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DevNewsBriefs/2014_10_06

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Distribution Summary 2014_10_06

http://getgalaxy.org
October 06, 2014 Galaxy Distribution News Brief



getgalaxy   

getgalaxy.org

galaxy-dist.readthedocs.org

bitbucket.org/galaxy/galaxy-dist

new:

$ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable 

upgrade:

$ hg pull 
$ hg update latest_2014.10.06


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:

  1. Config files moved into the sub-directory config/ .

  2. universe_wsgi.ini renamed to galaxy.ini and is now located in the config/ directory.

  3. Allow specifying of galaxy.ini defaults with environment variables.

  4. Removed unneeded contents of the root directory.
  5. Visualizations in Trackster now default to using config from new structure.
  6. Public release of Galaxy Ansible roles for installing, configuring, and managing

  7. Tool development simplified through GalaxyProject at GitHub

  8. Galaxy and Pulsar, a perfect team


PR#495 PR#501 discussion XynZwvnV G1SuUSxn s6pCnhMc ddTT39sA 8kFDSTBh
We thank Björn Grüning and other members of the community that helped to guide and support us through this transition.

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:

  1. You can now run many big tools on TACC's Stampede supercomputer (Official Beta(tm)!). Details here ...

  2. 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).

  3. 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.
  4. New ‘Dataset Chooser’ that allows the user to select one or more datasets from a particular source (current history, other histories, library datasets), example, wiki, and future upgrades.

  5. 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.
  6. 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

  7. 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


G4e5saQb fdlgSAYB PVdbbpQS lAFJnOfd nQmxOG60 m8gqYuTd

Improved

  1. Created a simple status.galaxyproject.org page to track UseGalaxy.org availability plus other primary servers. poeCC0KG

  2. Dynamic destination enhancements aimed at enabling co-locating data and (cloud) bursting. This was a complex upgrade, please review the links for full details: PR#465 lqqDhy6l

  3. jQuery updated to 1.11. Review more about the upgrade here. rhv5Nj7B

  4. Better reporting of details related to errors to facilitate troubleshooting. This enhancement only works with AJAX done through jQuery. anbum96x

  5. New APIs for managing permissions of libraries, library datasets plus folders, method to retrieve older versions of library datasets. woyoS8Wo

  6. Automatically re-queue jobs that fail under specific conditions (such as walltime timeouts) to alternate cluster destinations. 36HT4odq

  7. Optimize the job query to only select jobs ready to run at startup. XyHzzPGk

  8. Enable the specification of a UUID when using the upload tool. Contributed by Kyle Ellrott. PR#463 OF9fARUc

  9. UUID detection passed as input is now enabled. See the PR#471 for a first use case (added to Workflows). Our thanks again to Kyle Ellrott. 7MmRsXns 684L4W7D

  10. Upgrade to add a new search functionality when browsing or managing Data Library user roles through the UI. woyoS8Wo

  11. Enhanced the Data Libraries API to allow for copying hdas directly in, without re-uploading. lwBDzAEi

  12. 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

  13. Build sites admin files are now configurable to fully support display application functionality. YPxlmedb

  14. The tool_shed_repositories.py Tool Shed repo install

  15. Security enhancement that will permit the blocking of remote access if the user is not an admin. Thank you to James Johnson. Review the pull request and ticket for details. PR#468 qbmqjhor

  16. 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

  17. Added support for Illumina 1.8+ fastq headers to tools/fastq/fastq_paired_end_joiner. Thanks to Simone Leo. PR#281PR#177 YjjFv3Rv

  18. Updated wiki documentation for admin activities related to data integration. FinBeDet

  19. 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

Fixed

Images/NewsGraphics/2014_10_06_trello-5A2czklq.png
  1. Fastq groomer had a one-off difference with sequence count. d1IIKmGK

  2. Now job_files.py allows writing the VERSION_STRING back for a job. lWAPW3hd

  3. Corrected issue where the loading label in a history would duplicate if clicked multiple times (see pic). 5A2czklq

  4. The job lock function, located in the UI "Admin panel: Manage jobs" group, has been reintroduced. BTDaHy9m

  5. Bug fix for the testing framework associated with <repeat> tags. XjtA0ty5

  6. General Grid bug in Admin’s ‘Browse Installed Repositories’ page is now resolved. JwBOTgVl

  7. Fix "histories, set_as_current" failing when used without an existing session. KzqulfCU

  8. Bug fix for when CasperJS tests hang under certain conditions. IzAEX87N

  9. Fix for displaying wiggle ( .wig ) datasets in Trackster. hkFhaRnt

  10. Fix for usage case where Workflows would occasionally be multi-submitted to the job queue. 2l1cCAeS

  11. Galaxy no longer produces invalid tool detail JSON (and potentially elsewhere) due to "infinity" tool input values. TjbNbadP

  12. 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

  13. Failure to import ‘exported histories’ is now resolved (parameter ‘sanitation’ was the issue). OPeYs049

  14. Scratchbook was not displaying all file formats due to other recent changes, but now it does again. Ojx8UXc8

  15. Now use ‘log.debug’ instead of ‘warn’ for purposely disabled visualization plugins. 1TYOBGQ8

  16. Admin "manage data libraries" tool corrected to include all completion messages/buttons. eG8lkNbl

  17. PBKDF2 authentication no longer impacts FTP logins, using ProFTPD 1.3.5 (3rd party bug fix). 8oho1Ojy

  18. The "Manage library permissions" page now displays and functions correctly in all of the latest browsers. 9pwSPQdR

  19. Fixed bug with Pulsar regarding retry/resume of interrupted cURL transfers. ul77OiPm

Gossip

  1. In other news, please see our prior two Updates:
    September 2014 Galaxy Update
    October 2014 Galaxy Update

Security

<!> 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.

Upgrades

  1. Review instructions for core build: Getting the Stable Distribution

  2. Review reset for Toolshed repos: Resetting Metadata For Installed Repositories

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