mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-28 02:58:18 +08:00
Merge branch 'release_21.09' into dev
This commit is contained in:
mvdbeek
@@ -0,0 +1,681 @@
|
||||
|
||||
.. to_doc
|
||||
|
||||
21.09
|
||||
===============================
|
||||
|
||||
.. announce_start
|
||||
|
||||
Please note that the release is still being tested and finalized, and that these
|
||||
are pre-release notes.
|
||||
|
||||
Check back here for the official and comprehensive notes soon!
|
||||
|
||||
|
||||
Enhancements
|
||||
-------------------------------
|
||||
|
||||
.. major_feature
|
||||
|
||||
|
||||
.. feature
|
||||
|
||||
* New User Welcome page
|
||||
(thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
|
||||
`Pull Request 11085`_
|
||||
* GPU enabled jupyter notebook for machine learning powered by Jupyter lab and Tensorflow
|
||||
(thanks to `@anuprulez <https://github.com/anuprulez>`__).
|
||||
`Pull Request 11484`_
|
||||
* NCBI Datasets data source tool
|
||||
`Pull Request 11738`_
|
||||
* Feature/6965/change datatype and dbkey
|
||||
(thanks to `@assuntad23 <https://github.com/assuntad23>`__).
|
||||
`Pull Request 11799`_
|
||||
* Add "View Details" button for collections
|
||||
`Pull Request 12261`_
|
||||
* Vuefy and improve granularity for tool HTML sanitization
|
||||
`Pull Request 12283`_
|
||||
* Implement tool panel views.
|
||||
`Pull Request 12327`_
|
||||
* Implement news webhook to handle release announcements
|
||||
(thanks to `@hexylena <https://github.com/hexylena>`__).
|
||||
`Pull Request 12396`_
|
||||
.. enhancement_tag_viz
|
||||
|
||||
.. enhancement_tag_datatypes
|
||||
|
||||
* Convert/standardize to fstrings across `lib`
|
||||
`Pull Request 11338`_
|
||||
* Added documentation for FASTQ datatypes and implemented quality check
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 11931`_
|
||||
* Make dataset preview for h5mlm datatype
|
||||
(thanks to `@qiagu <https://github.com/qiagu>`__).
|
||||
`Pull Request 11935`_
|
||||
* Add datatypes for Structural Materials Hexrd application
|
||||
(thanks to `@jj-umn <https://github.com/jj-umn>`__).
|
||||
`Pull Request 11957`_
|
||||
* Adding new subclass types
|
||||
(thanks to `@maikenp <https://github.com/maikenp>`__).
|
||||
`Pull Request 12097`_
|
||||
* Converters: use target datatype
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12185`_
|
||||
* Add bref3 datatype
|
||||
(thanks to `@gallardoalba <https://github.com/gallardoalba>`__).
|
||||
`Pull Request 12199`_
|
||||
* Converters: add missing tests and add linting to converter tests
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12202`_
|
||||
* Converters: Unify converters to tabix and bgzip
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12213`_
|
||||
* Converters: Unify dcd, trr, xtc
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12224`_
|
||||
* converters: Unify bcf converters
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12225`_
|
||||
* Add "ExpressionSet RData object" Datatype
|
||||
(thanks to `@mtekman <https://github.com/mtekman>`__).
|
||||
`Pull Request 12336`_
|
||||
* also parse sam metadata from sam files
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12392`_
|
||||
* Add ONNX datatype
|
||||
(thanks to `@anuprulez <https://github.com/anuprulez>`__).
|
||||
`Pull Request 12429`_
|
||||
.. enhancement_tag_tools
|
||||
|
||||
* Changes to Collection Operation Help sections and parameter names
|
||||
`Pull Request 11068`_
|
||||
* Update bam.iobio interactive tool wrapper
|
||||
(thanks to `@luke-c-sargent <https://github.com/luke-c-sargent>`__).
|
||||
`Pull Request 11537`_
|
||||
* Add tool for exporting individual files to galaxy file source plugins.
|
||||
`Pull Request 11613`_
|
||||
* Update AskOmics interactive tool to 4.3.1
|
||||
(thanks to `@abretaud <https://github.com/abretaud>`__).
|
||||
`Pull Request 12159`_
|
||||
* add <creator> to the tool schema template, use live links in xsd
|
||||
`Pull Request 12242`_
|
||||
* Systematic handling of remotely required tool files.
|
||||
`Pull Request 12250`_
|
||||
* Allow bio.tools mappings for legacy tools.
|
||||
`Pull Request 12289`_
|
||||
* Allow skipping sanitization of / char in export_remote tool
|
||||
`Pull Request 12372`_
|
||||
* Lock location file before adding values
|
||||
`Pull Request 12446`_
|
||||
.. enhancement_tag_workflows
|
||||
|
||||
.. enhancement_tag_ui
|
||||
|
||||
* Beta history selenium updates and assorted bug fixes
|
||||
`Pull Request 12351`_
|
||||
* webpack dev server on remote galaxy server
|
||||
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
|
||||
`Pull Request 12356`_
|
||||
.. enhancement_tag_jobs
|
||||
|
||||
* SGE DRMAA example for queue, RAM and CPUs request
|
||||
(thanks to `@pcm32 <https://github.com/pcm32>`__).
|
||||
`Pull Request 12059`_
|
||||
* Allow specifying useful classes of tools for mapping in job conf YAML/XML
|
||||
`Pull Request 12258`_
|
||||
* Fix galaxy.json dynamic file collection in Pulsar.
|
||||
`Pull Request 12267`_
|
||||
* Default k8s_unschedulable_walltime_limit to None and allow for unlimi…
|
||||
(thanks to `@nuwang <https://github.com/nuwang>`__).
|
||||
`Pull Request 12317`_
|
||||
* Support setting per-job-environment container resolvers using the `container_resolvers` key in the environment config
|
||||
`Pull Request 12350`_
|
||||
* Add config options for controlling handler and runner monitor thread sleep.
|
||||
`Pull Request 12473`_
|
||||
.. enhancement_tag_admin
|
||||
|
||||
* Make conda_auto_init option overrridable
|
||||
(thanks to `@rhpvorderman <https://github.com/rhpvorderman>`__).
|
||||
`Pull Request 12200`_
|
||||
* Support setting the container resolvers configuration directly in the Galaxy app config
|
||||
`Pull Request 12344`_
|
||||
* Improve k8s docker image
|
||||
(thanks to `@nuwang <https://github.com/nuwang>`__).
|
||||
`Pull Request 12373`_
|
||||
* update admin user list DiskUsageColumn sorting for null values
|
||||
(thanks to `@cat-bro <https://github.com/cat-bro>`__).
|
||||
`Pull Request 12469`_
|
||||
* Make the subject and body of the mailing list join message configurable
|
||||
`Pull Request 12484`_
|
||||
.. enhancement
|
||||
|
||||
* Test configuration for running Selenium tests against beta history panel.
|
||||
`Pull Request 10965`_
|
||||
* Add `negate` attribute to validators .. and tests for all
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 11043`_
|
||||
* build list: list identifiers
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 11309`_
|
||||
* Prepare FastAPI route for quotas
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 11315`_
|
||||
* Create central pydantic models
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 11827`_
|
||||
* Use python:3.7-slim container instead of ubuntu
|
||||
(thanks to `@rhpvorderman <https://github.com/rhpvorderman>`__).
|
||||
`Pull Request 11855`_
|
||||
* add more examples for the file source plugins
|
||||
(thanks to `@bgruening <https://github.com/bgruening>`__).
|
||||
`Pull Request 11949`_
|
||||
* Migrate Libraries API (top level) to FastAPI
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 11983`_
|
||||
* Upgraded to v0.9.0 of irods client that supports parallel put/get
|
||||
(thanks to `@kxk302 <https://github.com/kxk302>`__).
|
||||
`Pull Request 11984`_
|
||||
* Improve handling of tags for collection manipulation tools
|
||||
(thanks to `@simonbray <https://github.com/simonbray>`__).
