October 2015 Galaxy Release (v 15.10)¶

Highlights¶

Reports Application: The reports web application has been greatly enhanced - including improved styling, new landing page, more reports, pagination, and sparklines. Huge thanks to Daniel Bouchard (@Airistotal) for these enhancements.
Upload: The Galaxy upload widget now features support for composite datatypes and improved styling.
Data Libraries: Improved API and UI for data libraries - including support for library folder management and search.

GitHub ¶

New

% git clone -b master https://github.com/galaxyproject/galaxy.git

Update to latest stable release

% git checkout master && pull --ff-only origin master

Update to exact version

% git checkout v15.10

BitBucket ¶

Upgrade

% hg pull
% hg update latest_15.10

See our wiki for additional details regarding the source code locations.

Deprecation Notices¶

The Mercurial repository at https://bitbucket.org/galaxy/galaxy-dist is deprecated. We recommend deployers to switch their instances to git and follow the master branch of GitHub repository https://github.com/galaxyproject/galaxy Details are available at https://galaxyproject.org/develop/source-code/ The next few releases will still be available on Bitbucket, but they may be less up to date than the corresponding GitHub branches.

The old UI of Data Libraries is deprecated and will be removed in the next release of Galaxy. The current Data Libraries Beta will replace it. The Data Library menu items were renamed accordingly.

The graphview visualization is deprecated and will be replaced in the next release of Galaxy.

The direct access to Tool Shed repositories through the Mercurial API is deprecated. It will be removed in a future release. Please use Planemo for uploading to the TS instead.

