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Galaxy March Release Summary

http://getgalaxy.org
March 2015 Galaxy Release (v 15.03)



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_15.03


Release Versioning

Starting with this distribution, an updated Galaxy release versioning system has been implemented. The versioning scheme is Ubuntu-style.

Releases versioning details are as follows:

  • A version_major key has been added to /api/configuration.

  • The file version.py is the source of version_major.

  • "Point" releases will be created periodically with updates to the release.
  • "Point" releases are versioned as YY.MM.point, where ».point« begins at .1 and increments for each point release.

  • The first version is »15.03«, where the tag for the release is »v15.03«.
  • Stable updates to »15.03« will be »15.03.1«, »15.03.2«, where the tag for the release is formatted as »v15.03.1«.
  • Backwards compatibility: The tag »latest_15.03« in Bitbucket will always point to the newest »15.03« changeset.
  • XvAhmlb0 ZHGSGosl

Release Branches

  • The Github master branch is similar to the former Bitbucket stable branch. The difference is that whereas individual commits to the current stable release were previously applied to the stable branch, they are now only applied in a group, when a "point" release is made (e.g. 15.03.1). 

  • The Bitbucket stable branch now works the same way as the Github master branch.
  • Permanent named branches are now created for each release. The 15.03 release is in the release_15.03 branch, which will be updated with additional changes throughout the lifecycle of this release, as was done with the Bitbucket stable branch in the past. When the Galaxy Team determines that a "point" release is necessary, this branch is merged to master and a point release tag is created. This branch exists in both the Github and Bitbucket versions of Galaxy.

Thus, if you would like to upgrade to the 15.03 release and ensure you do not subsequently upgrade to the release after 15.03 (i.e. 15.05) when it is made, you can use the release_15.03 branch. If you would always like to run the latest release (recommended), you should use the master (Git) or stable (Bitbucket) branch.

Tool Redesign

Much of Galaxy’s core tool set has been redesigned. Several contain new functionality. These tools are included in the Tool Shed and many are ready for use on Galaxy Main. Older Workflows may contain tools that automatically map to the new tools or Workflows may need minor adjustments. c6Lkejro

Be sure to check out the new Galaxy NGS 101 wiki (in progress).

Github

Galaxy on GitHub

Galaxy development has moved to Github, but stable/release changes are mirrored to Bitbucket. Deployers can continue to use Bitbucket as they have done in the past.

Infrastructure

  1. Mercurial egg updated to version (3.2.4). 9A9uIav0 NUqyskst

  2. SQLAlchemy upgrade to version 0.9.8. zGLtSgPW

  3. An invalid API key will now always return a »403« error. Triggers: API key is not found, is expired, or is not associated with an active account. n59kZhXk

  4. Python PEP-8 fixes and API documentation enhancements for Libraries API. Thanks to Nicola Soranzo. MD4iUtzk

  5. Moved the vast majority of the test-data out of GALAXY_ROOT (remaining tools excluded). kcYI9DnK xd7Uri9l

  6. New options that permits tools to access their $REPOSITORY_INSTALL_DIR location via PATH. 0pgF5PBQ

  7. To preserve the original deployment state, a new option to disable runtime egg fetching was created (a configurable environment variable - see ticket for details). lthRjVZq

  8. Enhancement to permit configuration to disable egg fetching or the use of eggs entirely. gfm6jilm

  9. Six egg added to eggs.galaxyproject.org. Pv84VVZR

  10. Reloading an external display application from disk can be done now without restarting Galaxy. 4ZlsSGA4

  11. Functional tool tests now output xunit or nosetests style XML. dpfrNZDq

  12. Expanded on Base, History, and HDA managers to provide a consistent facade for common model operations. 3A8nocpN

  13. Upgraded SQLAlchemy to incorporate two major revisions in this release. XbZwEuxx

  14. Removed use of the elementtree package and move to lxml.etree. JJDxFdzK

  15. Stopped aborted restart when stop_daemon() fails. Thank you Nicola Soranzo. 1nlG2OmX

  16. Merged rolling_restart.sh in run.sh by adding a new —wait parameter and other enhancements. Thank you Nicola Soranzo. QNKSMf2B S3WLFpGL jx0F2RKy

  17. Enhancements to galaxy.ini and integrated_tool_panel.xml documentation. Contributed by Nicola Soranzo. 4idoVDY8

  18. New configuration option to isolate tool commands in their own shell. kyS9dF0s

  19. Added a new configuration, template_cache_path, to reports_wsgi.ini.sample. Thank you Trevor Wennblom. 5vJ4EsDI

  20. Provide NGINX packages with the upload module. C3g6Ko8K

  21. Backported fixes for GATK wrappers to all relevant latest_* releases. i5hd7V1d GkQbKmvS

  22. Allow reloading External Display applications without restarting Galaxy. 02W1lMw7

  23. Restructured mvc/ui.js. HnnBFJy0

  24. Improved use of a SELECT statement to reliably retrieve table column names. Thank you James Johnson. oYkjj4T3

  25. Enhanced a method to use first component of X-Forwarded-{For,Host,Scheme} when redirecting to the Galaxy browser. BmbtnSon BmbtnSon