|
||||
`Pull Request 11992`_
|
||||
* Initial setup for migrating to declarative mapping
|
||||
`Pull Request 12042`_
|
||||
* Migrate model to declarative mapping
|
||||
`Pull Request 12045`_
|
||||
* Unify nested collection attribute or instance access
|
||||
`Pull Request 12056`_
|
||||
* Increase API tests coverage for Data Library GET permissions
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 12057`_
|
||||
* Tweak PR template to be a bit more flexible and lightweight.
|
||||
`Pull Request 12063`_
|
||||
* Declarative mappings + tests for all models
|
||||
`Pull Request 12064`_
|
||||
* Enable pytest class-based tests
|
||||
`Pull Request 12072`_
|
||||
* Rework variable name to clarify this is a wsgi application.
|
||||
`Pull Request 12090`_
|
||||
* Upgraded irods client to v1.0.0
|
||||
(thanks to `@kxk302 <https://github.com/kxk302>`__).
|
||||
`Pull Request 12101`_
|
||||
* Add configuration option to hide user account management interfaces
|
||||
`Pull Request 12103`_
|
||||
* Fix up some typing redundancy.
|
||||
`Pull Request 12108`_
|
||||
* Rename dataset_collections_service to dataset_collection_manager.
|
||||
`Pull Request 12110`_
|
||||
* allow jupyter IT to take multiple inputs
|
||||
`Pull Request 12113`_
|
||||
* docs: change GIEs label to interactive-tools
|
||||
`Pull Request 12114`_
|
||||
* Add FastAPI routes for Library Folders
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 12131`_
|
||||
* Change icon for "Share or Publish" in new history panel
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 12143`_
|
||||
* Cleanup use of refresh/undo/redo/sync icons
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 12145`_
|
||||
* Unify how the `GalaxyInteractorApi` handles JSON requests
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 12152`_
|
||||
* Hide masthead help resources if resource urls are unavailable
|
||||
`Pull Request 12198`_
|
||||
* Cancel in progress CI on same branch, cache yarn cache
|
||||
`Pull Request 12211`_
|
||||
* show target datatype in datatype conversion
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12230`_
|
||||
* Add a note to get Python extension and set interpreter
|
||||
(thanks to `@eancelet <https://github.com/eancelet>`__).
|
||||
`Pull Request 12234`_
|
||||
* Lint for whitespace in tool XML
|
||||
(thanks to `@neoformit <https://github.com/neoformit>`__).
|
||||
`Pull Request 12246`_
|
||||
* Use relative path in recursive discover_datasets tag
|
||||
`Pull Request 12254`_
|
||||
* Deprecate data manager version
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12255`_
|
||||
* Add linting for tool parameter validators
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12262`_
|
||||
* Create a bug-report issue template
|
||||
`Pull Request 12265`_
|
||||
* Enhance page functionalities in data-library folder
|
||||
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
|
||||
`Pull Request 12270`_
|
||||
* Parse edam operation and topic data from bio.tools if available.
|
||||
`Pull Request 12291`_
|
||||
* Refactor base toolbox code de-coupled from app & config into tool_util.
|
||||
`Pull Request 12292`_
|
||||
* Vueify Dataset Error Details Page and Form
|
||||
`Pull Request 12300`_
|
||||
* implement selecting a folder in file source (upload modal)
|
||||
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
|
||||
`Pull Request 12310`_
|
||||
* allow HTML in DatasetStorage view
|
||||
(thanks to `@bgruening <https://github.com/bgruening>`__).
|
||||
`Pull Request 12312`_
|
||||
* xsd: document the delta attribute of has_size assert
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12314`_
|
||||
* make linter accept from_tool_provided_metadata as means to specify the format for discovered datasets
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12319`_
|
||||
* Add Collection Import Pages
|
||||
`Pull Request 12324`_
|
||||
* Allow various configuration parameters to be set per host.
|
||||
`Pull Request 12328`_
|
||||
* Migrate group_roles endpoints to fastapi
|
||||
(thanks to `@ZimmerA <https://github.com/ZimmerA>`__).
|
||||
`Pull Request 12337`_
|
||||
* Restore Upload dialog in global Galaxy object
|
||||
`Pull Request 12339`_
|
||||
* Move page export button to title
|
||||
`Pull Request 12340`_
|
||||
* API test case to ensure model attributes get escaped during tool evaluation
|
||||
`Pull Request 12357`_
|
||||
* Provide more context in EDAM Tool Panel
|
||||
`Pull Request 12365`_
|
||||
* fix verify output for collections
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12376`_
|
||||
* Extend per_host configurations to include static directories and files.
|
||||
`Pull Request 12379`_
|
||||
* Display Tabular datasets as sortable tables, and PDF and HTML in embedded frames in Pages
|
||||
`Pull Request 12387`_
|
||||
* create dirs when needed for the pyfilesystem export plugins
|
||||
(thanks to `@bgruening <https://github.com/bgruening>`__).
|
||||
`Pull Request 12388`_
|
||||
* Debug Galaxy (that uses a Slurm cluster, not a LocalRunner) in VSCode
|
||||
(thanks to `@kxk302 <https://github.com/kxk302>`__).
|
||||
`Pull Request 12403`_
|
||||
* Don't allow beta history panel Selenium tests to fail.
|
||||
`Pull Request 12409`_
|
||||
* Selenium test for EDAM tool panel views.
|
||||
`Pull Request 12422`_
|
||||
* Spanish Translations for remaining untranslated UI components
|
||||
(thanks to `@hexylena <https://github.com/hexylena>`__).
|
||||
`Pull Request 12427`_
|
||||
* Improvements to Selenium testing
|
||||
`Pull Request 12433`_
|
||||
* Update refgenconf (refgenie) to 0.12.0. Requires version 0.4 of confi…
|
||||
`Pull Request 12435`_
|
||||
* Set default constructor for SA models
|
||||
`Pull Request 12438`_
|
||||
* FastAPI: add middelware to deal with file downloads
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 12441`_
|
||||
* Add options to override the history name and reuse histories in the tool test script
|
||||
`Pull Request 12466`_
|
||||
* let invalid profile trigger linter error
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12501`_
|
||||
.. small_enhancement
|
||||
|
||||
* Refactor Sharing
|
||||
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
|
||||
`Pull Request 11701`_
|
||||
* Migrate to SQLAlchemy 1.4
|
||||
`Pull Request 11737`_
|
||||
* Vueify Workflow Editor wrappers
|
||||
`Pull Request 11898`_
|
||||
* add double quotes to cp for from_work_dir
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 11960`_
|
||||
* Prettier version update to new release
|
||||
`Pull Request 12027`_
|
||||
* Vueify Tool Form Wrapper
|
||||
`Pull Request 12031`_
|
||||
* Normalize Vue mounts in analysis, admin endpoints
|
||||
`Pull Request 12040`_
|
||||
* Set cache_ok flag for SQLAlchemy custom types
|
||||
`Pull Request 12060`_
|
||||
* Update SQLAlchemy to 1.4.17
|
||||
`Pull Request 12089`_
|
||||
* Update dependency resolver docs and drop sample XML file in favor of direct configuration under the dependency_resolvers key of galaxy.yml
|
||||
`Pull Request 12105`_
|
||||
* No change; triggering CI
|
||||
`Pull Request 12111`_
|
||||
* Update SQLAlchemy to 1.4.18
|
||||
`Pull Request 12132`_
|
||||
* Refactoring: Remove ExportsHistoryMixin and ImportsHistoryMixin
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 12146`_
|
||||
* Remove unused legacy controller things
|
||||
`Pull Request 12172`_
|
||||
* Update SQLAlchmey to 1.4.19
|
||||
`Pull Request 12188`_
|
||||
* Refactor Histories API controller
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 12195`_
|
||||
* Converters: Unify molecules converters
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12214`_
|
||||
* Vueify Workflow Run form
|
||||
`Pull Request 12227`_
|
||||
* Update SQLAlchmey to 1.4.20
|
||||
`Pull Request 12229`_
|
||||
* Refactor History contents API
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 12231`_
|
||||
* Improve `GitHubSearch` class
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 12276`_
|
||||
* Some refactoring of interactive tool handling in k8s
|
||||
(thanks to `@nuwang <https://github.com/nuwang>`__).
