.. to_doc 17.05 =============================== .. announce_start Enhancements ------------------------------- .. major_feature .. feature * Recalculate user disk usage on logout. `Pull Request 3600`_ * Overlay search for tools, workflows, libraries and histories (thanks to `@anuprulez `__ and `@bgruening `__). `Pull Request 3460`_ * Webhook plugin: tool_list (thanks to `@blankclemens `__). `Pull Request 3753`_ * Add Cytoscape as the Galaxy charts plugin (thanks to `@anuprulez `__ and `@bgruening `__). `Pull Request 3817`_ * Ethercalc Interactive Environment (thanks to `@shiltemann `__). `Pull Request 3699`_ * Add a simple UI to manage tool dependencies (thanks to `@mvdbeek `__). `Pull Request 3479`_ * Add nrrd image datatype (thanks to `@ThomasWollmann `__). `Pull Request 3385`_ * NGL Viewer for molecule representation (thanks to `@anuprulez `__ and `@bgruening `__). `Pull Request 3601`_ * Add script to encode or decode the IDs that Galaxy exposes to users and admins (thanks to `@hexylena `__). `Pull Request 3622`_ * Support Docker Engine swarm mode for Interactive Environments. `Pull Request 3666`_ * Interactive Environment container waiting and swarm management. `Pull Request 3740`_ * Phylocanvas as a BioJS component for the Galaxy charts (thanks to `@anuprulez `__ `@bgruening `__). `Pull Request 3850`_ * Container interface abstraction. `Pull Request 3863`_ * Graphite support (thanks to `@hexylena `__). `Pull Request 3964`_ * Normalize the handling of steps and missing tools for the workflow editor. `Pull Request 3181`_ * Add possibility to load collection into data library (thanks to `@mvdbeek `__). `Pull Request 3559`_ * Prefer versioned Conda dependencies to unversioned Galaxy ones. `Pull Request 3708`_ * Speedup startup and toolbox operations (thanks to `@mvdbeek `__). `Pull Request 3909`_ .. enhancement * Add missing imports for documentation builds (thanks to `@athos-ribeiro `__). `Pull Request 3104`_ * Workflow editor UI touch up. `Pull Request 3407`_ * Add an example group filter for displaying tool panel sections (thanks to `@gregvonkuster `__). `Pull Request 3484`_ * Python3: use @six.add_metaclass() decorator (thanks to `@nsoranzo `__). `Pull Request 3491`_ * Improvements to build sites configuration. `Pull Request 3503`_ * Add peek and preview for compressed FASTQ datatype (thanks to `@mvdbeek `__). `Pull Request 3512`_ * Add ``refresh_on_change`` to tool XSD. `Pull Request 3515`_ * Store module step states as nested dictionaries, fix export for backward compatibility. `Pull Request 3522`_ * Add Jenkins documentation tasks to the release issue. `Pull Request 3523`_ * Allow decompressing tool test outputs. `Pull Request 3550`_ * Add a task to protect the release branch in GitHub. `Pull Request 3562`_ * Remove duplicated/unused display_migration_details() functions (thanks to `@nsoranzo `__). `Pull Request 3564`_ * Display the genbank datatype in upload. `Pull Request 3569`_ * Database migrations: improvements and fixes (thanks to `@nsoranzo `__). `Pull Request 3570`_ * Add d3_hierarchy subclass (thanks to `@jj-umn `__). `Pull Request 3580`_ * Clean up docker-compose resources better for Selenium tests. `Pull Request 3583`_ * Add option to send API key in header (thanks to `@jvolkening `__). `Pull Request 3584`_ * Increase patience of Galaxy tests throughout. `Pull Request 3589`_ * Introduce label and annotation attributes to subworkflows, fix annotation display, unify module form update handler. `Pull Request 3593`_ * Align architecture slides with training-material remarkjs template. `Pull Request 3594`_ * Revision of tool XML reloading feature. `Pull Request 3596`_ * Implement collection operation to relabel list identifiers from contents of a file. `Pull Request 3603`_ * Slow query logging. `Pull Request 3616`_ * Remove un-needed check in histories manager code. `Pull Request 3618`_ * Improve interaction between job state and purged datasets. `Pull Request 3619`_ * Usable slow query logging. `Pull Request 3625`_ * Allow composite datatypes of type auto_primary_file to automatically generate dataset. `Pull Request 3643`_ * Introduce labels for all workflow modules, remove name handling field for data inputs. `Pull Request 3644`_ * When using the new slow query logger, include parameters. `Pull Request 3649`_ * Allow nested parameters in the dynamic_tool rule -> argument (thanks to `@lecorguille `__). `Pull Request 3657`_ * By default, do not allow workflow invocations to schedule indefinitely. `Pull Request 3659`_ * Add the mzData datatype (thanks to `@lecorguille `__). `Pull Request 3661`_ * Display an error message when GIE loading raises an exception. `Pull Request 3662`_ * Set LDAP options