.. to_doc ------------------------------- 15.10 ------------------------------- Enhancements ------------------------------- .. enhancements * 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 `@erasche `__.) `Pull Request 803`_ * Explicit project procedure language on reversions and WIP. (Thanks to `@erasche `__.) `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 `@erasche `__.) `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 `@erasche `__.) `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 `@erasche `__.) `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 `@erasche `__.) `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 `@erasche `__.) `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 ------------------------------- .. 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 `@erasche `__.) `Pull Request 619`_ * Correct typo in tool shed action handler code. (Thanks to `@erasche `__.) `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 `@erasche `__.) `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 `@erasche `__.) `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`_ .. github_links .. _Pull Request 370: https://github.com/galaxyproject/galaxy/pull/370 .. _Pull Request 410: https://github.com/galaxyproject/galaxy/pull/410 .. _Pull Request 457: https://github.com/galaxyproject/galaxy/pull/457 .. _Pull Request 462: https://github.com/galaxyproject/galaxy/pull/462 .. _Pull Request 472: https://github.com/galaxyproject/galaxy/pull/472 .. _Pull Request 473: https://github.com/galaxyproject/galaxy/pull/473 .. _Pull Request 478: https://github.com/galaxyproject/galaxy/pull/478 .. _Pull Request 479: https://github.com/galaxyproject/galaxy/pull/479 .. _Pull Request 480: https://github.com/galaxyproject/galaxy/pull/480 .. _Pull Request 481: https://github.com/galaxyproject/galaxy/pull/481 .. _Pull Request 482: https://github.com/galaxyproject/galaxy/pull/482 .. _Pull Request 484: https://github.com/galaxyproject/galaxy/pull/484 .. _Pull Request 485: https://github.com/galaxyproject/galaxy/pull/485 .. _Pull Request 486: https://github.com/galaxyproject/galaxy/pull/486 .. _Pull Request 487: https://github.com/galaxyproject/galaxy/pull/487 .. _Pull Request 488: https://github.com/galaxyproject/galaxy/pull/488 .. _Pull Request 491: https://github.com/galaxyproject/galaxy/pull/491 .. _Pull Request 492: https://github.com/galaxyproject/galaxy/pull/492 .. _Pull Request 493: https://github.com/galaxyproject/galaxy/pull/493 .. _Pull Request 494: https://github.com/galaxyproject/galaxy/pull/494 .. _Pull Request 495: https://github.com/galaxyproject/galaxy/pull/495 .. _Pull Request 496: https://github.com/galaxyproject/galaxy/pull/496 .. _Pull Request 499: https://github.com/galaxyproject/galaxy/pull/499 .. _Pull Request 500: https://github.com/galaxyproject/galaxy/pull/500 .. _Pull Request 509: https://github.com/galaxyproject/galaxy/pull/509 .. _Pull Request 510: https://github.com/galaxyproject/galaxy/pull/510 .. _Pull Request 511: https://github.com/galaxyproject/galaxy/pull/511 .. _Pull Request 512: https://github.com/galaxyproject/galaxy/pull/512 .. _Pull Request 514: https://github.com/galaxyproject/galaxy/pull/514 .. _Pull Request 515: https://github.com/galaxyproject/galaxy/pull/515 .. _Pull Request 516: https://github.com/galaxyproject/galaxy/pull/516 .. _Pull Request 517: https://github.com/galaxyproject/galaxy/pull/517 .. _Pull Request 526: https://github.com/galaxyproject/galaxy/pull/526 .. _Pull Request 527: https://github.com/galaxyproject/galaxy/pull/527 .. _Pull Request 529: https://github.com/galaxyproject/galaxy/pull/529 .. _Pull Request 530: https://github.com/galaxyproject/galaxy/pull/530 .. _Pull Request 532: https://github.com/galaxyproject/galaxy/pull/532 .. _Pull Request 533: https://github.com/galaxyproject/galaxy/pull/533 .. _Pull Request 536: https://github.com/galaxyproject/galaxy/pull/536 .. _Pull Request 537: https://github.com/galaxyproject/galaxy/pull/537 .. _Pull Request 538: https://github.com/galaxyproject/galaxy/pull/538 .. _Pull Request 539: https://github.com/galaxyproject/galaxy/pull/539 .. _Pull Request 540: https://github.com/galaxyproject/galaxy/pull/540 .. _Pull Request 543: https://github.com/galaxyproject/galaxy/pull/543 .. _Pull Request 544: https://github.com/galaxyproject/galaxy/pull/544 .. _Pull Request 545: https://github.com/galaxyproject/galaxy/pull/545 .. _Pull Request 546: https://github.com/galaxyproject/galaxy/pull/546 .. _Pull Request 550: https://github.com/galaxyproject/galaxy/pull/550 .. _Pull Request 553: https://github.com/galaxyproject/galaxy/pull/553 .. _Pull Request 556: https://github.com/galaxyproject/galaxy/pull/556 .. _Pull Request 561: https://github.com/galaxyproject/galaxy/pull/561 .. _Pull Request 565: https://github.com/galaxyproject/galaxy/pull/565 .. _Pull Request 568: https://github.com/galaxyproject/galaxy/pull/568 .. _Pull Request 569: https://github.com/galaxyproject/galaxy/pull/569 .. _Pull Request 574: https://github.com/galaxyproject/galaxy/pull/574 .. _Pull Request 575: https://github.com/galaxyproject/galaxy/pull/575 .. _Pull Request 576: https://github.com/galaxyproject/galaxy/pull/576 .. _Pull Request 577: https://github.com/galaxyproject/galaxy/pull/577 .. _Pull Request 578: https://github.com/galaxyproject/galaxy/pull/578 .. _Pull Request 581: https://github.com/galaxyproject/galaxy/pull/581 .. _Pull Request 582: https://github.com/galaxyproject/galaxy/pull/582 .. _Pull Request 583: https://github.com/galaxyproject/galaxy/pull/583 .. _Pull Request 584: https://github.com/galaxyproject/galaxy/pull/584 .. _Pull Request 585: https://github.com/galaxyproject/galaxy/pull/585 .. _Pull Request 586: https://github.com/galaxyproject/galaxy/pull/586 .. _Pull Request 587: https://github.com/galaxyproject/galaxy/pull/587 .. _Pull Request 588: https://github.com/galaxyproject/galaxy/pull/588 .. _Pull Request 589: https://github.com/galaxyproject/galaxy/pull/589 .. _Pull Request 591: https://github.com/galaxyproject/galaxy/pull/591 .. _Pull Request 592: https://github.com/galaxyproject/galaxy/pull/592 .. _Pull Request 594: https://github.com/galaxyproject/galaxy/pull/594 .. _Pull Request 596: https://github.com/galaxyproject/galaxy/pull/596 .. _Pull Request 597: https://github.com/galaxyproject/galaxy/pull/597 .. _Pull Request 601: https://github.com/galaxyproject/galaxy/pull/601 .. _Pull Request 604: https://github.com/galaxyproject/galaxy/pull/604 .. _Pull Request 605: https://github.com/galaxyproject/galaxy/pull/605 .. _Pull Request 607: https://github.com/galaxyproject/galaxy/pull/607 .. _Pull Request 609: https://github.com/galaxyproject/galaxy/pull/609 .. _Pull Request 611: https://github.com/galaxyproject/galaxy/pull/611 .. _Pull Request 612: https://github.com/galaxyproject/galaxy/pull/612 .. _Pull Request 613: https://github.com/galaxyproject/galaxy/pull/613 .. _Pull Request 614: https://github.com/galaxyproject/galaxy/pull/614 .. _Pull Request 617: https://github.com/galaxyproject/galaxy/pull/617 .. _Pull Request 619: https://github.com/galaxyproject/galaxy/pull/619 .. _Pull Request 620: https://github.com/galaxyproject/galaxy/pull/620 .. _Pull Request 626: https://github.com/galaxyproject/galaxy/pull/626 .. _Pull Request 628: https://github.com/galaxyproject/galaxy/pull/628 .. _Pull Request 632: https://github.com/galaxyproject/galaxy/pull/632 .. _Pull Request 640: https://github.com/galaxyproject/galaxy/pull/640 .. _Pull Request 646: https://github.com/galaxyproject/galaxy/pull/646 .. _Pull Request 648: https://github.com/galaxyproject/galaxy/pull/648 .. _Pull Request 650: https://github.com/galaxyproject/galaxy/pull/650 .. _Pull Request 651: https://github.com/galaxyproject/galaxy/pull/651 .. _Pull Request 652: https://github.com/galaxyproject/galaxy/pull/652 .. _Pull Request 653: https://github.com/galaxyproject/galaxy/pull/653 .. _Pull Request 654: https://github.com/galaxyproject/galaxy/pull/654 .. _Pull Request 655: https://github.com/galaxyproject/galaxy/pull/655 .. _Pull Request 656: https://github.com/galaxyproject/galaxy/pull/656 .. _Pull Request 660: https://github.com/galaxyproject/galaxy/pull/660 .. _Pull Request 661: https://github.com/galaxyproject/galaxy/pull/661 .. _Pull Request 662: https://github.com/galaxyproject/galaxy/pull/662 .. _Pull Request 665: https://github.com/galaxyproject/galaxy/pull/665 .. _Pull Request 669: https://github.com/galaxyproject/galaxy/pull/669 .. _Pull Request 671: https://github.com/galaxyproject/galaxy/pull/671 .. _Pull Request 675: https://github.com/galaxyproject/galaxy/pull/675 .. _Pull Request 676: https://github.com/galaxyproject/galaxy/pull/676 .. _Pull Request 678: https://github.com/galaxyproject/galaxy/pull/678 .. _Pull Request 681: https://github.com/galaxyproject/galaxy/pull/681 .. _Pull Request 682: https://github.com/galaxyproject/galaxy/pull/682 .. _Pull Request 684: https://github.com/galaxyproject/galaxy/pull/684 .. _Pull Request 685: https://github.com/galaxyproject/galaxy/pull/685 .. _Pull Request 688: https://github.com/galaxyproject/galaxy/pull/688 .. _Pull Request 690: https://github.com/galaxyproject/galaxy/pull/690 .. _Pull Request 693: https://github.com/galaxyproject/galaxy/pull/693 .. _Pull Request 694: https://github.com/galaxyproject/galaxy/pull/694 .. _Pull Request 695: https://github.com/galaxyproject/galaxy/pull/695 .. _Pull Request 696: https://github.com/galaxyproject/galaxy/pull/696 .. _Pull Request 698: https://github.com/galaxyproject/galaxy/pull/698 .. _Pull Request 701: https://github.com/galaxyproject/galaxy/pull/701 .. _Pull Request 702: https://github.com/galaxyproject/galaxy/pull/702 .. _Pull Request 703: https://github.com/galaxyproject/galaxy/pull/703 .. _Pull Request 705: https://github.com/galaxyproject/galaxy/pull/705 .. _Pull Request 706: https://github.com/galaxyproject/galaxy/pull/706 .. _Pull Request 708: https://github.com/galaxyproject/galaxy/pull/708 .. _Pull Request 709: https://github.com/galaxyproject/galaxy/pull/709 .. _Pull Request 710: https://github.com/galaxyproject/galaxy/pull/710 .. _Pull Request 711: https://github.com/galaxyproject/galaxy/pull/711 .. _Pull Request 712: https://github.com/galaxyproject/galaxy/pull/712 .. _Pull Request 720: https://github.com/galaxyproject/galaxy/pull/720 .. _Pull Request 721: https://github.com/galaxyproject/galaxy/pull/721 .. _Pull Request 722: https://github.com/galaxyproject/galaxy/pull/722 .. _Pull Request 725: https://github.com/galaxyproject/galaxy/pull/725 .. _Pull Request 726: https://github.com/galaxyproject/galaxy/pull/726 .. _Pull Request 727: https://github.com/galaxyproject/galaxy/pull/727 .. _Pull Request 728: https://github.com/galaxyproject/galaxy/pull/728 .. _Pull Request 729: https://github.com/galaxyproject/galaxy/pull/729 .. _Pull Request 730: https://github.com/galaxyproject/galaxy/pull/730 .. _Pull Request 731: https://github.com/galaxyproject/galaxy/pull/731 .. _Pull Request 732: https://github.com/galaxyproject/galaxy/pull/732 .. _Pull Request 735: https://github.com/galaxyproject/galaxy/pull/735 .. _Pull Request 736: https://github.com/galaxyproject/galaxy/pull/736 .. _Pull Request 738: https://github.com/galaxyproject/galaxy/pull/738 .. _Pull Request 739: https://github.com/galaxyproject/galaxy/pull/739 .. _Pull Request 741: https://github.com/galaxyproject/galaxy/pull/741 .. _Pull Request 742: https://github.com/galaxyproject/galaxy/pull/742 .. _Pull Request 748: https://github.com/galaxyproject/galaxy/pull/748 .. _Pull Request 751: https://github.com/galaxyproject/galaxy/pull/751 .. _Pull Request 752: https://github.com/galaxyproject/galaxy/pull/752 .. _Pull Request 755: https://github.com/galaxyproject/galaxy/pull/755 .. _Pull Request 757: https://github.com/galaxyproject/galaxy/pull/757 .. _Pull Request 758: https://github.com/galaxyproject/galaxy/pull/758 .. _Pull Request 759: https://github.com/galaxyproject/galaxy/pull/759 .. _Pull Request 760: https://github.com/galaxyproject/galaxy/pull/760 .. _Pull Request 761: https://github.com/galaxyproject/galaxy/pull/761 .. _Pull Request 763: https://github.com/galaxyproject/galaxy/pull/763 .. _Pull Request 764: https://github.com/galaxyproject/galaxy/pull/764 .. _Pull Request 765: https://github.com/galaxyproject/galaxy/pull/765 .. _Pull Request 766: https://github.com/galaxyproject/galaxy/pull/766 .. _Pull Request 770: https://github.com/galaxyproject/galaxy/pull/770 .. _Pull Request 771: https://github.com/galaxyproject/galaxy/pull/771 .. _Pull Request 772: https://github.com/galaxyproject/galaxy/pull/772 .. _Pull Request 775: https://github.com/galaxyproject/galaxy/pull/775 .. _Pull Request 777: https://github.com/galaxyproject/galaxy/pull/777 .. _Pull Request 778: https://github.com/galaxyproject/galaxy/pull/778 .. _Pull Request 782: https://github.com/galaxyproject/galaxy/pull/782 .. _Pull Request 784: https://github.com/galaxyproject/galaxy/pull/784 .. _Pull Request 786: https://github.com/galaxyproject/galaxy/pull/786 .. _Pull Request 790: https://github.com/galaxyproject/galaxy/pull/790 .. _Pull Request 791: https://github.com/galaxyproject/galaxy/pull/791 .. _Pull Request 793: https://github.com/galaxyproject/galaxy/pull/793 .. _Pull Request 796: https://github.com/galaxyproject/galaxy/pull/796 .. _Pull Request 799: https://github.com/galaxyproject/galaxy/pull/799 .. _Pull Request 800: https://github.com/galaxyproject/galaxy/pull/800 .. _Pull Request 803: https://github.com/galaxyproject/galaxy/pull/803 .. _Pull Request 806: https://github.com/galaxyproject/galaxy/pull/806 .. _Pull Request 807: https://github.com/galaxyproject/galaxy/pull/807 .. _Pull Request 812: https://github.com/galaxyproject/galaxy/pull/812 .. _Pull Request 813: https://github.com/galaxyproject/galaxy/pull/813 .. _Pull Request 817: https://github.com/galaxyproject/galaxy/pull/817 .. _Pull Request 819: https://github.com/galaxyproject/galaxy/pull/819 .. _Pull Request 820: https://github.com/galaxyproject/galaxy/pull/820 .. _Pull Request 821: https://github.com/galaxyproject/galaxy/pull/821 .. _Pull Request 822: https://github.com/galaxyproject/galaxy/pull/822 .. _Pull Request 824: https://github.com/galaxyproject/galaxy/pull/824 .. _Pull Request 825: https://github.com/galaxyproject/galaxy/pull/825 .. _Pull Request 826: https://github.com/galaxyproject/galaxy/pull/826 .. _Pull Request 828: https://github.com/galaxyproject/galaxy/pull/828 .. _Pull Request 830: https://github.com/galaxyproject/galaxy/pull/830 .. _Pull Request 838: https://github.com/galaxyproject/galaxy/pull/838 .. _Pull Request 839: https://github.com/galaxyproject/galaxy/pull/839 .. _Pull Request 840: https://github.com/galaxyproject/galaxy/pull/840 .. _Pull Request 842: https://github.com/galaxyproject/galaxy/pull/842 .. _Pull Request 843: https://github.com/galaxyproject/galaxy/pull/843 .. _Pull Request 844: https://github.com/galaxyproject/galaxy/pull/844 .. _Pull Request 846: https://github.com/galaxyproject/galaxy/pull/846 .. _Pull Request 847: https://github.com/galaxyproject/galaxy/pull/847 .. _Pull Request 848: https://github.com/galaxyproject/galaxy/pull/848 .. _Pull Request 849: https://github.com/galaxyproject/galaxy/pull/849 .. _Pull Request 854: https://github.com/galaxyproject/galaxy/pull/854 .. _Pull Request 873: https://github.com/galaxyproject/galaxy/pull/873 .. _Pull Request 878: https://github.com/galaxyproject/galaxy/pull/878 .. _Pull Request 879: https://github.com/galaxyproject/galaxy/pull/879 .. _Pull Request 910: https://github.com/galaxyproject/galaxy/pull/910 .. _Pull Request 913: https://github.com/galaxyproject/galaxy/pull/913