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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