only once (thanks to `@nsoranzo `__). `Pull Request 3663`_ * Bump Jupyter container version to 16.01.1 . `Pull Request 3665`_ * Improve wording of getgalaxy in bootstrapping script for release notes. `Pull Request 3671`_ * Filter hda tags for tool parameters. `Pull Request 3688`_ * Add datatypes for soon coming PlantTribes Galaxy tools (thanks to `@gregvonkuster `__). `Pull Request 3698`_ * Touch up Galaxy testing documentation. `Pull Request 3715`_ * Add API and UI to remove requirements installed by Conda (thanks to `@mvdbeek `__). `Pull Request 3725`_ * Quota recalculation logic consolidation. `Pull Request 3734`_ * Percolator out datatypes (thanks to `@glormph `__). `Pull Request 3737`_ * Modify our docs in preparation for restructuring. `Pull Request 3738`_ * Update codefile documentation in tool XSD with info from old Wiki. `Pull Request 3739`_ * Mirror latest galaxy-lib changes for Conda and CWL improvements. `Pull Request 3742`_ * Add the possibility to uninstall Conda environments that are not in use by Galaxy (thanks to `@mvdbeek `__). `Pull Request 3750`_ * New Authentication section of the docs. `Pull Request 3751`_ * Bump routes requirement to 2.4.1 . `Pull Request 3752`_ * Abstract uWSGI handling into new galaxy.web.stack package. `Pull Request 3759`_ * i18n improvements and French localization. `Pull Request 3762`_ * Should exit immediately to avoid index error (thanks to `@hexylena `__). `Pull Request 3770`_ * Made collection operations help sections slightly more readable. `Pull Request 3784`_ * Avoid potential inconsistencies between differently stored labels. `Pull Request 3793`_ * Remove custom builds mako. `Pull Request 3794`_ * Small enhancements for collection builders. `Pull Request 3806`_ * Small improvements for driving Qunit tests. `Pull Request 3810`_ * Implement more upload testing in Selenium. `Pull Request 3811`_ * API & reports documentation improvements. `Pull Request 3812`_ * Make ToolConfWatcher watch ToolCache (thanks to `@mvdbeek `__). `Pull Request 3814`_ * Disable tool shed test function that fails frequently on Jenkins. `Pull Request 3819`_ * Restrict workflow scheduling within a history to a fixed, random handler. `Pull Request 3820`_ * Order processing evaluation of workflow invocations when scheduling. `Pull Request 3830`_ * Stricter checks for GFF/GFF3/GTF datatypes sniffing (thanks to `@nsoranzo `__). `Pull Request 3832`_ * Add root redirect for backbone router. `Pull Request 3837`_ * Allow explicit configuration of handlers for workflow scheduling. `Pull Request 3844`_ * Log reason when workflow scheduling of a step is delayed. `Pull Request 3849`_ * Update datatypes_conf.xml.sample (thanks to `@lecorguille `__). `Pull Request 3852`_ * Clean up old TODO into history tests. `Pull Request 3855`_ * Small changes to links and add Gitter (thanks to `@bgruening `__). `Pull Request 3861`_ * Use detect_errors="exit_code" in Trim tool (thanks to `@nsoranzo `__). `Pull Request 3869`_ * Synchronise against latest UCSC versions (thanks to `@bgruening `__). `Pull Request 3874`_ * Hardklor and kronik datatypes for proteomics (thanks to `@glormph `__). `Pull Request 3884`_ * History drag-and-drop feature with iframe support for run workflow form. `Pull Request 3886`_ * Update to a new Docker test image to fix dependency bugs. `Pull Request 3890`_ * Python3: Use shlex_quote() from six.moves instead of pipes.quote() (thanks to `@nsoranzo `__). `Pull Request 3891`_ * Add a validator that ensures a dataset's extra_files_path (thanks to `@gregvonkuster `__). `Pull Request 3918`_ * Update text.py Add interaction annotations to SnpEffDb metadata (thanks to `@jj-umn `__). `Pull Request 3938`_ * Collection operation: Filtering from a file. `Pull Request 3940`_ * Remove Google from OpenID providers in the sample. `Pull Request 3953`_ * Change 'User' menu to 'Login or Register' for anonymous users. `Pull Request 3955`_ * Stats docs (thanks to `@hexylena `__). `Pull Request 3968`_ * Enhance filenames with collection context when downloading datasets from GUI. `Pull Request 3985`_ * Displaying a message instead of just redirecting. `Pull Request 4000`_ * Implicitly set use_volumes = False if using Docker swarm. `Pull Request 4006`_ * Update Jupyter image to 17.05 . `Pull Request 4007`_ * Inline CSS in error report email (thanks to `@hexylena `__). `Pull Request 3445`_ * Improve routing for user preference views. `Pull Request 3446`_ * Tool documentation and testing improvements. `Pull Request 3457`_ * Update readme badges. `Pull Request 3465`_ * Lint some tools (thanks to `@nsoranzo `__). `Pull Request 3468`_ * Improve release issue docs. `Pull Request 3496`_ * Watch tool data table ``*.loc`` files, and