|
||||
`Pull Request 12285`_
|
||||
* Replace form-view imports in Visualizations with Vue component layer
|
||||
`Pull Request 12296`_
|
||||
* Fix histories content filtering by type
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 12303`_
|
||||
* Vueify Dataset Edit Attributes
|
||||
`Pull Request 12323`_
|
||||
* Vueify Generic Form Wrapper
|
||||
`Pull Request 12329`_
|
||||
* Refactor k8s IT checks to make logic more obvious
|
||||
(thanks to `@nuwang <https://github.com/nuwang>`__).
|
||||
`Pull Request 12360`_
|
||||
* Fix variable name typo in watchers
|
||||
(thanks to `@nuwang <https://github.com/nuwang>`__).
|
||||
`Pull Request 12368`_
|
||||
* FastAPI: deprecate url attribute (again)
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 12370`_
|
||||
* Avoid parsing the entire form model to the form display wrapper
|
||||
`Pull Request 12374`_
|
||||
* Remove tool_conf.xml.main which is no longer used
|
||||
(thanks to `@nuwang <https://github.com/nuwang>`__).
|
||||
`Pull Request 12380`_
|
||||
* Removing unused poolsize from code and config.
|
||||
(thanks to `@kxk302 <https://github.com/kxk302>`__).
|
||||
`Pull Request 12381`_
|
||||
* FastAPI: support reverse URL lookups
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 12391`_
|
||||
* Adapt quotas tests to use JSON payload
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 12417`_
|
||||
* Declarative mapping follow-up: model constructors cleanup
|
||||
`Pull Request 12424`_
|
||||
* Vuefy show_params.mako
|
||||
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
|
||||
`Pull Request 12432`_
|
||||
* Return `tool_name` only when `show_job` is full
|
||||
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
|
||||
`Pull Request 12457`_
|
||||
* Drop unused models: DeferredJob and TransferJob
|
||||
`Pull Request 12461`_
|
||||
* Drop bcftools requirement from set_metadata tool
|
||||
`Pull Request 12472`_
|
||||
* Revert "Install Tempita from a fork due to `use_2to3` deprecation"
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 12504`_
|
||||
* FastAPI: explicitly return empty response with 204 status
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 12505`_
|
||||
|
||||
|
||||
Fixes
|
||||
-------------------------------
|
||||
|
||||
.. major_bug
|
||||
|
||||
|
||||
.. bug_tag_viz
|
||||
|
||||
.. bug_tag_datatypes
|
||||
|
||||
* Fix edta metadata setting
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12273`_
|
||||
* mothur datatype: PairwiseDistanceMatrix sniffer may be too unspecific
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12280`_
|
||||
* Small fix in binary.py
|
||||
(thanks to `@melibleq <https://github.com/melibleq>`__).
|
||||
`Pull Request 12384`_
|
||||
* Fix cmap sniffer
|
||||
(thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
|
||||
`Pull Request 12509`_
|
||||
.. bug_tag_tools
|
||||
|
||||
* Fix typo in `interactivetool_jupyter_notebook.xml` help section
|
||||
(thanks to `@maximskorik <https://github.com/maximskorik>`__).
|
||||
`Pull Request 12077`_
|
||||
* Update interactivetool_pyiron.xml
|
||||
(thanks to `@gmauro <https://github.com/gmauro>`__).
|
||||
`Pull Request 12127`_
|
||||
* Fix patterns in Grep1 tool
|
||||
`Pull Request 12166`_
|
||||
* Restore Grep1 version 1.0.1
|
||||
`Pull Request 12252`_
|
||||
.. bug_tag_workflows
|
||||
|
||||
* Add switch for optional select in workflow editor
|
||||
`Pull Request 12138`_
|
||||
* Do not persist tool state when invoking workflow
|
||||
`Pull Request 12141`_
|
||||
* Fix failure to serialize invocation / drop stored_workflow_id from invocation API
|
||||
`Pull Request 12148`_
|
||||
* Fix various TRS bugs and add tests
|
||||
`Pull Request 12182`_
|
||||
* Fix simplified workflow run form config setting
|
||||
`Pull Request 12204`_
|
||||
* Fix expanding collections in invocation view
|
||||
`Pull Request 12216`_
|
||||
.. bug_tag_ui
|
||||
|
||||
* Swap to galaxy fork of bootstrap-tour
|
||||
`Pull Request 12210`_
|
||||
* Beta history annotation, title, and tag editor
|
||||
`Pull Request 12299`_
|
||||
* Fix typo in docs
|
||||
`Pull Request 12450`_
|
||||
.. bug_tag_jobs
|
||||
|
||||
* Handle k8s job creation failures
|
||||
(thanks to `@brinkmanlab <https://github.com/brinkmanlab>`__).
|
||||
`Pull Request 11715`_
|
||||
* More IT and k8s runner fixes
|
||||
(thanks to `@almahmoud <https://github.com/almahmoud>`__).
|
||||
`Pull Request 11989`_
|
||||
* Unquote globs in from_work_dir ouptuts
|
||||
`Pull Request 12049`_
|
||||
* quote extract_dataset_parts.sh call
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12183`_
|
||||
* Fix crash when uwsgi + mules has unhandled jobs at startup
|
||||
`Pull Request 12215`_
|
||||
* k8s - handle metadata explicitly instead of relying on legacy fallback
|
||||
(thanks to `@nuwang <https://github.com/nuwang>`__).
|
||||
`Pull Request 12243`_
|
||||
* Fix version command when using extended metadata
|
||||
`Pull Request 12245`_
|
||||
* Fix composite inputs when using Pulsar.
|
||||
`Pull Request 12259`_
|
||||
* Fix Pulsar dynamic output discovery for various simple tool specified patterns.
|
||||
`Pull Request 12260`_
|
||||
* Added additional guard conditions in k8s runner to prevent KeyError
|
||||
(thanks to `@nuwang <https://github.com/nuwang>`__).
|
||||
`Pull Request 12277`_
|
||||
* Fix Pulsar's ability to read tool provided metadata when path is overridden.
|
||||
`Pull Request 12284`_
|
||||
* Continue handler startup even if job working directory can't be recovered
|
||||
`Pull Request 12316`_
|
||||
* tmp_dir can be an expression or the string True - fix sample job_conf…
|
||||
(thanks to `@nuwang <https://github.com/nuwang>`__).
|
||||
`Pull Request 12361`_
|
||||
* Fail data manager job when processing table entry fails
|
||||
`Pull Request 12495`_
|
||||
.. bug_tag_admin
|
||||
|
||||
* change doc for ftp_upload_dir/site
|
||||
(thanks to `@lldelisle <https://github.com/lldelisle>`__).
|
||||
`Pull Request 12164`_
|
||||
.. bug
|
||||
|
||||
* Fix non-closing masthread downdown
|
||||
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
|
||||
`Pull Request 11962`_
|
||||
* Update tensorflow to 2.5.0.
|
||||
`Pull Request 12026`_
|
||||
* Fix query parameter in `/api/libraries/{id}/permissions`
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 12047`_
|
||||
* Add/drop index together with `job_id` column
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 12050`_
|
||||
* Fix pysam.view call
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12061`_
|
||||
* Open partfile in rb-mode in multipart uploading
|
||||
(thanks to `@bioflowy <https://github.com/bioflowy>`__).
|
||||
`Pull Request 12084`_
|
||||
* Make components full width
|
||||
(thanks to `@hexylena <https://github.com/hexylena>`__).
|
||||
`Pull Request 12085`_
|
||||
* Fix history audit table row trigger
|
||||
`Pull Request 12130`_
|
||||
* Update fastapi to 0.65.2 and dependencies
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 12136`_
|
||||
* Fix subworkflow tool state upgrade parsing
|
||||
`Pull Request 12139`_
|
||||
* adding test case for pair name, fixing other listpaired test case
|
||||
(thanks to `@assuntad23 <https://github.com/assuntad23>`__).
|
||||
`Pull Request 12154`_
|
||||
* Fix remote files upload from other pages
|
||||
(thanks to `@almahmoud <https://github.com/almahmoud>`__).
