$ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable
$ hg pull
New! Galaxy Reorganized
Certain files in the Galaxy clone root directory have been renamed, moved, removed, and/or have modified usage.
There is configuration resolution solution in place that will automatically use the config files in the old locations if they exist, or the new locations if they do not. Administrator can also move any non .sample versions of modified files into config/ to match the new directory structure.
Specifically, the following changes were made:
Config files moved into the sub-directory config/ .
universe_wsgi.ini renamed to galaxy.ini and is now located in the config/ directory.
Allow specifying of galaxy.ini defaults with environment variables.
- Removed unneeded contents of the root directory.
- Visualizations in Trackster now default to using config from new structure.
Public release of Galaxy Ansible roles for installing, configuring, and managing
Tool development simplified through GalaxyProject at GitHub
New! History and Dataset Functions
Several enhancements and improvements have been made to facilitate easier viewing and manipulation of data within the Galaxy UI and Job execution choices. These include:
The current/active dataset (the dataset being shown/manipulated in the center panel of 'analyze data') is now highlighted. Hovering over a history dataset lights up the other datasets from which it was derived (Edit: this was mistakenly reported as a released feature).
- One can now view datasets within collections that are within published or page embedded histories (as well as admin views), plus other dataset collection test and design improvements, including drill-down and fold-down viewing methods.
- The scroll position of the history panel is now stored and will persist across page loads. In other words, if you've scrolled to a dataset at the beginning/bottom of your history, the history panel will open to that same position when re-loaded. The scroll position will reset to the top when the history is switched or a new dataset is added.
Datasets that time-out (and fail) in a smaller queue are automatically resubmitted to the longer running queue. This ‘re-submitted’ state is displayed when a dataset is fully expanded in the history panel. 6BFJfDqX
When deleting the current history from the history options, the most recent history is set as the new current one instead of creating a new history. A new history is still created if the user is anonymous or if there are no non-deleted histories remaining. jPMEX46R
New APIs for managing permissions of libraries, library datasets plus folders, method to retrieve older versions of library datasets. woyoS8Wo
Automatically re-queue jobs that fail under specific conditions (such as walltime timeouts) to alternate cluster destinations. 36HT4odq
Optimize the job query to only select jobs ready to run at startup. XyHzzPGk
Upgrade to add a new search functionality when browsing or managing Data Library user roles through the UI. woyoS8Wo
Enhanced the Data Libraries API to allow for copying hdas directly in, without re-uploading. lwBDzAEi
Clarification about config requirements related to Virtual Environments (virtualenv and Python version checks, before executing run.sh. Thanks goes to Lance Parsons. hcUU4kzU. Duplicate of PR#486 IAN9mx71
Build sites admin files are now configurable to fully support display application functionality. YPxlmedb
The tool_shed_repositories.py Tool Shed repo install
Admin jobs page now includes more information about recently run jobs. Useful for getting a global view of jobs and for reviewing jobs that are not tracked in the UI history (such as history import/export jobs). Thanks to Kyle Ellrott. PR#466 PR#467 (add 466 ticket here) fjXBjXti
Function ‘migration 104’ was using a ‘Session()’ object and this conflicted with threadlocal configuration. Fix removed threadlocal from universe_wsgi.ini.sample, the root cause of ‘103 is not 105' migration errors seen lately. PR#439 EVVA5mmZ
Fastq groomer had a one-off difference with sequence count. d1IIKmGK
Now job_files.py allows writing the VERSION_STRING back for a job. lWAPW3hd
Corrected issue where the loading label in a history would duplicate if clicked multiple times (see pic). 5A2czklq
The job lock function, located in the UI "Admin panel: Manage jobs" group, has been reintroduced. BTDaHy9m
Bug fix for the testing framework associated with <repeat> tags. XjtA0ty5
General Grid bug in Admin’s ‘Browse Installed Repositories’ page is now resolved. JwBOTgVl
Fix "histories, set_as_current" failing when used without an existing session. KzqulfCU
Fix for displaying wiggle ( .wig ) datasets in Trackster. hkFhaRnt
Fix for usage case where Workflows would occasionally be multi-submitted to the job queue. 2l1cCAeS
Galaxy no longer produces invalid tool detail JSON (and potentially elsewhere) due to "infinity" tool input values. TjbNbadP
Issues with cluster jobs running as real user with LSF/drmaa are now resolved. Big thanks to Chong Chen and IBM. See ticket for full details: 5moWcFEd
Failure to import ‘exported histories’ is now resolved (parameter ‘sanitation’ was the issue). OPeYs049
Scratchbook was not displaying all file formats due to other recent changes, but now it does again. Ojx8UXc8
Now use ‘log.debug’ instead of ‘warn’ for purposely disabled visualization plugins. 1TYOBGQ8
Admin "manage data libraries" tool corrected to include all completion messages/buttons. eG8lkNbl
The "Manage library permissions" page now displays and functions correctly in all of the latest browsers. 9pwSPQdR
On July 31st, we fixed a serious security vulnerability in Galaxy and notified the community. Please upgrade immediately if you haven’t done so already: Instructions. Stay connected! We both email and tweet security alerts.
Review instructions for core build: Getting the Stable Distribution
Review reset for Toolshed repos: Resetting Metadata For Installed Repositories