Release Notes¶

Greatly enhance the reports application - including improved styling, new landing page, pagination, and sparklines. Huge thanks to @Airistotal. Pull Request 370, Pull Request 410, Pull Request 609, Pull Request 472, Pull Request 576, Pull Request 678 Pull Request 675, Pull Request 584
Enhanced upload tool - with support for composite types and improved styling. Pull Request 605, Pull Request 620, Pull Request 577, Pull Request 628
Improved API and UI for data libraries - including new support for library folder management and search. Pull Request 806, Pull Request 820
Expose more history panel options for collection datasets. Pull Request 854
Improve UI encapsulation for panel rendering, iframes and tool forms. Pull Request 706, Pull Request 739, Pull Request 786
Implement whitelist for tools that generate HTML. Pull Request 510
Add regex_replace tool dependency install action. Pull Request 457
Document Galaxy interactive environments (GIEs). (Thanks to @hexylena.) Pull Request 803
Explicit project procedure language on reversions and WIP. (Thanks to @hexylena.) Pull Request 556
Readme improvemenets - GitHub issues, security email contact and CI testing (Thanks to @nsoranzo.) Pull Request 574
Remove history controller methods. Pull Request 578
Remove older references to get_disk_size and associated methods in histories code. Pull Request 582
Cleanup of the Tool Shed’s url handling methods. Pull Request 586
Remove old cloudlaunch in favor of new web application. Pull Request 597
Enable a Grunt develop mode. Pull Request 601
Allow tools to explicitly produce nested collections. Pull Request 538
Update output actions code for some collection operations. Pull Request 544
Allow discover_datasets tag to use format attribute (instead of ext). Pull Request 764
Implement min and max attributes for multiple data input parameters. Pull Request 765
Style fixes a test fixes for all tool shed code. (Thanks to @nsoranzo.) Pull Request 650
Style fixes for lib/galaxy_utils/. (Thanks to @nsoranzo.) Pull Request 604
Style fixes for test/. (Thanks to @nsoranzo.) Pull Request 653
Style fixes for contrib/ and lib/tool_shed/. (Thanks to @nsoranzo.) Pull Request 708
Style fixes violated when merging from release_15.07. (Thanks to @nsoranzo.) Pull Request 688
Style fixes for tool shed database migrations. (Thanks to @nsoranzo.) Pull Request 770
Changed refresh time on reports homepage (Thanks to @Airistotal.) Pull Request 609
Remove unused fastx_clipper_sequences.txt file. (Thanks to @lparsons.) Pull Request 611
Move manual_builds.txt to manual_builds.txt.sample. (Thanks to @lparsons.) Pull Request 612
Expose tool shed version through API. Pull Request 613
Improvements to history API allowing fetching of histories shared with given user. Pull Request 614
Allow deserializing dataset permissions via the API. Pull Request 640, Pull Request 496
Merge nearly-identical methods in shed_util_common module. Pull Request 651
Expose tool config file path to admins via the API. Pull Request 652
Add Galaxy developer documentation section to docs. (Thanks to @hexylena.) Pull Request 654
Password reset improvements. Pull Request 655
Allow accessing repeat and conditional elements in workflow post job action parameters. Pull Request 662
Use new path variable syntax available since Routes 1.9. (Thanks to @nsoranzo.) Pull Request 665
Lazy-load histories into multi-history view. Pull Request 676
Use standard Galaxy message box styles on tool help texts that use rST admonitions. Pull Request 685
Set a default value for copy history dialog radio input (to copy all). Pull Request 693
Remove various code duplication. (Thanks to @hexylena.) Pull Request 694
Use setup.py for Python all installations during dependency installation. (Thanks to @bgruening.) Pull Request 698
Reorganize procedures documentation content. (Thanks to @nsoranzo.) Pull Request 702
Upgrade sqlalchemy to 1.0.8. Pull Request 709
Enhance GenomeSpace tools to report the GS tool name. Pull Request 711
Add Oxli datatypes. (Thanks to @dib-lab.) Pull Request 721
Extend root controller to allow specifying a history id. Pull Request 725
Fix multi-history copy/new to set the history as current. Pull Request 727
Fix workflow post job actions when rerunning a job. Pull Request 730
Trigger iframe event for history. Pull Request 732
Add testing environment variable GALAXY_TEST_LOGGING_CONFIG. Pull Request 738
Do not explicitly require pexpect Python dependency. Pull Request 741
API and UI enhancements for history copying. Pull Request 742
Remove deprecated objectstore options from sample documentation. Pull Request 748
Improved jobs API documentation. Pull Request 751
Improved state tracking of collections in history panel. Pull Request 755, Pull Request 819
Updates and fixes for dockerized Galaxy testing. Pull Request 759
When submitting tool error reports, include ‘old’ tool id as part of subject line. Pull Request 761
Eliminate use of bare exceptions from code. Pull Request 763
Add encoded IDs to job error reports and also include a link to show_params Pull Request 771
In log of collecting job metrics, print id of has_metrics object Pull Request 772
Add docker command wrapper. (Thanks to @scholtalbers.) Pull Request 777
Unify the docker command, command_inject, and command_wrapper (Thanks to @hexylena.) Pull Request 782
Test case to prevent regression of #753. Pull Request 784
Refactor interactive environment launching to use Docker’s -P option. (Thanks to @hexylena.) Pull Request 790
Print has_metrics class name instead of object memory address. (Thanks to @nsoranzo.) Pull Request 791
Improved state tracking of datasets in the history panel. Pull Request 793
Add sentry configuration option and doc to galaxy.ini.sample. Pull Request 799
Small tweaks to tool loading. Pull Request 813
Implment request timing middleware via statsd. Pull Request 821
Various small run_tests.sh fixes/enhancements. Pull Request 825
Remove test broken after #786. (Thanks to @nsoranzo.) Pull Request 828
Improved file handling in local runner. Pull Request 830
Swap debug mode to be off by default in galaxy.ini.sample. Pull Request 840
Update documentation for the gff_filter_by_attribute tool (Thanks to @bgruening.) Pull Request 842
Allow reuse of parent /tmp directory in dockerized testing. Pull Request 843
More small adjustments to test script run_tests.sh. Pull Request 844
UCSC tool cleanup - remove unused, deprecated code and add citations to existing tools. Pull Request 846
Add more distribution tool citations. Pull Request 847
Remove unused echo tool Pull Request 848
Update interactive environments for this release. (Thanks to @hexylena.) Pull Request 849
Enhancements for IPython interactive environment allowing it run in certain deployments. (Thanks to @scholtalbers.) Pull Request 462
Update style tools grunt-contrib-less, grunt-spritesmith. Pull Request 473
Preserve tags and annotations when copying datasets between histories. Pull Request 482
Implement grunt task for compiling handlerbars templates. Pull Request 484
Improve shortcut logic in Python job code. Pull Request 488
Do not render dataset selector when there are no datasets to select in history. Pull Request 491
Clean up the formatting on mapping.py Pull Request 492
Allow interactive environments to have their own static base url. Pull Request 500
Improve history dataset manager testing to verify set order of tags. Pull Request 493
Enhance directory handling for tool shed installations. (Thanks to @gregvonkuster.) Pull Request 511
Improved tag handling for anonymous users. Pull Request 516
Allow uninstalling multiple toolshed repositories at once. Pull Request 517
Allow the user to add the dataset for Trackster visualization to and existing visualization. Pull Request 526
Tool extract_genomic_dna tool to support for 2bit files from local data. (Thanks to @yhoogstrate.) Pull Request 529
Remove unused serializer _get_history_data. Pull Request 530
Render nice_size on the client. Pull Request 532
Swap track_jobs_in_database to be True by default. Pull Request 533
Update client libs: farbtastic, jqtouch, bib2json Pull Request 536
Standardize nice_size() import. (Thanks to @nsoranzo.) Pull Request 537
Remove older, unused history CSS rules. Pull Request 539
Allow ordering of the history index list using an order query parameter. Pull Request 540
Improve job config error message when no handler elements are defined. Pull Request 543
Allow use of History disk_size as a column in queries. Pull Request 550
Implement API for dealing with converted datasets. Pull Request 553
Include tool shed API information in Galaxy’s documentation. Pull Request 569
Stop creating unneeded database/message.mako.py file. Pull Request 575
Page Saved Histories at 10 histories. Pull Request 581
Remove older references to get_disk_size and associated methods. Pull Request 582
Remove osme unused files in /static. Pull Request 583
Minor cleanup of some Python iterator usages. Pull Request 589
Minor tool shed code style cleanup. Pull Request 591
Include valid_tools as part of metadata returned with the repository install information. Pull Request 592
New API for published histories. Pull Request 594