|
||||
`Pull Request 12155`_
|
||||
* Add timeout to all urlopen and requests.* methods
|
||||
`Pull Request 12173`_
|
||||
* Allow ``decompress="true"`` in test comparison methods
|
||||
`Pull Request 12187`_
|
||||
* Fix TRS search if search term contains -
|
||||
`Pull Request 12196`_
|
||||
* Allow leading whitespace in TRS search term
|
||||
`Pull Request 12197`_
|
||||
* xsd: fix typo
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12206`_
|
||||
* Work around null hid
|
||||
`Pull Request 12217`_
|
||||
* Assorted fixes to debugging documentation
|
||||
`Pull Request 12218`_
|
||||
* Don't let reports auto-create database tables
|
||||
`Pull Request 12220`_
|
||||
* Small fixes for beta history panel.
|
||||
`Pull Request 12228`_
|
||||
* Fix fugue pencil on old sharing not showing up correctly.
|
||||
`Pull Request 12235`_
|
||||
* Fix string formatting bug in test interactor
|
||||
`Pull Request 12253`_
|
||||
* Added check to install 'fs.sshfs' package
|
||||
(thanks to `@kjetilkl <https://github.com/kjetilkl>`__).
|
||||
`Pull Request 12269`_
|
||||
* fix type of `page` and `page_limit` in Libraries Folder permissions
|
||||
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
|
||||
`Pull Request 12271`_
|
||||
* Improve handling of unexpected values in is_empty_file
|
||||
`Pull Request 12275`_
|
||||
* Beta history: Dataset Collection API fix for updating tags
|
||||
`Pull Request 12286`_
|
||||
* Allow scrolling in autocomplete options, fix search word filtering
|
||||
`Pull Request 12290`_
|
||||
* Add a GDPR-friendly user purge to pgcleanup
|
||||
`Pull Request 12293`_
|
||||
* Fix admin user manage
|
||||
`Pull Request 12295`_
|
||||
* reword history import button text
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12304`_
|
||||
* Fix order of dataset instances
|
||||
`Pull Request 12305`_
|
||||
* Fix recursive file list in posix remote files
|
||||
(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
|
||||
`Pull Request 12307`_
|
||||
* linter support for `format_source` in static collection elements
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12309`_
|
||||
* Make authnz end session endpoint optional to support various …
|
||||
(thanks to `@nuwang <https://github.com/nuwang>`__).
|
||||
`Pull Request 12311`_
|
||||
* Use workflow step title as defined in the workflow model
|
||||
`Pull Request 12320`_
|
||||
* Gitlab Error report - Remove previously required urllib
|
||||
(thanks to `@selten <https://github.com/selten>`__).
|
||||
`Pull Request 12333`_
|
||||
* Identify tool by name, owner, toolshed
|
||||
(thanks to `@pvanheus <https://github.com/pvanheus>`__).
|
||||
`Pull Request 12338`_
|
||||
* Fix for empty docker_volumes/singularity_volumes in job config
|
||||
`Pull Request 12341`_
|
||||
* Fix up plugin_config module modifying configuration dictionaries.
|
||||
`Pull Request 12354`_
|
||||
* Remove NetworkException catch clauses, so if irods server is down, NetworkException percolates up, preventing a silent failure and alerting us
|
||||
(thanks to `@kxk302 <https://github.com/kxk302>`__).
|
||||
`Pull Request 12363`_
|
||||
* Bump tensorflow from 2.5.0 to 2.5.1 in /lib/galaxy/dependencies
|
||||
`Pull Request 12378`_
|
||||
* Added missing triggers package to galaxy data
|
||||
(thanks to `@nuwang <https://github.com/nuwang>`__).
|
||||
`Pull Request 12389`_
|
||||
* Fix hids, alignment, other style issues in beta history.
|
||||
`Pull Request 12406`_
|
||||
* Fixes to selenium testing with beta history panel enabled.
|
||||
`Pull Request 12407`_
|
||||
* Downgrade Cheetah3 to 3.2.6.post1
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 12408`_
|
||||
* Install Tempita from a fork due to `use_2to3` deprecation
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 12413`_
|
||||
* Fix flaky failing workflow editor selenium test.
|
||||
`Pull Request 12423`_
|
||||
* Bump sqlparse from 0.4.1 to 0.4.2 in /lib/galaxy/dependencies
|
||||
`Pull Request 12436`_
|
||||
* Fix keycloak user creation username handling.
|
||||
`Pull Request 12444`_
|
||||
* Make Role description field optional
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 12447`_
|
||||
* Drop sylink to tool_conf.xml.main
|
||||
`Pull Request 12451`_
|
||||
* Fix history contents API update batch with collections
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 12456`_
|
||||
* Remove default pagination in `LibraryPopulator.get_permissions()`
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 12463`_
|
||||
* Drop tool_name from dataset details
|
||||
`Pull Request 12465`_
|
||||
* stripping whitespace on urls when uploading
|
||||
(thanks to `@assuntad23 <https://github.com/assuntad23>`__).
|
||||
`Pull Request 12474`_
|
||||
* removing appended name field for default_value
|
||||
(thanks to `@assuntad23 <https://github.com/assuntad23>`__).
|
||||
`Pull Request 12481`_
|
||||
* Explicitly set `page_limit` in `test_get_library_available_permissions`
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 12483`_
|
||||
* Update dataset edit toggle button to refer to dataset instead of coll…
|
||||
`Pull Request 12485`_
|
||||
* Handle deleted panel views in the UI.
|
||||
`Pull Request 12488`_
|
||||
* Fix bug when restarting Galaxy in selenium integration tests.
|
||||
`Pull Request 12489`_
|
||||
* revert a change to xsd
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12494`_
|
||||
* Add PostgreSQL < 9.5 deprecation notice to 21.05 release announce
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 12496`_
|
||||
* Fix indention for admin panel links
|
||||
`Pull Request 12497`_
|
||||
|
||||
.. include:: 21.09_prs.rst
|
||||
|
||||
@@ -0,0 +1,50 @@
|
||||
|
||||
===========================================================
|
||||
September 2021 Galaxy Release (v 21.09)
|
||||
===========================================================
|
||||
|
||||
.. include:: _header.rst
|
||||
|
||||
Highlights
|
||||
===========================================================
|
||||
|
||||
Please note that the release is still being tested and finalized, and that these
|
||||
are pre-release notes.
|
||||
|
||||
Check back here for the official and comprehensive notes soon!
|
||||
|
||||
**Feature1**
|
||||
Feature description.
|
||||
|
||||
**Feature2**
|
||||
Feature description.
|
||||
|
||||
**Feature3**
|
||||
Feature description.
|
||||
|
||||
Also check out the `21.09 user release notes <21.09_announce_user.html>`__
|
||||
|
||||
Get Galaxy
|
||||
==========
|
||||
|
||||
The code lives at `GitHub <https://github.com/galaxyproject/galaxy>`__ and you should have `Git <https://git-scm.com/>`__ to obtain it.
|
||||
|
||||
To get a new Galaxy repository run:
|
||||
.. code-block:: shell
|
||||
|
||||
$ git clone -b release_21.09 https://github.com/galaxyproject/galaxy.git
|
||||
|
||||
To update an existing Galaxy repository run:
|
||||
.. code-block:: shell
|
||||
|
||||
$ git fetch origin && git checkout release_21.09 && git pull --ff-only origin release_21.09
|
||||
|
||||
See the `community hub <https://galaxyproject.org/develop/source-code/>`__ for additional details on source code locations.
|
||||
|
||||
Release Notes
|
||||
===========================================================
|
||||
|
||||
.. include:: 21.09.rst
|
||||
:start-after: announce_start
|
||||
|
||||
.. include:: _thanks.rst
|
||||
@@ -0,0 +1,152 @@
|
||||
|
||||
===========================================================
|
||||
September 2021 Galaxy Release (v 21.09)
|
||||
===========================================================
|
||||
|
||||
.. include:: _header.rst
|
||||
|
||||
Highlights
|
||||
===========================================================
|
||||
|
||||
Please note that the release is still being tested and finalized, and that these
|
||||
are pre-release notes.
|
||||
|
||||
Check back here for the official and comprehensive notes soon!
|
||||
|
||||
**Feature1**
|
||||
Feature description.
|
||||
|
||||
**Feature2**
|
||||
Feature description.
