We made Galaxy more lively and responsive. Homepage, published workflows, published/saved histories, and data libraries should all load much faster now. Importing data from FTP will also take less of your time.
Web Server and Configuration
The default web server used by Galaxy has changed from Paste to uWSGI and the default configuration file for Galaxy is now config/galaxy.yml instead of config/galaxy.ini. To minimize the impact of this change on existing Galaxy instances, if a Galaxy has a galaxy.ini file configured, it will continue to use Paste by default unless additional steps are taken by the administrator
Dataset Collection Usability
This release has significantly improved the usability of Galaxy dataset collections. Dozens of improvements to collections have been made, some of the key highlights include:
* Data library folders can now be sent to histories as a dataset collection. * Failed dataset collection elements can now be fixed using job re-running * Collections now appear with state and progress bars in the history panel and contained datasets are hidden by default * We added intuitive workflow post job actions for dataset collections * The web interface now supports collections with arbitrary nesting and size * More robust nametag discovery and propagation when using collections
The architecture for the client code that powers the Galaxy user interface has been significantly overhauled. The code base has been converted to ES6, Yarn now powers the build and dependency management of the code, Prettier is now used to ensure consistent code formatting, and the VueJS framework has been integrated.
New BAM datatypes Previously Galaxy only supported coordinate sorted BAM files by default (the bam datatype). In addition, this release of Galaxy now supports three new types of BAM: * qname_sorted.bam, that ensures that the file is queryname sorted (e.g. SO:queryname); * qname_input_sorted.bam, that can be used to describe the output of aligners which generally keep mate pairs adjacent * unsorted.bam, that makes no assumptions about the sort order of the file.
Experimental Job Caching Galaxy can now be configured to allow users the option of skipping duplicated jobs if one with identical parameters has been previously executed and simply reuse the previously generated outputs.