  26. Migrated shed_tool_conf.xml into /config. Contributed by Nitesh Turaga. 6olcQrhR

  27. Made installation of tool repositories more robust by setting time to "Epoch" instead of throwing server error when repository_metadata.time_last_tested is unset. o09VBhr1

  28. Change to allow anonymous users (those not logged into a Galaxy account) to view Pages with embedded Histories. 9Om6Odj2

  29. The GET /api/jobs request/response functionality has been expanded. Details in ticket. Thank you Thomas McGowan. H0Bvd737

  30. SQlite query result rows can now be fetched by javascript visualization libs. Thanks to James Johnson. S3R9AdA9

  31. Moved blastdb_p.loc.sample to the NCBI BLAST Tool Shed repository. Thanks to Lance Parsons. lpZNmEzj

  32. Clearer error messages where parameter validation fails. Thanks to Peter Cock. dRaX5reV

  33. Added pkg_resources to load required Mako packages. Thanks to Lance Parsons. JdxJ11U0

  34. Updated the Dockerfile template to the latest version our Galaxy Docker Container (updated at Galaxy release). Thanks to Björn Grüning. Z45ZZ9C2

  35. Added a new API method to remove items from tool data tables. Thanks to Anthony Bretaud. 51JsMj0b

  36. Create attribute »optional« for data column parameters. A compliment to »force_select«. G5YtpQZK

  37. Enhanced the collect_primary_datasets() method to allow assignment of the defined output parameter for 3rd-party tools that manage tool outputs internally. pncHLXdw

New and Improved

  1. Data Source/Provider Functions: filtering of transferred lines based on parsed column values. jBMtQm0w

  2. Updated the Tuxedo RNA-seq tools to version 2.2.1 and created new wrappers for Cuffquant and Cuffnorm. In the Tool Shed and installed on http://usegalaxy.org. bfr0jKut

  3. New Multiple Histories View. XLkP9pCr

  4. Enhancement for how the »Available Genomes List« is generated for the display application IGV. 1T49snMh

  5. Enhanced the Data Managers' reference genome retrieval protocol to function better with UCSC's updated file naming/paths. Created a new Data Manager for dbkeys/Genome Builds. Find these in the Tool Shed. kPkwDHmi pmd6gSS6

  6. External Display Applications can now use Tool Data Tables. b5kX6Eje

  7. Data Managers can now populate Tool Data Tables that are undeclared. 2FV2aVIH

  8. Tool Data Tables can load from a URL instead of a path. xTsc9ojY

  9. Tuned and enhanced the determine_output_formats() method for tools. jeMaAiap

  10. Many changes have been made in order to support full usability of Dataset Collections in the near term. Latest progress includes:
    • Tools can now be written to explicitly produce one or more Dataset Collections. ndVQmt3G RA15wpMH

    • Tools may now use $input.element_identifier during tool evaluation for input data parameters (useful for Workflows/Dataset Collections). W5IChoLS

    • Implementation of Dataset Collections »list of pairs«. Additional work is in-progress (see ticket). 8hEO00xj

    • Dataset Collections updated to permit »Drag & Drop« functionality (»copy datasets« is still an option). Zmy8aiFP

  11. New ZebrafishMine Data Source tool. u5OlE4kZ

  12. New datatypes. Thanks to Björn Grüning.

    • Added SnpEff datatypes. accZ8KdI

    • Added CompressedArchive as a new datatype that does not uncompress during data upload. 1xtvpWil

    • Added Arff datatype. fdVfagbS

    • Added »RNA dotplot matrix« as a new datatype. vNmGhAGE

  13. API updated to include options for selecting data from or downloading (as a tar ball) tool-data content. Thank you Kyle Ellrott. 1874DlBw

  14. Allow BAM's set_meta() function to use SAMTools 1 to generate the index (when $PATH points to SAMTools 1). wVN3wSiT

  15. Upload UI enhancements that added »select all« functionality to severall operations. Contributed by Jennifer Cabral. X4WscBt8