|
||||
|
||||
**Feature3**
|
||||
Feature description.
|
||||
|
||||
|
||||
New Visualizations
|
||||
===========================================================
|
||||
|
||||
.. visualizations
|
||||
|
||||
New Datatypes
|
||||
===========================================================
|
||||
|
||||
.. datatypes
|
||||
* Convert/standardize to fstrings across `lib`
|
||||
`Pull Request 11338`_
|
||||
* Added documentation for FASTQ datatypes and implemented quality check
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 11931`_
|
||||
* Make dataset preview for h5mlm datatype
|
||||
(thanks to `@qiagu <https://github.com/qiagu>`__).
|
||||
`Pull Request 11935`_
|
||||
* Add datatypes for Structural Materials Hexrd application
|
||||
(thanks to `@jj-umn <https://github.com/jj-umn>`__).
|
||||
`Pull Request 11957`_
|
||||
* Adding new subclass types
|
||||
(thanks to `@maikenp <https://github.com/maikenp>`__).
|
||||
`Pull Request 12097`_
|
||||
* Converters: use target datatype
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12185`_
|
||||
* Add bref3 datatype
|
||||
(thanks to `@gallardoalba <https://github.com/gallardoalba>`__).
|
||||
`Pull Request 12199`_
|
||||
* Converters: add missing tests and add linting to converter tests
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12202`_
|
||||
* Converters: Unify converters to tabix and bgzip
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12213`_
|
||||
* Converters: Unify molecules converters
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12214`_
|
||||
* Converters: Unify dcd, trr, xtc
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12224`_
|
||||
* converters: Unify bcf converters
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12225`_
|
||||
* Fix edta metadata setting
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12273`_
|
||||
* mothur datatype: PairwiseDistanceMatrix sniffer may be too unspecific
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12280`_
|
||||
* Add "ExpressionSet RData object" Datatype
|
||||
(thanks to `@mtekman <https://github.com/mtekman>`__).
|
||||
`Pull Request 12336`_
|
||||
* Small fix in binary.py
|
||||
(thanks to `@melibleq <https://github.com/melibleq>`__).
|
||||
`Pull Request 12384`_
|
||||
* also parse sam metadata from sam files
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 12392`_
|
||||
* Add ONNX datatype
|
||||
(thanks to `@anuprulez <https://github.com/anuprulez>`__).
|
||||
`Pull Request 12429`_
|
||||
* Drop bcftools requirement from set_metadata tool
|
||||
`Pull Request 12472`_
|
||||
* Fix cmap sniffer
|
||||
(thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
|
||||
`Pull Request 12509`_
|
||||
|
||||
Builtin Tool Updates
|
||||
===========================================================
|
||||
|
||||
.. tools
|
||||
* Changes to Collection Operation Help sections and parameter names
|
||||
`Pull Request 11068`_
|
||||
* GPU enabled jupyter notebook for machine learning powered by Jupyter lab and Tensorflow
|
||||
(thanks to `@anuprulez <https://github.com/anuprulez>`__).
|
||||
`Pull Request 11484`_
|
||||
* Update bam.iobio interactive tool wrapper
|
||||
(thanks to `@luke-c-sargent <https://github.com/luke-c-sargent>`__).
|
||||
`Pull Request 11537`_
|
||||
* Add tool for exporting individual files to galaxy file source plugins.
|
||||
`Pull Request 11613`_
|
||||
* NCBI Datasets data source tool
|
||||
`Pull Request 11738`_
|
||||
* Fix typo in `interactivetool_jupyter_notebook.xml` help section
|
||||
(thanks to `@maximskorik <https://github.com/maximskorik>`__).
|
||||
`Pull Request 12077`_
|
||||
* Update interactivetool_pyiron.xml
|
||||
(thanks to `@gmauro <https://github.com/gmauro>`__).
|
||||
`Pull Request 12127`_
|
||||
* Update AskOmics interactive tool to 4.3.1
|
||||
(thanks to `@abretaud <https://github.com/abretaud>`__).
|
||||
`Pull Request 12159`_
|
||||
* Fix patterns in Grep1 tool
|
||||
`Pull Request 12166`_
|
||||
* Remove unused legacy controller things
|
||||
`Pull Request 12172`_
|
||||
* add <creator> to the tool schema template, use live links in xsd
|
||||
`Pull Request 12242`_
|
||||
* Systematic handling of remotely required tool files.
|
||||
`Pull Request 12250`_
|
||||
* Restore Grep1 version 1.0.1
|
||||
`Pull Request 12252`_
|
||||
* Vuefy and improve granularity for tool HTML sanitization
|
||||
`Pull Request 12283`_
|
||||
* Allow bio.tools mappings for legacy tools.
|
||||
`Pull Request 12289`_
|
||||
* Allow skipping sanitization of / char in export_remote tool
|
||||
`Pull Request 12372`_
|
||||
* Lock location file before adding values
|
||||
`Pull Request 12446`_
|
||||
|
||||
Release Testing Team
|
||||
===========================================================
|
||||
|
||||
A special thanks to the release testing team for testing many of the new features and reporting many bugs:
|
||||
|
||||
<team members go here>
|
||||
|
||||
Release Notes
|
||||
===========================================================
|
||||
|
||||
Please see the `full release notes <21.09_announce.html>`_ for more details.
|
||||
|
||||
.. include:: 21.09_prs.rst
|
||||
|
||||
.. include:: _thanks.rst
|
||||
@@ -0,0 +1,269 @@
|
||||
|
||||
.. github_links
|
||||
.. _Pull Request 10965: https://github.com/galaxyproject/galaxy/pull/10965
|
||||
.. _Pull Request 11043: https://github.com/galaxyproject/galaxy/pull/11043
|
||||
.. _Pull Request 11068: https://github.com/galaxyproject/galaxy/pull/11068
|
||||
.. _Pull Request 11085: https://github.com/galaxyproject/galaxy/pull/11085
|
||||
.. _Pull Request 11309: https://github.com/galaxyproject/galaxy/pull/11309
|
||||
.. _Pull Request 11315: https://github.com/galaxyproject/galaxy/pull/11315
|
||||
.. _Pull Request 11338: https://github.com/galaxyproject/galaxy/pull/11338
|
||||
.. _Pull Request 11484: https://github.com/galaxyproject/galaxy/pull/11484
|
||||
.. _Pull Request 11537: https://github.com/galaxyproject/galaxy/pull/11537
|
||||
.. _Pull Request 11613: https://github.com/galaxyproject/galaxy/pull/11613
|
||||
.. _Pull Request 11701: https://github.com/galaxyproject/galaxy/pull/11701
|
||||
.. _Pull Request 11715: https://github.com/galaxyproject/galaxy/pull/11715
|
||||
.. _Pull Request 11737: https://github.com/galaxyproject/galaxy/pull/11737
|
||||
.. _Pull Request 11738: https://github.com/galaxyproject/galaxy/pull/11738
|
||||
.. _Pull Request 11799: https://github.com/galaxyproject/galaxy/pull/11799
|
||||
.. _Pull Request 11827: https://github.com/galaxyproject/galaxy/pull/11827
|
||||
.. _Pull Request 11855: https://github.com/galaxyproject/galaxy/pull/11855
|
||||
.. _Pull Request 11898: https://github.com/galaxyproject/galaxy/pull/11898
|
||||
.. _Pull Request 11931: https://github.com/galaxyproject/galaxy/pull/11931
