl Download and install GFF data sets  
bp_load_gff.pl Load a Bio::DB::GFF database from GFF files.  
cgi-bin/gbrowse_gmap  
docs/pod/BIOSQL_ADAPTER_HOWTO.pod  
docs/pod/CONFIGURE_HOWTO.pod  
docs/pod/CONTROLLER.pod  
docs/pod/DAS_HOWTO.pod  
docs/pod/FAQ.pod  
docs/pod/GBROWSE_IMG.pod  
docs/pod/GENBANK_HOWTO.pod  
docs/pod/INSTALL.MacOSX.pod  
docs/pod/INSTALL.pod  
docs/pod/MAKE_IMAGES_HOWTO.pod  
docs/pod/ORACLE_AND_POSTGRESQL.pod  
docs/pod/README-berkeley-gadfly.pod  
docs/pod/README-chado.pod  
docs/pod/README-gff-files.pod  
docs/pod/README-lucegene.pod  
gbrowse_clean.pl Clean up sessions and other temporary gbrowse2 files  
gbrowse_grow_cloud-vol.pl Grow the GBrowse volume by the requested amount  
gbrowse_key_img  
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  
ncbi_2_gff.pl Massage NCBI chromosome annotation into GFF-format suitable for Bio::DB::GFF  
process_gadfly.pl Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser  
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  

Other Files

README.IF.GBROWSE.ISNT.WORKING
README.fedora_and_selinux
README.gff3
docs/README.AWS
docs/README.tutorial
docs/developer_notes/README.rearchitecture
docs/developer_notes/README.sharing_tracks
htdocs/annotation_help.html
htdocs/cloud_index.html
htdocs/example_scripts/README
htdocs/example_scripts/index.html
htdocs/gbrowse_karyotype_help.html
htdocs/gbrowse_syn_help.html
htdocs/general_help.html
htdocs/index.html
htdocs/tutorial/conf_files/HEADER.html
htdocs/tutorial/data_files/HEADER.html
htdocs/tutorial/tutorial.html
htdocs/tutorial/tutorial.phyTreeEdit.html
htdocs/vbox_index.html
libalign/README
sample_data/admin_uploads/README