GBrowse
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down then throws an error (once) and then reverts to local rendering for a period of time.
* Updated installer to give dire warning if installing into /usr/local/apache
and there doesn't appear to be an apache instance there.
* Support truetype fonts (need Bio::Graphics 2.33 or higher; set truetype=1 in GBrowse.conf, and
optionally pass font names like "Helvetica-12:Italic" to the track "font" option).
* Clicking on the "Go" button when an annotation plugin is selected now turns on the corresponding track.
* Clicking on the "Go" button when a filter plugin is selected opens up the configuration dialog.
* Added Juan Tena's split_wig.pl script, which is useful for uploading WIG files from genomes with lots
of scaffolds.
* Fix performance problems when using in-memory databases composed of multiple GFF3 files. The fix is
a hack that involves overwriting the Bio::DB::SeqFeature::Store::LoadHelper module!
2.54
* Version 2.53 introduced a bad bug into track configuration such
that semantic zooming no longer works for user-provided
configuration. This has now been fixed.
2.53
* Fix a variety of semantic zooming inconsistencies.
* Code simplification in data source.
2.52
* Avoid clipping the subtrack selection link on long track titles.
* Require Bio::Graphics version 2.31 to avoid bug in wiggle xyplot generation.
2.51
* Fix "can't call FETCH without object reference" errors during ./Build test.
* Fix pod documentation for gbrowse_grow_cloud_vol.pl.
* Remove gbrowse_attach_slaves.pl.
* Volumes added to cloud instance have deleteOnTermination set to true.
2.50
* Add gbrowse_import_ucsc_db.pl, which will create a fully functional starter database
from a UCSC data source (e.g. 'hg19').
* Add VirtualBox and EC2 virtual machine support (see http://gmod.org/wiki/GBrowse2_VMs).
* Prompt user before overwriting a customized config file.
2.49
* Add new "metadata" option in track stanzas for making subtracks selectable via
structured metadata; see http://gmod.org/wiki/Creating_and_Managing_Subtracks_with_GBrowse2
for details.
* Specify which database to use for search result karyotype display using following
syntax:
[builtin:karyotype]
database = my_database
* Fixed error reporting when uploading badly-formatted WIG files.
* Do something sensible when user tries to upload a bigwig file.
* Some support for UCSC-style uploads with "track type=bigWig bigDataUrl=http://something...".
2.48
* Fix track-level genbank and fasta dumping.
* Fix (mostly) the batch and sequence dumping plugins.
2.47
* Fix bugs in demo mode.
* Fix session locking bug; FastCGI performance subjectively improved.
* Revert to using inline imagemaps when not running in an accelerated environment.
* Require Bio::Graphics version 2.26, so that transparency is supported.
2.46
* Support for transparent overlay tracks. These will appear as a user settable formatting option
for any track with subtracks. To make this default for a track set "bump = overlap" and consider
setting "color_series = 1" in order for background colors to be assigned automatically;
* When downloading vista tracks, default download format to "vista_wiggle".
* Fix signal handling under FastCGI in order to kill runaway rendering processes
when server restarted.
2.45
* Restore h_feat & h_region functionality to gbrowse_img.
* Fix gbrowse_img documentation to point to correct example URLs on WormBase.
* Fix persistent grey screen when clicking on snapshot thumbnail.
* Fix URL-escaped characters appearing in snapshot name.
2.44
* Modest performance improvements when rendering multiple tracks.
* Set absolute cap of 5000 features per track to avoid performance issues on NGS data.
This cap can be changed by setting "maximum features" in the [GENERAL] section. Set
to 0 to return to unlimited behavior.
* Imagemap is now generated in such a way that time-consuming callbacks are only executed when
mouse hovers or clicks on the feature. This noticeably speeds up track generation time. Drawback
is that this increases the delay before balloon pops up on the hover operation when run in
cgi-bin mode (still fast in FastCGI mode). Restore original behavior by setting
"inline imagemaps" (or "inline imagemap") to true in [TRACK DEFAULTS]
or individual track definitions.
* Can now close tracks from main view even when corresponding track checkbox not showing
in the track listing.
* Default to flock locking instead of NFS locking; the former seems to be faster.
* Enable shared session locking to improve performance.
* Fix bad database pathnames in yeast configuration file examples.
* Fix track finder plugin to avoid annoying extra refresh after leaving text entry field.
* Fix broken sorting of subtracks.
* Improve dynamic range of wiggle tracks.
* mod_perl is no longer supported due to unfixable issues with zombie processes.
2.43
* Fix semantic zooming bug which caused features to disappear when feature type changed between
semantic zooming levels. Also speeded up rendering process.
2.42
* Improve user interface when a new openid user first logs in.
* Fix outgoing mail, which was broken.
2.41
* Quash bugs related to miscalculating semantic zooming settings.
* Fix inability to close tracks in the overview by clicking on their close box.
2.40
* Quash a few uninitialized variable warnings when bringing up track configuration dialog.
* Fix inability to toggle visibility & favorite status of plugin tracks from the
track titlebar.
* Added caching of inverted configuration file data structure to speed up track
rendering on really huge configuration files with many stanzas. Cache structure
is stored in /tmp/bio_graphics_ff_cache_$UID
* Add ability to save and restore named snapshots of current state.
* Changed behavior of render slave to a prefork model. Activate by including
PREFORK=5 (or other desired number of servers) in /etc/default/gbrowse-slave.
* Added support script for Amazon cloud image: gbrowse_attach_slaves.pl creates
slave instances for AMI ami-c6ca31af.
* Change default tmpfile location to /var/tmp/gbrowse2 (was /tmp/gbrowse2).
2.39
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