|
||||
.. _Pull Request 11935: https://github.com/galaxyproject/galaxy/pull/11935
|
||||
.. _Pull Request 11937: https://github.com/galaxyproject/galaxy/pull/11937
|
||||
.. _Pull Request 11949: https://github.com/galaxyproject/galaxy/pull/11949
|
||||
.. _Pull Request 11957: https://github.com/galaxyproject/galaxy/pull/11957
|
||||
.. _Pull Request 11960: https://github.com/galaxyproject/galaxy/pull/11960
|
||||
.. _Pull Request 11962: https://github.com/galaxyproject/galaxy/pull/11962
|
||||
.. _Pull Request 11983: https://github.com/galaxyproject/galaxy/pull/11983
|
||||
.. _Pull Request 11984: https://github.com/galaxyproject/galaxy/pull/11984
|
||||
.. _Pull Request 11989: https://github.com/galaxyproject/galaxy/pull/11989
|
||||
.. _Pull Request 11992: https://github.com/galaxyproject/galaxy/pull/11992
|
||||
.. _Pull Request 12026: https://github.com/galaxyproject/galaxy/pull/12026
|
||||
.. _Pull Request 12027: https://github.com/galaxyproject/galaxy/pull/12027
|
||||
.. _Pull Request 12031: https://github.com/galaxyproject/galaxy/pull/12031
|
||||
.. _Pull Request 12040: https://github.com/galaxyproject/galaxy/pull/12040
|
||||
.. _Pull Request 12042: https://github.com/galaxyproject/galaxy/pull/12042
|
||||
.. _Pull Request 12045: https://github.com/galaxyproject/galaxy/pull/12045
|
||||
.. _Pull Request 12047: https://github.com/galaxyproject/galaxy/pull/12047
|
||||
.. _Pull Request 12049: https://github.com/galaxyproject/galaxy/pull/12049
|
||||
.. _Pull Request 12050: https://github.com/galaxyproject/galaxy/pull/12050
|
||||
.. _Pull Request 12056: https://github.com/galaxyproject/galaxy/pull/12056
|
||||
.. _Pull Request 12057: https://github.com/galaxyproject/galaxy/pull/12057
|
||||
.. _Pull Request 12059: https://github.com/galaxyproject/galaxy/pull/12059
|
||||
.. _Pull Request 12060: https://github.com/galaxyproject/galaxy/pull/12060
|
||||
.. _Pull Request 12061: https://github.com/galaxyproject/galaxy/pull/12061
|
||||
.. _Pull Request 12063: https://github.com/galaxyproject/galaxy/pull/12063
|
||||
.. _Pull Request 12064: https://github.com/galaxyproject/galaxy/pull/12064
|
||||
.. _Pull Request 12072: https://github.com/galaxyproject/galaxy/pull/12072
|
||||
.. _Pull Request 12077: https://github.com/galaxyproject/galaxy/pull/12077
|
||||
.. _Pull Request 12084: https://github.com/galaxyproject/galaxy/pull/12084
|
||||
.. _Pull Request 12085: https://github.com/galaxyproject/galaxy/pull/12085
|
||||
.. _Pull Request 12089: https://github.com/galaxyproject/galaxy/pull/12089
|
||||
.. _Pull Request 12090: https://github.com/galaxyproject/galaxy/pull/12090
|
||||
.. _Pull Request 12097: https://github.com/galaxyproject/galaxy/pull/12097
|
||||
.. _Pull Request 12101: https://github.com/galaxyproject/galaxy/pull/12101
|
||||
.. _Pull Request 12103: https://github.com/galaxyproject/galaxy/pull/12103
|
||||
.. _Pull Request 12105: https://github.com/galaxyproject/galaxy/pull/12105
|
||||
.. _Pull Request 12108: https://github.com/galaxyproject/galaxy/pull/12108
|
||||
.. _Pull Request 12110: https://github.com/galaxyproject/galaxy/pull/12110
|
||||
.. _Pull Request 12111: https://github.com/galaxyproject/galaxy/pull/12111
|
||||
.. _Pull Request 12113: https://github.com/galaxyproject/galaxy/pull/12113
|
||||
.. _Pull Request 12114: https://github.com/galaxyproject/galaxy/pull/12114
|
||||
.. _Pull Request 12127: https://github.com/galaxyproject/galaxy/pull/12127
|
||||
.. _Pull Request 12130: https://github.com/galaxyproject/galaxy/pull/12130
|
||||
.. _Pull Request 12131: https://github.com/galaxyproject/galaxy/pull/12131
|
||||
.. _Pull Request 12132: https://github.com/galaxyproject/galaxy/pull/12132
|
||||
.. _Pull Request 12136: https://github.com/galaxyproject/galaxy/pull/12136
|
||||
.. _Pull Request 12138: https://github.com/galaxyproject/galaxy/pull/12138
|
||||
.. _Pull Request 12139: https://github.com/galaxyproject/galaxy/pull/12139
|
||||
.. _Pull Request 12140: https://github.com/galaxyproject/galaxy/pull/12140
|
||||
.. _Pull Request 12141: https://github.com/galaxyproject/galaxy/pull/12141
|
||||
.. _Pull Request 12143: https://github.com/galaxyproject/galaxy/pull/12143
|
||||
.. _Pull Request 12145: https://github.com/galaxyproject/galaxy/pull/12145
|
||||
.. _Pull Request 12146: https://github.com/galaxyproject/galaxy/pull/12146
|
||||
.. _Pull Request 12148: https://github.com/galaxyproject/galaxy/pull/12148
|
||||
.. _Pull Request 12152: https://github.com/galaxyproject/galaxy/pull/12152
|
||||
.. _Pull Request 12154: https://github.com/galaxyproject/galaxy/pull/12154
|
||||
.. _Pull Request 12155: https://github.com/galaxyproject/galaxy/pull/12155
|
||||
.. _Pull Request 12159: https://github.com/galaxyproject/galaxy/pull/12159
|
||||
.. _Pull Request 12164: https://github.com/galaxyproject/galaxy/pull/12164
|
||||
.. _Pull Request 12166: https://github.com/galaxyproject/galaxy/pull/12166
|
||||
.. _Pull Request 12172: https://github.com/galaxyproject/galaxy/pull/12172
|
||||
.. _Pull Request 12173: https://github.com/galaxyproject/galaxy/pull/12173
|
||||
.. _Pull Request 12182: https://github.com/galaxyproject/galaxy/pull/12182
|
||||
.. _Pull Request 12183: https://github.com/galaxyproject/galaxy/pull/12183
|
||||
.. _Pull Request 12185: https://github.com/galaxyproject/galaxy/pull/12185
|
||||
.. _Pull Request 12187: https://github.com/galaxyproject/galaxy/pull/12187
|
||||
.. _Pull Request 12188: https://github.com/galaxyproject/galaxy/pull/12188
|
||||
.. _Pull Request 12195: https://github.com/galaxyproject/galaxy/pull/12195
|
||||
.. _Pull Request 12196: https://github.com/galaxyproject/galaxy/pull/12196
|
||||
.. _Pull Request 12197: https://github.com/galaxyproject/galaxy/pull/12197
|
||||
.. _Pull Request 12198: https://github.com/galaxyproject/galaxy/pull/12198
|
||||
.. _Pull Request 12199: https://github.com/galaxyproject/galaxy/pull/12199
|
||||
.. _Pull Request 12200: https://github.com/galaxyproject/galaxy/pull/12200
|
||||
.. _Pull Request 12202: https://github.com/galaxyproject/galaxy/pull/12202
|
||||
.. _Pull Request 12204: https://github.com/galaxyproject/galaxy/pull/12204
|
||||
.. _Pull Request 12206: https://github.com/galaxyproject/galaxy/pull/12206
|
||||
.. _Pull Request 12210: https://github.com/galaxyproject/galaxy/pull/12210
|
||||
.. _Pull Request 12211: https://github.com/galaxyproject/galaxy/pull/12211
|
||||
.. _Pull Request 12213: https://github.com/galaxyproject/galaxy/pull/12213
|
||||
.. _Pull Request 12214: https://github.com/galaxyproject/galaxy/pull/12214
|
||||
.. _Pull Request 12215: https://github.com/galaxyproject/galaxy/pull/12215
|
||||
.. _Pull Request 12216: https://github.com/galaxyproject/galaxy/pull/12216
|
||||
.. _Pull Request 12217: https://github.com/galaxyproject/galaxy/pull/12217