  16. Modified API protocol when removing or refreshing a data table. x2DLSNlN

  17. History API Prototypes:
    • Consumers can filter index lists with a larger set of per-model options. n72g8sZG

    • New use of limit, offset in index calls. 7QH3vxRO

  18. Updated location for new Tool’s »Tool Shed URL«: Tool Options pull down menu. (see graphic at right) 8GdLuEj2

  19. Tool Panel »search« function optimized. 6Bvbduci

  20. Allowing Workflow step dependencies when no input/output files exist. h5qZlgU8

  21. Workflow steps are now assigned UUIDs. 4U9e1och

  22. Updated the Workflow API by replacing preferred usage terminology (s/usage/invocation). XNInq5KH

  23. Tuning for History panel functions: Dataset search, multi-select Datasets to perform batch operations, related database modifications. D4nLl5Ky

  24. To enhance sharing of a History or Page, the forms now accept user IDs. Contributed by Eric Rasche. qzYtnG4T DCjT4KdQ

  25. Load the »Available Genomes« list from data tables for visualizations (Trackster). Thanks to Anthony Bretaudeau. x8LMSD7Z

  26. The History »Options« menu has been updated to better compliment other recent UI changes. EEsM0abM

  27. Several improvements to the History list view. ltNMDNbZ

  28. New Fetch Genome Data Manager updated to create the metadata needed by Trackster. IKdX0vX5

  29. Addressed »multipart-upload« by using Swift as an object storage backend. Thank you Charles Hsu. U4kJBMk9

  30. Added Planemo test file to Tool Shed upload »blacklist«. Thanks to Björn Grüning. 0Z1tfTVU

  31. Added tool tests functions to assert properties about command, standard output, and standard error. kNgOADAF

Fixed

  1. Fixed tool shed tests by creating database directory when one is missing from the repository. Thank you Jennifer Cabral. mKBDDG8j

  2. Fixed provenance API request bug when data element has job == None. Thank you Kyle Ellrott. fPVKzBZ6

  3. Resolved a bug in Users API preventing administrators from creating users when allow_user_creation was False. aLqEOOyd

  4. Fixed a GATK Evaluation Bug. PXClb3PT

  5. Corrected an "over-sanitized" info message after renaming a history (html was displaying). MtAQNOqC

  6. Discovered and fixed issue with Paired list collection creator (key renaming broken). QklilFk3

  7. Fix for preventing non-admins from running Data Managers through the API.EeHJP167

  8. Egg-fetching related bugfixes. 9L0HlQ0u

  9. Fixes for resetting metadata on ToolShed Repositories. lGmlkvdr

  10. Small fixes for updated workflow scheduler. fF7pUNIG

  11. Change to use samtools version 1.x to generate BAM indexes if it is first in $PATH. UOVlg7nL

  12. Removed displayed paragraph tags from history/rename feedback messages V4VMvDeY

  13. Fixed Picard index Data Manager so that it no longer indicates failure (red dataset result in admin history) when it is actually successful. b1cHiIw0

  14. Corrected certain UI confirmation dialogs that were non-functional. LWkgOJRV

  15. Fix for installing .loc files from the Tool Shed to respect shed_tool_data_path in galaxy.ini.sample. njgEucfY

  16. Galaxy Report Webapp is now functioning when a MySQL database is used (functionality was already intact when PostgreSQL was used). Q91djTUc

  17. The Test ToolShed RSS feed no longer fails when time_last_tested == None. RrVBYIBZ

  18. Fetching zip-safe eggs that depend on other eggs were failing - this has been corrected. HWuxsftB

  19. Logging out through External authentication external_auth_logout_url now resets impersonation correctly (logs out of impersonated account). 4SX0BZKA

  20. Fixed tabular dataset display so that it sets the correct extension and mime-type when preview=False and to_ext is not provided. uZnZdFGu

  21. Additions to the js environment by require.js now correctly apply cache busting (avoiding user errors). s2klR2Bb

  22. Corrected a re-run operation that was reporting incorrect dataset names. eniXoRB6

  23. Fixed a history dataset counter that was not updating after a tool run. 2slkkPQW

  24. Several Fixes for Tool Data Tables. scA7eWKH

  25. Fixed History, HDA, and UI post-managers-refactoring. UPiay3qr

  26. Corrected Workflow/Visualization links that were including an extraneous slash »/». dtccfVRK

  27. Replaced missing get_initial_value function in LibraryDatasetToolParameter. MVOasuZY

  28. Correction for Tool Shed not having config.shed_tool_data_path. Og1WxqSA

  29. Fixed bug in multi-history view that wasn’t rendering well in Safari. oCU2Kvkt

  30. Resolved processing naming conflicts with uWSGI and Control Queues. ahDk0lx4

News and Community

Security

  1. Various low-vulnerability-level security fixes. U6yj2pPr

  2. Galaxy logs no longer leak database connection information. VjEqTxlT

  3. The email for resetting an account password is now a link. SKjU40t6

  4. New »shared secret« between Galaxy and upstream proxies, thereby preventing a specific potential impersonation attack. Thank you Eric Rasche. jTHrXHol

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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