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@gmod/jbrowse

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JBrowse - client-side genome browser

jbrowse.org

GMOD/jbrowse

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--- layout: post title: JBrowse 1.11.2 maintenance release date: 2014-02-10 tags: ["Software releases"] --- JBrowse 1.11.2 has been released, with some new controls to adjust the size of quantitative tracks (thanks to Evan Briones at University of Arizona!), added support for the new text-based `tracks.conf` files to `generate-names.pl`, and quite a few other small improvements. Files for download: * [JBrowse-1.11.2.zip](/wordpress/wp-content/plugins/download-monitor/download.php?id=91 "download JBrowse-1.11.2.zip") - 4.7M file SHA1 5714343563074b96046acf86fb66d6d32a8bacea * [JBrowse-1.11.2-dev.zip](http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=92 "download JBrowse-1.11.2-dev.zip") - 26M file SHA1 47f432620a2b1d0c1aa2529f42e1a75fe4898447 ## Minor improvements * Added some user interface elements to set the height in pixels of a single quantitative track, or of all visible quantitative tracks. Thanks to Evan Briones for implementing this! * Added a `JBrowse/View/FeatureGlyph/Diamond` glyph that draws diamond-shaped features instead of boxes. Thanks to OICR Co-op student Kevin Mohamed for implementing this! * Reference sequence tracks now display a "no sequence" message instead of a bunch of blank blocks when the reference sequence basepairs aren't available. Thanks to Kevin Mohamed for implementing this ([issue #422](https://github.com/gmod/jbrowse/issues/422)). * Persistent session state is now stored on a per-dataset basis, which improves user experience when switching between multiple datasets in JBrowse. Thanks to Richard Hayes for pointing this issue out, and Kevin Mohamed for the fix ([issue #410](https://github.com/gmod/jbrowse/issues/410)). * "Hide sites not passing ..." settings in VCF track menus now show the filter's long description when hovered over. Thanks to Keiran Raine for suggesting this ([issue #420](https://github.com/gmod/jbrowse/issues/420)). * Tweaked display of track labels and added a slight border at the top edge of each track to make it more clear which track data belongs to. Thanks to Keiran Raine for suggesting this, and Kevin Mohamed for the initial implementation ([issue #432](https://github.com/gmod/jbrowse/issues/432)). * Added a `--config` option to `flatfile-to-json.pl` that accepts additional configuration variables that will be merged into the top level of the track configuration. Thanks to Mikael Brandström Durling for the initial implementation of this. ## Bug fixes * `generate-names.pl` now indexes VCF files from track definitions in `tracks.conf` files. Thanks to Paul Halle for pointing this out ([issue #434](https://github.com/gmod/jbrowse/issues/434)). * Added a missing dependency for the server side formatting tools on List::MoreUtil 0.28 or higher. Thanks to Cris Lawrence and Keiran Raine for troubleshooting this!