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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 1.10.9 maintenance release date: 2013-11-08 tags: ["Software releases"] --- JBrowse 1.10.9 has been released, with new incremental-updating support in `generate-names.pl`, along with some other bug fixes and small improvements. Files for download: * [JBrowse-1.10.9.zip](/wordpress/wp-content/plugins/download-monitor/download.php?id=79 "download JBrowse-1.10.9.zip") - 4.6M file SHA1 e05f599c8692489e7c184cfd6c340afc79519a38 * [JBrowse-1.10.9-dev.zip](http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=80 "download JBrowse-1.10.9-dev.zip") - 26M file SHA1 e74d9b8ab21aa31e9ce09ff996ec45916b934821 ## Minor improvements * `generate-names.pl` now supports a `--incremental` or `-i` option that adds names to an existing index. Thanks to Richard Hayes for reminding me that this wasn't done yet ([issue #373](https://github.com/gmod/jbrowse/issues/373)). * Added a lower-performance, but more backward-compatible indexing backend to generate-names.pl that can be activated by passing the `--safeMode` command-line argument. The recent performance improvements to generate-names.pl have apparently tickled some bugs that are present in some installations. Thanks to Josie Reinhardt and GitHub user raj76 for their continued help troubleshooting this. If you find that name indexing is not working correctly, try running it again with `--safeMode`, and report to the mailing list if it helps. * Added support for using the JBrowse in-memory GFF3 adaptor to display web-accessible GFF3 files directly. See docs/tutorial/data_files/volvox.gff3.conf for an example configuration. Thanks to David Goodstein and Richard Hayes for motivating this. ## Bug fixes * `flatfile-to-json.pl` now depends on the latest Bio::GFF3::LowLevel::Parser 1.8, which fixes a bug in which features with no ID, Parent, or Derives_from attributes were not being included in parsed data. Thanks to Gwendoline Andres for pointing this out. * Tweak BioPerl-handling code in biodb-to-json.pl to hopefully work better with BioSQL backends. Thanks to Brian Osborne for pointing this out.