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Fill in release notes for 15.10.

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John Chilton
2015-10-14 17:05:06 +01:00
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-------------------------------
15.10
-------------------------------
Enhancements
-------------------------------
.. enhancements
* Greatly enhance the reports application - including improved styling,
new landing page, pagination, and sparklines. Huge thanks to
`@Airistotal <https://github.com/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 <https://github.com/erasche>`__.)
`Pull Request 803`_
* Explicit project procedure language on reversions and WIP. (Thanks to `@erasche
<https://github.com/erasche>`__.)
`Pull Request 556`_
* Readme improvemenets - GitHub issues, security email contact and CI testing
(Thanks to `@nsoranzo <https://github.com/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 <https://github.com/galaxyproject/cloudlaunch>`__.
`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 <https://github.com/nsoranzo>`__.)
`Pull Request 650`_
* Style fixes for ``lib/galaxy_utils/``. (Thanks to `@nsoranzo
<https://github.com/nsoranzo>`__.)
`Pull Request 604`_
* Style fixes for ``test/``. (Thanks to `@nsoranzo
<https://github.com/nsoranzo>`__.)
`Pull Request 653`_
* Style fixes for ``contrib/`` and ``lib/tool_shed/``. (Thanks to `@nsoranzo
<https://github.com/nsoranzo>`__.)
`Pull Request 708`_
* Style fixes violated when merging from ``release_15.07``. (Thanks to `@nsoranzo
<https://github.com/nsoranzo>`__.)
`Pull Request 688`_
* Style fixes for tool shed database migrations. (Thanks to
`@nsoranzo <https://github.com/nsoranzo>`__.)
`Pull Request 770`_
* Changed refresh time on reports homepage (Thanks to `@Airistotal
<https://github.com/Airistotal>`__.)
`Pull Request 609`_
* Remove unused ``fastx_clipper_sequences.txt`` file.
(Thanks to `@lparsons <https://github.com/lparsons>`__.)
`Pull Request 611`_
* Move ``manual_builds.txt`` to ``manual_builds.txt.sample``.
(Thanks to `@lparsons <https://github.com/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 <https://github.com/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 <https://github.com/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 <https://github.com/erasche>`__.)
`Pull Request 694`_
* Use ``setup.py`` for Python all installations during dependency installation.
(Thanks to `@bgruening <https://github.com/bgruening>`__.)
`Pull Request 698`_
* Reorganize procedures documentation content. (Thanks to `@nsoranzo <https://github.com/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 <https://github.com/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
<https://github.com/scholtalbers>`__.)
`Pull Request 777`_
* Unify the docker command, command_inject, and command_wrapper (Thanks to
`@erasche <https://github.com/erasche>`__.)
`Pull Request 782`_
* Test case to prevent regression of `#753
<https://github.com/galaxyproject/galaxy/issues/753>`__.
`Pull Request 784`_
* Refactor interactive environment launching to use Docker's ``-P`` option.
(Thanks to `@erasche <https://github.com/erasche>`__.)
`Pull Request 790`_
* Print ``has_metrics`` class name instead of object memory address. (Thanks to
`@nsoranzo <https://github.com/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
<https://github.com/galaxyproject/galaxy/issues/786>`__. (Thanks to
`@nsoranzo <https://github.com/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 <https://github.com/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 <https://github.com/erasche>`__.)
`Pull Request 849`_
* Enhancements for IPython interactive environment allowing it run in certain
deployments.
(Thanks to `@scholtalbers <https://github.com/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 <https://github.com/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 <https://github.com/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 <https://github.com/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 <https://github.com/ericenns>`__.)
`Pull Request 568`_
* Tool lineage fixes.
(Thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
`Pull Request 596`_
* Fix bug in reload API where id wasn't recognised.
(Thanks to `@erasche <https://github.com/erasche>`__.)
`Pull Request 619`_
* Correct typo in tool shed action handler code.
(Thanks to `@erasche <https://github.com/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 <https://github.com/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 <https://github.com/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 <https://github.com/yhoogstrate>`__.)
`Pull Request 588`_
* Ensure removal of temporary tool shed files.
`Pull Request 607`_
* Bug fix in Reports
(Thanks to `@Airistotal <https://github.com/Airistotal>`__.)
`Pull Request 626`_
* Cleaner commit history for `#629
<https://github.com/galaxyproject/galaxy/issues/629>`__ and array syntax for
pathspec
(Thanks to `@chambm <https://github.com/chambm>`__.)
`Pull Request 632`_
* add missing js build
`Pull Request 648`_
* Reports - Small bug fixes
(Thanks to `@Airistotal <https://github.com/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 <https://github.com/Airistotal>`__.)
`Pull Request 669`_
* Don't overwrite $R_LIBS path during installation.
(Thanks to `@bgruening <https://github.com/bgruening>`__.)
`Pull Request 671`_
* Fix tool shed installation issue
(`#525 <https://github.com/galaxyproject/galaxy/issues/525>`__).
(Thanks to `@mvdbeek <https://github.com/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 <https://github.com/nsoranzo>`__.)
`Pull Request 696`_
* Fix regression introduced in tool shed code this cycle.
(Thanks to `@nsoranzo <https://github.com/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 <https://github.com/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 <https://github.com/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 <https://github.com/mr-c>`__.)
`Pull Request 729`_
* Fix more API tests.
(Thanks to `@nsoranzo <https://github.com/nsoranzo>`__.)
`Pull Request 731`_
* Fixes for framework test cases.
(Thanks to `@nsoranzo <https://github.com/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 <https://github.com/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 <https://github.com/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 <https://github.com/nsoranzo>`__.)
`Pull Request 838`_
* Expose all API keys to admins under ``REMOTE_USER``.
(Thanks to `@erasche <https://github.com/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
doc/source/releases/15.10_announce.rst
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===========================================================
October 2015 Galaxy Release (v 15.10)
===========================================================
.. include:: _header.rst
Schedule
Highlights
===========================================================
* Planned Freeze Date: October 5, 2015
* Planned Release Date: October 26, 2015
**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 <https://github.com/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 <https://github.com/galaxyproject/galaxy>`__
===========================================================
New
.. code-block:: shell
% git clone -b master https://github.com/galaxyproject/galaxy.git
Update to latest stable release
.. code-block:: shell
% git checkout master && pull --ff-only origin master
Update to exact version
.. code-block:: shell
% git checkout v15.10
`BitBucket <https://bitbucket.org/galaxy/galaxy-dist>`__
===========================================================
Upgrade
.. code-block:: shell
% hg pull
% hg update latest_15.10
See `our wiki <https://wiki.galaxyproject.org/Develop/SourceCode>`__ for additional details regarding the source code locations.
Deprecation Notice
===========================================================
The graphview visualization is deprecated and will be replaced in the next
release of Galaxy.
Release Notes
===========================================================
.. include:: 15.10.rst
:start-after: enhancements
.. include:: _thanks.rst
doc/source/releases/16.01_announce.rst
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===========================================================
January 2016 Galaxy Release (v 16.01)
===========================================================
Schedule
===========================================================
* Planned Freeze Date: 2016-01-04
* Planned Release Date: 2016-01-25