reload if modified (thanks to `@mvdbeek `__). `Pull Request 3533`_ .. small_enhancement * Attempt work around for race-y sort of condition in Selenium sizzle checkers. `Pull Request 3451`_ * Webhooks: add tests (thanks to `@anatskiy `__). `Pull Request 3469`_ * Disable transiently failing tour test. `Pull Request 3599`_ * Selenium testing improvements. `Pull Request 3716`_ * Merge ConfiguresGalaxyMixin.reload_toolbox() in _configure_toolbox() (thanks to `@nsoranzo `__). `Pull Request 3732`_ * Abstraction for re-use between collection creators. `Pull Request 3781`_ * Merge ToolConfWatchers and separate from Toolbox (thanks to `@mvdbeek `__). `Pull Request 3821`_ * Attempt to improve the robustness and verboseness of the test_sharing_valid Selenium test. `Pull Request 3841`_ * Routes cleanup. `Pull Request 3895`_ * Standardize usage of log.exception . `Pull Request 3933`_ * Followup to exception refactoring. `Pull Request 3959`_ * Use container-based infrastructure (sudo: false) in TravisCI (thanks to `@nsoranzo `__). `Pull Request 3977`_ * Improve implicit workflow connection test case. `Pull Request 3991`_ Fixes ------------------------------- .. major_bug .. bug * Fix tag escaping. `Pull Request 3720`_ * Fix kombu documentation link in galaxy.ini.sample . `Pull Request 3629`_ * Fix for EtherCalc IE image specification. `Pull Request 3825`_ * Fix margin style values for color picker element. `Pull Request 3965`_ * 17.05 rstudio fixes / one small GIE fix (thanks to `@hexylena `__). `Pull Request 3975`_ * Fix transiently failing Selenium upload test. `Pull Request 3587`_ * Fix webhook search overlay interfering with masthead load. `Pull Request 3731`_ * Fix collection operations in workflows. `Pull Request 3848`_ * Remove old, unused search controller. `Pull Request 3894`_ * Deduplicate obsolete API readme. `Pull Request 3777`_ * Assorted fixes for dockerized test setup. `Pull Request 3755`_ * Another fix for Selenium testing on Jenkins. `Pull Request 3422`_ * Fix most broken Selenium tests. `Pull Request 3440`_ * Fix for transiently failing workflow test. `Pull Request 3668`_ * Fix selenium workflow tests broken with `#3181 `__. `Pull Request 3504`_ * Fix integration test for default Conda mapping. `Pull Request 3508`_ * Various fixes for test image Docker user switching. `Pull Request 3443`_ * Fix Travix builds which use flake8-docstrings (thanks to `@nsoranzo `__). `Pull Request 3981`_ * Azure - Leasing container sometimes breaks things in Docker Galaxy (thanks to `@zfrenchee `__). `Pull Request 3263`_ * run_tests.sh: a small typo (thanks to `@anatskiy `__). `Pull Request 3322`_ * Fix cycle detection for single node workflows. `Pull Request 3374`_ * Small selenium hack to fix occasionally failing collection upload tests. `Pull Request 3967`_ * Bug fix in mulled.py (thanks to `@abdulrahmanazab `__). `Pull Request 3434`_ * Do not select first value as default if select value is optional. `Pull Request 3472`_ * jsonify initial value when returned through to_dict caller. `Pull Request 3513`_ * Fix output test assert check (thanks to `@jvolkening `__). `Pull Request 3530`_ * Fix output tests for checksum example tools. `Pull Request 3545`_ * Update Nagios check. `Pull Request 3568`_ * Set 'deleted' to True when purging a history dataset association (thanks to `@nsoranzo `__). `Pull Request 3572`_ * Update tool XSD for (hopefully deprecated) change_format syntax. `Pull Request 3579`_ * Remove broken tour step. `Pull Request 3582`_ * Avoid step duplication when ordering steps on the fly. `Pull Request 3590`_ * Minor fix of core.galaxy-ui tour. `Pull Request 3608`_ * Fix RELEASE_ISSUE_TEMPLATE in bootstrap_history.py (thanks to `@nsoranzo `__). `Pull Request 3653`_ * Update dynamic_tool_destination.py (thanks to `@lecorguille `__). `Pull Request 3655`_ * Ignore Node modules installed for the GIE proxy when linting. `Pull Request 3664`_ * Logout recalc improvements. `Pull Request 3669`_ * Strip broken autocomplete feature, webbrowsers console error is an artifact. `Pull Request 3676`_ * Generate primary composite file after extra files collection. `Pull Request 3678`_ * Fix tool search index building for tools with slash in id and not from ToolShed. `Pull Request 3680`_ * Set $HOME to a temp directory rather than conda_prefix because conda_prefix may not be writable either. `Pull Request 3701`_ * Properly handle boolean values when parsed to a string-based/default tool parameter. `Pull Request 3702`_ * Mothur datatypes: fix metadata failure for large count tables (thanks to `@shiltemann `__). `Pull Request 3706`_ * Filename handling for FTP upload. `Pull Request 3722`_ * Do not require stored workflow id for