|
||||
.. _Pull Request 12218: https://github.com/galaxyproject/galaxy/pull/12218
|
||||
.. _Pull Request 12220: https://github.com/galaxyproject/galaxy/pull/12220
|
||||
.. _Pull Request 12221: https://github.com/galaxyproject/galaxy/pull/12221
|
||||
.. _Pull Request 12224: https://github.com/galaxyproject/galaxy/pull/12224
|
||||
.. _Pull Request 12225: https://github.com/galaxyproject/galaxy/pull/12225
|
||||
.. _Pull Request 12227: https://github.com/galaxyproject/galaxy/pull/12227
|
||||
.. _Pull Request 12228: https://github.com/galaxyproject/galaxy/pull/12228
|
||||
.. _Pull Request 12229: https://github.com/galaxyproject/galaxy/pull/12229
|
||||
.. _Pull Request 12230: https://github.com/galaxyproject/galaxy/pull/12230
|
||||
.. _Pull Request 12231: https://github.com/galaxyproject/galaxy/pull/12231
|
||||
.. _Pull Request 12234: https://github.com/galaxyproject/galaxy/pull/12234
|
||||
.. _Pull Request 12235: https://github.com/galaxyproject/galaxy/pull/12235
|
||||
.. _Pull Request 12242: https://github.com/galaxyproject/galaxy/pull/12242
|
||||
.. _Pull Request 12243: https://github.com/galaxyproject/galaxy/pull/12243
|
||||
.. _Pull Request 12245: https://github.com/galaxyproject/galaxy/pull/12245
|
||||
.. _Pull Request 12246: https://github.com/galaxyproject/galaxy/pull/12246
|
||||
.. _Pull Request 12250: https://github.com/galaxyproject/galaxy/pull/12250
|
||||
.. _Pull Request 12252: https://github.com/galaxyproject/galaxy/pull/12252
|
||||
.. _Pull Request 12253: https://github.com/galaxyproject/galaxy/pull/12253
|
||||
.. _Pull Request 12254: https://github.com/galaxyproject/galaxy/pull/12254
|
||||
.. _Pull Request 12255: https://github.com/galaxyproject/galaxy/pull/12255
|
||||
.. _Pull Request 12258: https://github.com/galaxyproject/galaxy/pull/12258
|
||||
.. _Pull Request 12259: https://github.com/galaxyproject/galaxy/pull/12259
|
||||
.. _Pull Request 12260: https://github.com/galaxyproject/galaxy/pull/12260
|
||||
.. _Pull Request 12261: https://github.com/galaxyproject/galaxy/pull/12261
|
||||
.. _Pull Request 12262: https://github.com/galaxyproject/galaxy/pull/12262
|
||||
.. _Pull Request 12265: https://github.com/galaxyproject/galaxy/pull/12265
|
||||
.. _Pull Request 12266: https://github.com/galaxyproject/galaxy/pull/12266
|
||||
.. _Pull Request 12267: https://github.com/galaxyproject/galaxy/pull/12267
|
||||
.. _Pull Request 12269: https://github.com/galaxyproject/galaxy/pull/12269
|
||||
.. _Pull Request 12270: https://github.com/galaxyproject/galaxy/pull/12270
|
||||
.. _Pull Request 12271: https://github.com/galaxyproject/galaxy/pull/12271
|
||||
.. _Pull Request 12273: https://github.com/galaxyproject/galaxy/pull/12273
|
||||
.. _Pull Request 12275: https://github.com/galaxyproject/galaxy/pull/12275
|
||||
.. _Pull Request 12276: https://github.com/galaxyproject/galaxy/pull/12276
|
||||
.. _Pull Request 12277: https://github.com/galaxyproject/galaxy/pull/12277
|
||||
.. _Pull Request 12280: https://github.com/galaxyproject/galaxy/pull/12280
|
||||
.. _Pull Request 12283: https://github.com/galaxyproject/galaxy/pull/12283
|
||||
.. _Pull Request 12284: https://github.com/galaxyproject/galaxy/pull/12284
|
||||
.. _Pull Request 12285: https://github.com/galaxyproject/galaxy/pull/12285
|
||||
.. _Pull Request 12286: https://github.com/galaxyproject/galaxy/pull/12286
|
||||
.. _Pull Request 12289: https://github.com/galaxyproject/galaxy/pull/12289
|
||||
.. _Pull Request 12290: https://github.com/galaxyproject/galaxy/pull/12290
|
||||
.. _Pull Request 12291: https://github.com/galaxyproject/galaxy/pull/12291
|
||||
.. _Pull Request 12292: https://github.com/galaxyproject/galaxy/pull/12292
|
||||
.. _Pull Request 12293: https://github.com/galaxyproject/galaxy/pull/12293
|
||||
.. _Pull Request 12295: https://github.com/galaxyproject/galaxy/pull/12295
|
||||
.. _Pull Request 12296: https://github.com/galaxyproject/galaxy/pull/12296
|
||||
.. _Pull Request 12299: https://github.com/galaxyproject/galaxy/pull/12299
|
||||
.. _Pull Request 12300: https://github.com/galaxyproject/galaxy/pull/12300
|
||||
.. _Pull Request 12303: https://github.com/galaxyproject/galaxy/pull/12303
|
||||
.. _Pull Request 12304: https://github.com/galaxyproject/galaxy/pull/12304
|
||||
.. _Pull Request 12305: https://github.com/galaxyproject/galaxy/pull/12305
|
||||
.. _Pull Request 12307: https://github.com/galaxyproject/galaxy/pull/12307
|
||||
.. _Pull Request 12309: https://github.com/galaxyproject/galaxy/pull/12309
|
||||
.. _Pull Request 12310: https://github.com/galaxyproject/galaxy/pull/12310
|
||||
.. _Pull Request 12311: https://github.com/galaxyproject/galaxy/pull/12311
|
||||
.. _Pull Request 12312: https://github.com/galaxyproject/galaxy/pull/12312
|
||||
.. _Pull Request 12314: https://github.com/galaxyproject/galaxy/pull/12314
|
||||
.. _Pull Request 12316: https://github.com/galaxyproject/galaxy/pull/12316
|
||||
.. _Pull Request 12317: https://github.com/galaxyproject/galaxy/pull/12317
|
||||
.. _Pull Request 12319: https://github.com/galaxyproject/galaxy/pull/12319
|
||||
.. _Pull Request 12320: https://github.com/galaxyproject/galaxy/pull/12320
|
||||
.. _Pull Request 12323: https://github.com/galaxyproject/galaxy/pull/12323
|
||||
.. _Pull Request 12324: https://github.com/galaxyproject/galaxy/pull/12324
|
||||
.. _Pull Request 12327: https://github.com/galaxyproject/galaxy/pull/12327
|
||||
.. _Pull Request 12328: https://github.com/galaxyproject/galaxy/pull/12328
|
||||
.. _Pull Request 12329: https://github.com/galaxyproject/galaxy/pull/12329
|
||||
.. _Pull Request 12333: https://github.com/galaxyproject/galaxy/pull/12333
|
||||
.. _Pull Request 12334: https://github.com/galaxyproject/galaxy/pull/12334
|
||||
.. _Pull Request 12336: https://github.com/galaxyproject/galaxy/pull/12336
|
||||
.. _Pull Request 12337: https://github.com/galaxyproject/galaxy/pull/12337
|
||||
.. _Pull Request 12338: https://github.com/galaxyproject/galaxy/pull/12338
|
||||
.. _Pull Request 12339: https://github.com/galaxyproject/galaxy/pull/12339
|
||||
.. _Pull Request 12340: https://github.com/galaxyproject/galaxy/pull/12340
|
||||
.. _Pull Request 12341: https://github.com/galaxyproject/galaxy/pull/12341
|
||||
.. _Pull Request 12344: https://github.com/galaxyproject/galaxy/pull/12344
|
||||
.. _Pull Request 12350: https://github.com/galaxyproject/galaxy/pull/12350
|
||||
.. _Pull Request 12351: https://github.com/galaxyproject/galaxy/pull/12351
|
||||
.. _Pull Request 12352: https://github.com/galaxyproject/galaxy/pull/12352
|
||||
.. _Pull Request 12354: https://github.com/galaxyproject/galaxy/pull/12354
|
||||
.. _Pull Request 12356: https://github.com/galaxyproject/galaxy/pull/12356
|
||||
.. _Pull Request 12357: https://github.com/galaxyproject/galaxy/pull/12357