Fixes¶

Fix batch mode input in new tool form UI. (Thanks to @ericenns.) Pull Request 568
Tool lineage fixes. (Thanks to @nsoranzo.) Pull Request 596
Fix bug in reload API where id wasn’t recognised. (Thanks to @hexylena.) Pull Request 619
Correct typo in tool shed action handler code. (Thanks to @hexylena.) Pull Request 561
Small fixes for UI functional tests. Pull Request 485, Pull Request 487
Bug fixes related style adjustments. (Thanks in part to @nsoranzo.) Pull Request 478, Pull Request 479, Pull Request 480, Pull Request 481
Fixes to make Sweepster functional. Pull Request 486
Add client to ignore so that tox locally doesn’t try to test JavaScript. Pull Request 494
Fix for server error when installing certain repositories. Pull Request 495
Fix BBI data provider underflow bug when computing standard deviation. Pull Request 499
Add numpad support to integer inputs. Pull Request 509
Fix for rdata datatype. Pull Request 512
Fix for toolshed escape method, where an error/log message contains non- ASCII characters. Pull Request 514
Restore line wrongly removed in fa7c5c5 and again in 9805294 . (Thanks to @nsoranzo.) Pull Request 515
Ensure file exists before attempting chmod in tool shed install code. Pull Request 545
Filter deleted library datasets when using the library data parameter. Pull Request 546
Correct examples in workflow invocation documentation. Pull Request 565
Fix the CSS class for reports brand. Pull Request 585
Retab .loc.sample files. Pull Request 587
liftOver.loc was not accessible in local data (Thanks to @yhoogstrate.) Pull Request 588
Ensure removal of temporary tool shed files. Pull Request 607
Bug fix in Reports (Thanks to @Airistotal.) Pull Request 626
Cleaner commit history for #629 and array syntax for pathspec (Thanks to @chambm.) Pull Request 632
add missing js build Pull Request 648
Reports - Small bug fixes (Thanks to @Airistotal.) Pull Request 656
Fix tool image paths Pull Request 660
remove reports style that affected the whole application Pull Request 661
Fix centering bug in firefox (Thanks to @Airistotal.) Pull Request 669
Don’t overwrite $R_LIBS path during installation. (Thanks to @bgruening.) Pull Request 671
Fix tool shed installation issue (#525). (Thanks to @mvdbeek.) Pull Request 681
Return copied collection from manager copy method. Pull Request 682
Fix multi-history fetch flag to allow re-fetching after collection sort. Pull Request 695
Small fixes for LDAP auth. (Thanks to @nsoranzo.) Pull Request 696
Fix regression introduced in tool shed code this cycle. (Thanks to @nsoranzo.) Pull Request 701
Fix workflow editor post job action argument display. Pull Request 703
Fix to get custom tabular datatypes. (Thanks to @richard-burhans.) Pull Request 705
Fix for logging in using OpenID when the OpenID isn’t associated. Pull Request 712
Misc fixes. (Thanks to @nsoranzo.) Pull Request 720
Fix history option flags. Pull Request 726
Fix Galaxy.user in client code to be available when not using a require. Pull Request 728
Remove no-op __init__ methods from lib/galaxy/datatypes/binary.py. (Thanks to @mr-c.) Pull Request 729
Fix more API tests. (Thanks to @nsoranzo.) Pull Request 731
Fixes for framework test cases. (Thanks to @nsoranzo.) Pull Request 752, Pull Request 757
Bugfix in test error reporting handling code. Pull Request 760
Tool form error messages and rerun fixes. Pull Request 766
Quote value to fix configparser error in interactive environments. (Thanks to @hexylena.) Pull Request 775
Fix upload event binding. Pull Request 778
Fix _JAVA_OPTIONS example in job_conf.xml.sample_advanced. Pull Request 796
Fix errors when starting ./run_tests.sh -with_framework_test_tools -api. (Thanks to @nsoranzo.) Pull Request 800
Tweak password reset email template to truly be plain text. Pull Request 812
Fix returned tuple from creating_job. Pull Request 817
Fix database initialization when galaxy.ini doesn’t exist. Pull Request 822
Fix default value for optional select fields. Pull Request 826
Use dependency handling in lib/galaxy/datatypes/. (Thanks to @nsoranzo.) Pull Request 838
Expose all API keys to admins under REMOTE_USER. (Thanks to @hexylena.) Pull Request 873
Various fixes for data libraries. Pull Request 878
Minor fixes to the history UI. Pull Request 910
Fix command quoting and remove size from text input for Cut tool. Pull Request 913

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Thanks for using Galaxy!

The Galaxy Team