subworkflows. `Pull Request 3723`_ * Remove outdated items from tool cache when reloading the toolbox (thanks to `@mvdbeek `__). `Pull Request 3729`_ * Change API path in docstrings to correct /api/dependency_resolvers/* (thanks to `@mvdbeek `__). `Pull Request 3749`_ * Wiki to hub link update. `Pull Request 3754`_ * Fix KeyError when getting request and response content-type headers (thanks to `@nsoranzo `__). `Pull Request 3757`_ * Fix for uploading rdata datasets when explicitly declaring datatype. `Pull Request 3766`_ * Fixes for users API. `Pull Request 3771`_ * Fix XSS vulnerability in grids. `Pull Request 3776`_ * Layered routing fix for when controller route fails and client route does not exist. `Pull Request 3783`_ * Fix collection operations not having a history. `Pull Request 3786`_ * Fix problem with cleaning up jobs in local runner. `Pull Request 3803`_ * Have tool-search listen to change as well as keyup. `Pull Request 3808`_ * Fix BED dataset display in Trackster (thanks to `@hrhotz `__). `Pull Request 3822`_ * More CONVERTER fixes for restricting tools' Python environment. `Pull Request 3824`_ * Have IGV bigWig display application make use of build_sites/ site_type config instead of direct filename. `Pull Request 3828`_ * Properly handle multiple hidden datasets when populating data select options. `Pull Request 3842`_ * Fix for direct message routing using a 'real' exchange like RabbitMQ. `Pull Request 3846`_ * Fix setting UUID on steps when copying steps from another workflow. `Pull Request 3856`_ * Fix certain aspects of collection reductions in conditionals/repeats. `Pull Request 3864`_ * Fix multiple collection reductions on multiple data parameters. `Pull Request 3875`_ * Fix inability for viz to raise loading with non-ascii messages (thanks to `@hexylena `__). `Pull Request 3881`_ * Fix new history endpoint providing custom builds metadata. `Pull Request 3887`_ * Remove unused model import from users API. `Pull Request 3888`_ * Cytoscape bugfix for SIF files (thanks to `@bgruening `__). `Pull Request 3896`_ * Add missing trigger event to drop handler in content selector. `Pull Request 3897`_ * Fix Instance is not bound to a Session (thanks to `@mvdbeek `__). `Pull Request 3904`_ * Fix library parameter style width to avoid second line. `Pull Request 3926`_ * More careful inspection of fixes for MAF tools requiring Galaxy. `Pull Request 3935`_ * Containers interface and GIE bugfixes. `Pull Request 3941`_ * Show default value for runtime values. `Pull Request 3943`_ * Fix JJ's column_join tool depending on Galaxy at runtime. `Pull Request 3961`_ * Fix edge case for workflow mapping handling when tools not available. `Pull Request 3962`_ * Tour fixes (thanks to `@nsoranzo `__). `Pull Request 3970`_ * Fix some typos in config/galaxy.ini.sample (thanks to `@nsoranzo `__). `Pull Request 3971`_ * Add two tools from str_fm repository to galaxy module whitelist. `Pull Request 3973`_ * Remote user logout fixes, rework header handling a bit. `Pull Request 3976`_ * Fixes to get GIEs working on Mac OS X. `Pull Request 3978`_ * Rework Jupyter IE for additional_ids handling. `Pull Request 3980`_ * Update Babel to a version compat. with sphinx. `Pull Request 3986`_ * Use the configured tool_path when loading data managers. `Pull Request 3989`_ * Typo in remote user / user preferences exception (thanks to `@hexylena `__). `Pull Request 4015`_ * Fix setting up explicit container resolution from a container resolution config file. `Pull Request 4020`_ * Fix spelling error in error message (thanks to `@pvanheus `__). `Pull Request 4026`_ * Fixes for containerized job executions. `Pull Request 4033`_ * Try activating Conda environment again if previous activation failed (thanks to `@mvdbeek `__). `Pull Request 4035`_ * HTCondor fix for running containers (thanks to `@bgruening `__). `Pull Request 4038`_ * Fix destructive tag rerender to be a simpler, more precise html replacement. `Pull Request 4052`_ * Fix for S3ObjectStore _clean_cache method. `Pull Request 4055`_ * Correct webhooks to use Galaxy.root and be compatible with proxy_prefix (thanks to `@hexylena `__). `Pull Request 4065`_ * Fix global grid action event handler. `Pull Request 4068`_ * Fix various transiently failing Selenium tests. `Pull Request 3450`_ * Do not modify self.app.config.tool_data_path and self.app.config.tool_data_table_config_path during metadata setting (thanks to `@mvdbeek `__). `Pull Request 4089`_ * Open Babel update for datatype converters (thanks to `@bgruening `__). `Pull Request 4094`_ * Change to only inheriting 'name' tags. `Pull Request 4104`_ * Fixes repeat handling in workflow editor, store values as passed from UI. `Pull