|
||||
.. _Pull Request 12360: https://github.com/galaxyproject/galaxy/pull/12360
|
||||
.. _Pull Request 12361: https://github.com/galaxyproject/galaxy/pull/12361
|
||||
.. _Pull Request 12363: https://github.com/galaxyproject/galaxy/pull/12363
|
||||
.. _Pull Request 12365: https://github.com/galaxyproject/galaxy/pull/12365
|
||||
.. _Pull Request 12368: https://github.com/galaxyproject/galaxy/pull/12368
|
||||
.. _Pull Request 12370: https://github.com/galaxyproject/galaxy/pull/12370
|
||||
.. _Pull Request 12372: https://github.com/galaxyproject/galaxy/pull/12372
|
||||
.. _Pull Request 12373: https://github.com/galaxyproject/galaxy/pull/12373
|
||||
.. _Pull Request 12374: https://github.com/galaxyproject/galaxy/pull/12374
|
||||
.. _Pull Request 12376: https://github.com/galaxyproject/galaxy/pull/12376
|
||||
.. _Pull Request 12378: https://github.com/galaxyproject/galaxy/pull/12378
|
||||
.. _Pull Request 12379: https://github.com/galaxyproject/galaxy/pull/12379
|
||||
.. _Pull Request 12380: https://github.com/galaxyproject/galaxy/pull/12380
|
||||
.. _Pull Request 12381: https://github.com/galaxyproject/galaxy/pull/12381
|
||||
.. _Pull Request 12382: https://github.com/galaxyproject/galaxy/pull/12382
|
||||
.. _Pull Request 12384: https://github.com/galaxyproject/galaxy/pull/12384
|
||||
.. _Pull Request 12387: https://github.com/galaxyproject/galaxy/pull/12387
|
||||
.. _Pull Request 12388: https://github.com/galaxyproject/galaxy/pull/12388
|
||||
.. _Pull Request 12389: https://github.com/galaxyproject/galaxy/pull/12389
|
||||
.. _Pull Request 12390: https://github.com/galaxyproject/galaxy/pull/12390
|
||||
.. _Pull Request 12391: https://github.com/galaxyproject/galaxy/pull/12391
|
||||
.. _Pull Request 12392: https://github.com/galaxyproject/galaxy/pull/12392
|
||||
.. _Pull Request 12396: https://github.com/galaxyproject/galaxy/pull/12396
|
||||
.. _Pull Request 12401: https://github.com/galaxyproject/galaxy/pull/12401
|
||||
.. _Pull Request 12403: https://github.com/galaxyproject/galaxy/pull/12403
|
||||
.. _Pull Request 12405: https://github.com/galaxyproject/galaxy/pull/12405
|
||||
.. _Pull Request 12406: https://github.com/galaxyproject/galaxy/pull/12406
|
||||
.. _Pull Request 12407: https://github.com/galaxyproject/galaxy/pull/12407
|
||||
.. _Pull Request 12408: https://github.com/galaxyproject/galaxy/pull/12408
|
||||
.. _Pull Request 12409: https://github.com/galaxyproject/galaxy/pull/12409
|
||||
.. _Pull Request 12413: https://github.com/galaxyproject/galaxy/pull/12413
|
||||
.. _Pull Request 12417: https://github.com/galaxyproject/galaxy/pull/12417
|
||||
.. _Pull Request 12420: https://github.com/galaxyproject/galaxy/pull/12420
|
||||
.. _Pull Request 12422: https://github.com/galaxyproject/galaxy/pull/12422
|
||||
.. _Pull Request 12423: https://github.com/galaxyproject/galaxy/pull/12423
|
||||
.. _Pull Request 12424: https://github.com/galaxyproject/galaxy/pull/12424
|
||||
.. _Pull Request 12426: https://github.com/galaxyproject/galaxy/pull/12426
|
||||
.. _Pull Request 12427: https://github.com/galaxyproject/galaxy/pull/12427
|
||||
.. _Pull Request 12429: https://github.com/galaxyproject/galaxy/pull/12429
|
||||
.. _Pull Request 12430: https://github.com/galaxyproject/galaxy/pull/12430
|
||||
.. _Pull Request 12432: https://github.com/galaxyproject/galaxy/pull/12432
|
||||
.. _Pull Request 12433: https://github.com/galaxyproject/galaxy/pull/12433
|
||||
.. _Pull Request 12434: https://github.com/galaxyproject/galaxy/pull/12434
|
||||
.. _Pull Request 12435: https://github.com/galaxyproject/galaxy/pull/12435
|
||||
.. _Pull Request 12436: https://github.com/galaxyproject/galaxy/pull/12436
|
||||
.. _Pull Request 12438: https://github.com/galaxyproject/galaxy/pull/12438
|
||||
.. _Pull Request 12441: https://github.com/galaxyproject/galaxy/pull/12441
|
||||
.. _Pull Request 12444: https://github.com/galaxyproject/galaxy/pull/12444
|
||||
.. _Pull Request 12446: https://github.com/galaxyproject/galaxy/pull/12446
|
||||
.. _Pull Request 12447: https://github.com/galaxyproject/galaxy/pull/12447
|
||||
.. _Pull Request 12448: https://github.com/galaxyproject/galaxy/pull/12448
|
||||
.. _Pull Request 12450: https://github.com/galaxyproject/galaxy/pull/12450
|
||||
.. _Pull Request 12451: https://github.com/galaxyproject/galaxy/pull/12451
|
||||
.. _Pull Request 12456: https://github.com/galaxyproject/galaxy/pull/12456
|
||||
.. _Pull Request 12457: https://github.com/galaxyproject/galaxy/pull/12457
|
||||
.. _Pull Request 12461: https://github.com/galaxyproject/galaxy/pull/12461
|
||||
.. _Pull Request 12462: https://github.com/galaxyproject/galaxy/pull/12462
|
||||
.. _Pull Request 12463: https://github.com/galaxyproject/galaxy/pull/12463
|
||||
.. _Pull Request 12465: https://github.com/galaxyproject/galaxy/pull/12465
|
||||
.. _Pull Request 12466: https://github.com/galaxyproject/galaxy/pull/12466
|
||||
.. _Pull Request 12469: https://github.com/galaxyproject/galaxy/pull/12469
|
||||
.. _Pull Request 12471: https://github.com/galaxyproject/galaxy/pull/12471
|
||||
.. _Pull Request 12472: https://github.com/galaxyproject/galaxy/pull/12472
|
||||
.. _Pull Request 12473: https://github.com/galaxyproject/galaxy/pull/12473
|
||||
.. _Pull Request 12474: https://github.com/galaxyproject/galaxy/pull/12474
|
||||
.. _Pull Request 12481: https://github.com/galaxyproject/galaxy/pull/12481
|
||||
.. _Pull Request 12483: https://github.com/galaxyproject/galaxy/pull/12483
|
||||
.. _Pull Request 12484: https://github.com/galaxyproject/galaxy/pull/12484
|
||||
.. _Pull Request 12485: https://github.com/galaxyproject/galaxy/pull/12485
|
||||
.. _Pull Request 12488: https://github.com/galaxyproject/galaxy/pull/12488
|
||||
.. _Pull Request 12489: https://github.com/galaxyproject/galaxy/pull/12489
|
||||
.. _Pull Request 12494: https://github.com/galaxyproject/galaxy/pull/12494
|
||||
.. _Pull Request 12495: https://github.com/galaxyproject/galaxy/pull/12495
|
||||
.. _Pull Request 12496: https://github.com/galaxyproject/galaxy/pull/12496
|
||||
.. _Pull Request 12497: https://github.com/galaxyproject/galaxy/pull/12497
|
||||
.. _Pull Request 12501: https://github.com/galaxyproject/galaxy/pull/12501
|
||||
.. _Pull Request 12504: https://github.com/galaxyproject/galaxy/pull/12504
|
||||
.. _Pull Request 12505: https://github.com/galaxyproject/galaxy/pull/12505
|
||||
.. _Pull Request 12509: https://github.com/galaxyproject/galaxy/pull/12509
|
||||
.. _Pull Request 12511: https://github.com/galaxyproject/galaxy/pull/12511
|
||||
.. _Pull Request 12521: https://github.com/galaxyproject/galaxy/pull/12521
|
||||
.. _Pull Request 12532: https://github.com/galaxyproject/galaxy/pull/12532
|
||||
Reference in New Issue
Block a user