Request 4107`_ .. github_links .. _Pull Request 3104: https://github.com/galaxyproject/galaxy/pull/3104 .. _Pull Request 3181: https://github.com/galaxyproject/galaxy/pull/3181 .. _Pull Request 3263: https://github.com/galaxyproject/galaxy/pull/3263 .. _Pull Request 3322: https://github.com/galaxyproject/galaxy/pull/3322 .. _Pull Request 3374: https://github.com/galaxyproject/galaxy/pull/3374 .. _Pull Request 3385: https://github.com/galaxyproject/galaxy/pull/3385 .. _Pull Request 3407: https://github.com/galaxyproject/galaxy/pull/3407 .. _Pull Request 3420: https://github.com/galaxyproject/galaxy/pull/3420 .. _Pull Request 3422: https://github.com/galaxyproject/galaxy/pull/3422 .. _Pull Request 3434: https://github.com/galaxyproject/galaxy/pull/3434 .. _Pull Request 3440: https://github.com/galaxyproject/galaxy/pull/3440 .. _Pull Request 3443: https://github.com/galaxyproject/galaxy/pull/3443 .. _Pull Request 3445: https://github.com/galaxyproject/galaxy/pull/3445 .. _Pull Request 3446: https://github.com/galaxyproject/galaxy/pull/3446 .. _Pull Request 3450: https://github.com/galaxyproject/galaxy/pull/3450 .. _Pull Request 3451: https://github.com/galaxyproject/galaxy/pull/3451 .. _Pull Request 3457: https://github.com/galaxyproject/galaxy/pull/3457 .. _Pull Request 3460: https://github.com/galaxyproject/galaxy/pull/3460 .. _Pull Request 3465: https://github.com/galaxyproject/galaxy/pull/3465 .. _Pull Request 3468: https://github.com/galaxyproject/galaxy/pull/3468 .. _Pull Request 3469: https://github.com/galaxyproject/galaxy/pull/3469 .. _Pull Request 3472: https://github.com/galaxyproject/galaxy/pull/3472 .. _Pull Request 3478: https://github.com/galaxyproject/galaxy/pull/3478 .. _Pull Request 3479: https://github.com/galaxyproject/galaxy/pull/3479 .. _Pull Request 3484: https://github.com/galaxyproject/galaxy/pull/3484 .. _Pull Request 3491: https://github.com/galaxyproject/galaxy/pull/3491 .. _Pull Request 3496: https://github.com/galaxyproject/galaxy/pull/3496 .. _Pull Request 3503: https://github.com/galaxyproject/galaxy/pull/3503 .. _Pull Request 3504: https://github.com/galaxyproject/galaxy/pull/3504 .. _Pull Request 3508: https://github.com/galaxyproject/galaxy/pull/3508 .. _Pull Request 3512: https://github.com/galaxyproject/galaxy/pull/3512 .. _Pull Request 3513: https://github.com/galaxyproject/galaxy/pull/3513 .. _Pull Request 3515: https://github.com/galaxyproject/galaxy/pull/3515 .. _Pull Request 3522: https://github.com/galaxyproject/galaxy/pull/3522 .. _Pull Request 3523: https://github.com/galaxyproject/galaxy/pull/3523 .. _Pull Request 3530: https://github.com/galaxyproject/galaxy/pull/3530 .. _Pull Request 3531: https://github.com/galaxyproject/galaxy/pull/3531 .. _Pull Request 3533: https://github.com/galaxyproject/galaxy/pull/3533 .. _Pull Request 3545: https://github.com/galaxyproject/galaxy/pull/3545 .. _Pull Request 3550: https://github.com/galaxyproject/galaxy/pull/3550 .. _Pull Request 3553: https://github.com/galaxyproject/galaxy/pull/3553 .. _Pull Request 3559: https://github.com/galaxyproject/galaxy/pull/3559 .. _Pull Request 3562: https://github.com/galaxyproject/galaxy/pull/3562 .. _Pull Request 3564: https://github.com/galaxyproject/galaxy/pull/3564 .. _Pull Request 3565: https://github.com/galaxyproject/galaxy/pull/3565 .. _Pull Request 3568: https://github.com/galaxyproject/galaxy/pull/3568 .. _Pull Request 3569: https://github.com/galaxyproject/galaxy/pull/3569 .. _Pull Request 3570: https://github.com/galaxyproject/galaxy/pull/3570 .. _Pull Request 3572: https://github.com/galaxyproject/galaxy/pull/3572 .. _Pull Request 3576: https://github.com/galaxyproject/galaxy/pull/3576 .. _Pull Request 3579: https://github.com/galaxyproject/galaxy/pull/3579 .. _Pull Request 3580: https://github.com/galaxyproject/galaxy/pull/3580 .. _Pull Request 3582: https://github.com/galaxyproject/galaxy/pull/3582 .. _Pull Request 3583: https://github.com/galaxyproject/galaxy/pull/3583 .. _Pull Request 3584: https://github.com/galaxyproject/galaxy/pull/3584 .. _Pull Request 3587: https://github.com/galaxyproject/galaxy/pull/3587 .. _Pull Request 3589: https://github.com/galaxyproject/galaxy/pull/3589 .. _Pull Request 3590: https://github.com/galaxyproject/galaxy/pull/3590 .. _Pull Request 3593: https://github.com/galaxyproject/galaxy/pull/3593 .. _Pull Request 3594: https://github.com/galaxyproject/galaxy/pull/3594 .. _Pull Request 3596: https://github.com/galaxyproject/galaxy/pull/3596 .. _Pull Request 3599: https://github.com/galaxyproject/galaxy/pull/3599 .. _Pull Request 3600: https://github.com/galaxyproject/galaxy/pull/3600 .. _Pull Request 3601: https://github.com/galaxyproject/galaxy/pull/3601 .. _Pull Request 3603: https://github.com/galaxyproject/galaxy/pull/3603 .. _Pull Request 3608: https://github.com/galaxyproject/galaxy/pull/3608 .. _Pull Request 3616: https://github.com/galaxyproject/galaxy/pull/3616 .. _Pull Request 3618: https://github.com/galaxyproject/galaxy/pull/3618 .. _Pull Request 3619: https://github.com/galaxyproject/galaxy/pull/3619 .. _Pull Request 3622: https://github.com/galaxyproject/galaxy/pull/3622 .. _Pull Request 3625: https://github.com/galaxyproject/galaxy/pull/3625 .. _Pull Request 3629: https://github.com/galaxyproject/galaxy/pull/3629 .. _Pull Request 3641: https://github.com/galaxyproject/galaxy/pull/3641 .. _Pull Request 3643: https://github.com/galaxyproject/galaxy/pull/3643 .. _Pull Request 3644: https://github.com/galaxyproject/galaxy/pull/3644 .. _Pull Request 3649: https://github.com/galaxyproject/galaxy/pull/3649 .. _Pull Request 3652: https://github.com/galaxyproject/galaxy/pull/3652 .. _Pull Request 3653: https://github.com/galaxyproject/galaxy/pull/3653 .. _Pull Request 3654: https://github.com/galaxyproject/galaxy/pull/3654 .. _Pull Request 3655: https://github.com/galaxyproject/galaxy/pull/3655 .. _Pull Request 3657: https://github.com/galaxyproject/galaxy/pull/3657 .. _Pull Request 3659: https://github.com/galaxyproject/galaxy/pull/3659 .. _Pull Request 3661: https://github.com/galaxyproject/galaxy/pull/3661 .. _Pull Request 3662: https://github.com/galaxyproject/galaxy/pull/3662 .. _Pull Request 3663: https://github.com/galaxyproject/galaxy/pull/3663 .. _Pull Request 3664: https://github.com/galaxyproject/galaxy/pull/3664 .. _Pull Request 3665: https://github.com/galaxyproject/galaxy/pull/3665 .. _Pull Request 3666: https://github.com/galaxyproject/galaxy/pull/3666 .. _Pull Request 3668: https://github.com/galaxyproject/galaxy/pull/3668 .. _Pull Request 3669: https://github.com/galaxyproject/galaxy/pull/3669 .. _Pull Request 3671: https://github.com/galaxyproject/galaxy/pull/3671 .. _Pull Request 3674: https://github.com/galaxyproject/galaxy/pull/3674 .. _Pull Request 3676: https://github.com/galaxyproject/galaxy/pull/3676 .. _Pull Request 3678: https://github.com/galaxyproject/galaxy/pull/3678 .. _Pull Request 3680: https://github.com/galaxyproject/galaxy/pull/3680 .. _Pull Request 3688: https://github.com/galaxyproject/galaxy/pull/3688 .. _Pull Request 3696: https://github.com/galaxyproject/galaxy/pull/3696 .. _Pull Request 3698: https://github.com/galaxyproject/galaxy/pull/3698 .. _Pull Request 3699: https://github.com/galaxyproject/galaxy/pull/3699 .. _Pull Request 3701: https://github.com/galaxyproject/galaxy/pull/3701 .. _Pull Request 3702: https://github.com/galaxyproject/galaxy/pull/3702 .. _Pull Request 3704: https://github.com/galaxyproject/galaxy/pull/3704 .. _Pull Request 3706: https://github.com/galaxyproject/galaxy/pull/3706 .. _Pull Request 3708: https://github.com/galaxyproject/galaxy/pull/3708 .. _Pull Request 3715: https://github.com/galaxyproject/galaxy/pull/3715 .. _Pull Request 3716: https://github.com/galaxyproject/galaxy/pull/3716 .. _Pull Request 3718: https://github.com/galaxyproject/galaxy/pull/3718 .. _Pull Request 3719: https://github.com/galaxyproject/galaxy/pull/3719 .. _Pull Request 3720: https://github.com/galaxyproject/galaxy/pull/3720 .. _Pull Request 3722: https://github.com/galaxyproject/galaxy/pull/3722 .. _Pull Request 3723: https://github.com/galaxyproject/galaxy/pull/3723 .. _Pull Request 3725: https://github.com/galaxyproject/galaxy/pull/3725 .. _Pull Request 3729: https://github.com/galaxyproject/galaxy/pull/3729 .. _Pull Request 3731: https://github.com/galaxyproject/galaxy/pull/3731 .. _Pull Request 3732: https://github.com/galaxyproject/galaxy/pull/3732 .. _Pull Request 3734: https://github.com/galaxyproject/galaxy/pull/3734 .. _Pull Request 3737: https://github.com/galaxyproject/galaxy/pull/3737 .. _Pull Request 3738: https://github.com/galaxyproject/galaxy/pull/3738 .. _Pull Request 3739: https://github.com/galaxyproject/galaxy/pull/3739 .. _Pull Request 3740: https://github.com/galaxyproject/galaxy/pull/3740 .. _Pull Request 3742: https://github.com/galaxyproject/galaxy/pull/3742 .. _Pull Request 3746: https://github.com/galaxyproject/galaxy/pull/3746 .. _Pull Request 3749: https://github.com/galaxyproject/galaxy/pull/3749 .. _Pull Request 3750: https://github.com/galaxyproject/galaxy/pull/3750 .. _Pull Request 3751: https://github.com/galaxyproject/galaxy/pull/3751 .. _Pull Request 3752: https://github.com/galaxyproject/galaxy/pull/3752 .. _Pull Request 3753: https://github.com/galaxyproject/galaxy/pull/3753 .. _Pull Request 3754: https://github.com/galaxyproject/galaxy/pull/3754 .. _Pull Request 3755: https://github.com/galaxyproject/galaxy/pull/3755 .. _Pull Request 3757: https://github.com/galaxyproject/galaxy/pull/3757 .. _Pull Request 3759: https://github.com/galaxyproject/galaxy/pull/3759 .. _Pull Request 3760: https://github.com/galaxyproject/galaxy/pull/3760 .. _Pull Request 3762: https://github.com/galaxyproject/galaxy/pull/3762 .. _Pull Request 3766: https://github.com/galaxyproject/galaxy/pull/3766 .. _Pull Request 3768: https://github.com/galaxyproject/galaxy/pull/3768 .. _Pull Request 3770: https://github.com/galaxyproject/galaxy/pull/3770 .. _Pull Request 3771: https://github.com/galaxyproject/galaxy/pull/3771 .. _Pull Request 3776: https://github.com/galaxyproject/galaxy/pull/3776 .. _Pull Request 3777: https://github.com/galaxyproject/galaxy/pull/3777 .. _Pull Request 3781: https://github.com/galaxyproject/galaxy/pull/3781 .. _Pull Request 3783: https://github.com/galaxyproject/galaxy/pull/3783 .. _Pull Request 3784: https://github.com/galaxyproject/galaxy/pull/3784 .. _Pull Request 3786: https://github.com/galaxyproject/galaxy/pull/3786 .. _Pull Request 3793: https://github.com/galaxyproject/galaxy/pull/3793 .. _Pull Request 3794: https://github.com/galaxyproject/galaxy/pull/3794 .. _Pull Request 3799: https://github.com/galaxyproject/galaxy/pull/3799 .. _Pull Request 3803: https://github.com/galaxyproject/galaxy/pull/3803 .. _Pull Request 3805: https://github.com/galaxyproject/galaxy/pull/3805 .. _Pull Request 3806: https://github.com/galaxyproject/galaxy/pull/3806 .. _Pull Request 3808: https://github.com/galaxyproject/galaxy/pull/3808 .. _Pull Request 3809: https://github.com/galaxyproject/galaxy/pull/3809 .. _Pull Request 3810: https://github.com/galaxyproject/galaxy/pull/3810 .. _Pull Request 3811: https://github.com/galaxyproject/galaxy/pull/3811 .. _Pull Request 3812: https://github.com/galaxyproject/galaxy/pull/3812 .. _Pull Request 3814: https://github.com/galaxyproject/galaxy/pull/3814 .. _Pull Request 3817: https://github.com/galaxyproject/galaxy/pull/3817 .. _Pull Request 3819: https://github.com/galaxyproject/galaxy/pull/3819 .. _Pull Request 3820: https://github.com/galaxyproject/galaxy/pull/3820 .. _Pull Request 3821: https://github.com/galaxyproject/galaxy/pull/3821 .. _Pull Request 3822: https://github.com/galaxyproject/galaxy/pull/3822 .. _Pull Request 3824: https://github.com/galaxyproject/galaxy/pull/3824 .. _Pull Request 3825: https://github.com/galaxyproject/galaxy/pull/3825 .. _Pull Request 3828: https://github.com/galaxyproject/galaxy/pull/3828 .. _Pull Request 3830: https://github.com/galaxyproject/galaxy/pull/3830 .. _Pull Request 3832: https://github.com/galaxyproject/galaxy/pull/3832 .. _Pull Request 3837: https://github.com/galaxyproject/galaxy/pull/3837 .. _Pull Request 3841: https://github.com/galaxyproject/galaxy/pull/3841 .. _Pull Request 3842: https://github.com/galaxyproject/galaxy/pull/3842 .. _Pull Request 3844: https://github.com/galaxyproject/galaxy/pull/3844 .. _Pull Request 3846: https://github.com/galaxyproject/galaxy/pull/3846 .. _Pull Request 3848: https://github.com/galaxyproject/galaxy/pull/3848 .. _Pull Request 3849: https://github.com/galaxyproject/galaxy/pull/3849 .. _Pull Request 3850: https://github.com/galaxyproject/galaxy/pull/3850 .. _Pull Request 3852: https://github.com/galaxyproject/galaxy/pull/3852 .. _Pull Request 3855: https://github.com/galaxyproject/galaxy/pull/3855 .. _Pull Request 3856: https://github.com/galaxyproject/galaxy/pull/3856 .. _Pull Request 3857: https://github.com/galaxyproject/galaxy/pull/3857 .. _Pull Request 3861: https://github.com/galaxyproject/galaxy/pull/3861 .. _Pull Request 3863: https://github.com/galaxyproject/galaxy/pull/3863 .. _Pull Request 3864: https://github.com/galaxyproject/galaxy/pull/3864 .. _Pull Request 3868: https://github.com/galaxyproject/galaxy/pull/3868 .. _Pull Request 3869: https://github.com/galaxyproject/galaxy/pull/3869 .. _Pull Request 3871: https://github.com/galaxyproject/galaxy/pull/3871 .. _Pull Request 3874: https://github.com/galaxyproject/galaxy/pull/3874 .. _Pull Request 3875: https://github.com/galaxyproject/galaxy/pull/3875 .. _Pull Request 3881: https://github.com/galaxyproject/galaxy/pull/3881 .. _Pull Request 3884: https://github.com/galaxyproject/galaxy/pull/3884 .. _Pull Request 3886: https://github.com/galaxyproject/galaxy/pull/3886 .. _Pull Request 3887: https://github.com/galaxyproject/galaxy/pull/3887 .. _Pull Request 3888: https://github.com/galaxyproject/galaxy/pull/3888 .. _Pull Request 3889: https://github.com/galaxyproject/galaxy/pull/3889 .. _Pull Request 3890: https://github.com/galaxyproject/galaxy/pull/3890 .. _Pull Request 3891: https://github.com/galaxyproject/galaxy/pull/3891 .. _Pull Request 3894: https://github.com/galaxyproject/galaxy/pull/3894 .. _Pull Request 3895: https://github.com/galaxyproject/galaxy/pull/3895 .. _Pull Request 3896: https://github.com/galaxyproject/galaxy/pull/3896 .. _Pull Request 3897: https://github.com/galaxyproject/galaxy/pull/3897 .. _Pull Request 3904: https://github.com/galaxyproject/galaxy/pull/3904 .. _Pull Request 3909: https://github.com/galaxyproject/galaxy/pull/3909 .. _Pull Request 3918: https://github.com/galaxyproject/galaxy/pull/3918 .. _Pull Request 3920: https://github.com/galaxyproject/galaxy/pull/3920 .. _Pull Request 3926: https://github.com/galaxyproject/galaxy/pull/3926 .. _Pull Request 3931: https://github.com/galaxyproject/galaxy/pull/3931 .. _Pull Request 3933: https://github.com/galaxyproject/galaxy/pull/3933 .. _Pull Request 3935: https://github.com/galaxyproject/galaxy/pull/3935 .. _Pull Request 3938: https://github.com/galaxyproject/galaxy/pull/3938 .. _Pull Request 3940: https://github.com/galaxyproject/galaxy/pull/3940 .. _Pull Request 3941: https://github.com/galaxyproject/galaxy/pull/3941 .. _Pull Request 3943: https://github.com/galaxyproject/galaxy/pull/3943 .. _Pull Request 3953: https://github.com/galaxyproject/galaxy/pull/3953 .. _Pull Request 3955: https://github.com/galaxyproject/galaxy/pull/3955 .. _Pull Request 3956: https://github.com/galaxyproject/galaxy/pull/3956 .. _Pull Request 3959: https://github.com/galaxyproject/galaxy/pull/3959 .. _Pull Request 3961: https://github.com/galaxyproject/galaxy/pull/3961 .. _Pull Request 3962: https://github.com/galaxyproject/galaxy/pull/3962 .. _Pull Request 3964: https://github.com/galaxyproject/galaxy/pull/3964 .. _Pull Request 3965: https://github.com/galaxyproject/galaxy/pull/3965 .. _Pull Request 3967: https://github.com/galaxyproject/galaxy/pull/3967 .. _Pull Request 3968: https://github.com/galaxyproject/galaxy/pull/3968 .. _Pull Request 3970: https://github.com/galaxyproject/galaxy/pull/3970 .. _Pull Request 3971: https://github.com/galaxyproject/galaxy/pull/3971 .. _Pull Request 3973: https://github.com/galaxyproject/galaxy/pull/3973 .. _Pull Request 3975: https://github.com/galaxyproject/galaxy/pull/3975 .. _Pull Request 3976: https://github.com/galaxyproject/galaxy/pull/3976 .. _Pull Request 3977: https://github.com/galaxyproject/galaxy/pull/3977 .. _Pull Request 3978: https://github.com/galaxyproject/galaxy/pull/3978 .. _Pull Request 3979: https://github.com/galaxyproject/galaxy/pull/3979 .. _Pull Request 3980: https://github.com/galaxyproject/galaxy/pull/3980 .. _Pull Request 3981: https://github.com/galaxyproject/galaxy/pull/3981 .. _Pull Request 3985: https://github.com/galaxyproject/galaxy/pull/3985 .. _Pull Request 3986: https://github.com/galaxyproject/galaxy/pull/3986 .. _Pull Request 3988: https://github.com/galaxyproject/galaxy/pull/3988 .. _Pull Request 3989: https://github.com/galaxyproject/galaxy/pull/3989 .. _Pull Request 3991: https://github.com/galaxyproject/galaxy/pull/3991 .. _Pull Request 3996: https://github.com/galaxyproject/galaxy/pull/3996 .. _Pull Request 4000: https://github.com/galaxyproject/galaxy/pull/4000 .. _Pull Request 4004: https://github.com/galaxyproject/galaxy/pull/4004 .. _Pull Request 4006: https://github.com/galaxyproject/galaxy/pull/4006 .. _Pull Request 4007: https://github.com/galaxyproject/galaxy/pull/4007 .. _Pull Request 4009: https://github.com/galaxyproject/galaxy/pull/4009 .. _Pull Request 4012: https://github.com/galaxyproject/galaxy/pull/4012 .. _Pull Request 4015: https://github.com/galaxyproject/galaxy/pull/4015 .. _Pull Request 4017: https://github.com/galaxyproject/galaxy/pull/4017 .. _Pull Request 4020: https://github.com/galaxyproject/galaxy/pull/4020 .. _Pull Request 4026: https://github.com/galaxyproject/galaxy/pull/4026 .. _Pull Request 4033: https://github.com/galaxyproject/galaxy/pull/4033 .. _Pull Request 4035: https://github.com/galaxyproject/galaxy/pull/4035 .. _Pull Request 4038: https://github.com/galaxyproject/galaxy/pull/4038 .. _Pull Request 4052: https://github.com/galaxyproject/galaxy/pull/4052 .. _Pull Request 4055: https://github.com/galaxyproject/galaxy/pull/4055 .. _Pull Request 4058: https://github.com/galaxyproject/galaxy/pull/4058 .. _Pull Request 4065: https://github.com/galaxyproject/galaxy/pull/4065 .. _Pull Request 4068: https://github.com/galaxyproject/galaxy/pull/4068 .. _Pull Request 4089: https://github.com/galaxyproject/galaxy/pull/4089 .. _Pull Request 4094: https://github.com/galaxyproject/galaxy/pull/4094 .. _Pull Request 4104: https://github.com/galaxyproject/galaxy/pull/4104 .. _Pull Request 4107: https://github.com/galaxyproject/galaxy/pull/4107