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Merge pull request #17259 from dannon/release_notes_23.2
[23.2] Initial release notes for 23.2
This commit is contained in:
Martin Cech
@@ -0,0 +1,950 @@
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.. to_doc
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23.2
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===============================
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.. announce_start
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|
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Enhancements
|
||||
-------------------------------
|
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|
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.. major_feature
|
||||
|
||||
|
||||
.. feature
|
||||
|
||||
* Make form repeat blocks reorderable
|
||||
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
|
||||
`Pull Request 14892`_
|
||||
* Tool Shed 2.0
|
||||
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
|
||||
`Pull Request 15639`_
|
||||
* Limit number of celery task executions per second per user
|
||||
(thanks to `@claudiofr <https://github.com/claudiofr>`__).
|
||||
`Pull Request 16232`_
|
||||
* Notifications admin panel
|
||||
(thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
|
||||
`Pull Request 16278`_
|
||||
* Add Invenio RDM repository integration
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16381`_
|
||||
* Add new cns, cnr and cnn datatypes (cnvkit tools)
|
||||
(thanks to `@khaled196 <https://github.com/khaled196>`__).
|
||||
`Pull Request 16503`_
|
||||
* Create reusable `FilterMenu` with advanced options
|
||||
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
|
||||
`Pull Request 16522`_
|
||||
* Support new genome browser chain file format
|
||||
(thanks to `@claudiofr <https://github.com/claudiofr>`__).
|
||||
`Pull Request 16576`_
|
||||
* Workflow Comments 💬
|
||||
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
|
||||
`Pull Request 16612`_
|
||||
* Create `GDateTime` component
|
||||
(thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
|
||||
`Pull Request 16622`_
|
||||
* History MultiView drag-drop on history picker creates new history
|
||||
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
|
||||
`Pull Request 16644`_
|
||||
* Workflow Embed
|
||||
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
|
||||
`Pull Request 16657`_
|
||||
* Add EGI Check-in as OIDC authentication option
|
||||
(thanks to `@enolfc <https://github.com/enolfc>`__).
|
||||
`Pull Request 16782`_
|
||||
* Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including
|
||||
Podman job_conf
|
||||
(thanks to `@sveinugu <https://github.com/sveinugu>`__).
|
||||
`Pull Request 16795`_
|
||||
* Galaxy help forum integration
|
||||
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
|
||||
`Pull Request 16798`_
|
||||
* Allow to permanently delete non-deleted items in Storage Dashboard Visualizations
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16944`_
|
||||
* Allow switching histories from Storage Dashboard Visualizations
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16945`_
|
||||
* Add support for larch datatypes
|
||||
(thanks to `@patrick-austin <https://github.com/patrick-austin>`__).
|
||||
`Pull Request 17080`_
|
||||
.. enhancement_tag_viz
|
||||
|
||||
.. enhancement_tag_datatypes
|
||||
|
||||
* Implement display function for all datatypes
|
||||
(thanks to `@SergeyYakubov <https://github.com/SergeyYakubov>`__).
|
||||
`Pull Request 15447`_
|
||||
* Add stl datatype
|
||||
(thanks to `@TanguyGen <https://github.com/TanguyGen>`__).
|
||||
`Pull Request 16478`_
|
||||
* Bump samtools converters
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 16668`_
|
||||
* Add docx datatype
|
||||
(thanks to `@yvanlebras <https://github.com/yvanlebras>`__).
|
||||
`Pull Request 16713`_
|
||||
* Optimize object store cache operations
|
||||
(thanks to `@SergeyYakubov <https://github.com/SergeyYakubov>`__).
|
||||
`Pull Request 17025`_
|
||||
.. enhancement_tag_tools
|
||||
|
||||
* Update cellxgene interactive tool to 1.1.1
|
||||
(thanks to `@pcm32 <https://github.com/pcm32>`__).
|
||||
`Pull Request 15313`_
|
||||
* Update interactivetool_mgnify_notebook to v1.2.2
|
||||
(thanks to `@SandyRogers <https://github.com/SandyRogers>`__).
|
||||
`Pull Request 16517`_
|
||||
* Refactor Tool Panel views structures and combine ToolBox and ToolBoxWorkflow into one component
|
||||
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
|
||||
`Pull Request 16739`_
|
||||
.. enhancement_tag_workflows
|
||||
|
||||
* Implement default locations for data and collection parameters
|
||||
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
|
||||
`Pull Request 14955`_
|
||||
* Delete non-terminal jobs and subworkflow invocations when canceling invocation
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16252`_
|
||||
* Make it obvious that `WorkflowInvocationStep` is clickable/expandable
|
||||
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
|
||||
`Pull Request 16507`_
|
||||
* Galaxy Markdown - add workflow image and license to Galaxy markdown
|
||||
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
|
||||
`Pull Request 16672`_
|
||||
* Implement instance URLs in Galaxy markdown
|
||||
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
|
||||
`Pull Request 16675`_
|
||||
* Improve invocation error reporting
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16917`_
|
||||
* Remove "Create Workflow" form and allow workflow creation in editor
|
||||
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
|
||||
`Pull Request 16938`_
|
||||
* Fix invocation report to target correct workflow version
|
||||
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
|
||||
`Pull Request 17008`_
|
||||
* Require name for workflows on save, set default to Unnamed Workflow
|
||||
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
|
||||
`Pull Request 17038`_
|
||||
.. enhancement_tag_ui
|
||||
|
||||
* Client import sorting
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 16345`_
|
||||
.. enhancement_tag_jobs
|
||||
|
||||
* Towards SQLAlchemy 2.0 (upgrades to SQLAlchemy Core usage)
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16264`_
|
||||
* Add HEAD route to job_files endpoint
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17072`_
|
||||
.. enhancement_tag_admin
|
||||
|
||||
* Add carbon emissions admin configuration options
|
||||
(thanks to `@Renni771 <https://github.com/Renni771>`__).
|
||||
`Pull Request 16307`_
|
||||
* Augment pgcleanup to allow periodically deleting old datasets
|
||||
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
|
||||
`Pull Request 16340`_
|
||||
* Support configuring job metrics inline, update documentation
|
||||
(thanks to `@natefoo <https://github.com/natefoo>`__).
|
||||
`Pull Request 17178`_
|
||||
.. enhancement
|
||||
|
||||
* Add parameter name to validation errors
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 15440`_
|
||||
* Add framework test for profile behavior of `format="input"`
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 15482`_
|
||||
* Add ability to assert metadata properties on input dataset parameters
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 15825`_
|
||||
* Vueify _fieldDialog
|
||||
(thanks to `@assuntad23 <https://github.com/assuntad23>`__).
|
||||
`Pull Request 16236`_
|
||||
* Update Python dependencies
|
||||
(thanks to `@galaxybot <https://github.com/galaxybot>`__).
|
||||
`Pull Request 16305`_
|
||||
* Add Python string formatting best practices
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 16312`_
|
||||
* Migrate a part of the users API to FastAPI
|
||||
(thanks to `@heisner-tillman <https://github.com/heisner-tillman>`__).
|
||||
`Pull Request 16341`_
|
||||
* Update Python dependencies
|
||||
(thanks to `@galaxybot <https://github.com/galaxybot>`__).
|
||||
`Pull Request 16360`_
|
||||
* Exclude auto-generated schema file from labeler
|
||||
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
|
||||
`Pull Request 16378`_
|
||||
* Update Python dependencies
|
||||
(thanks to `@galaxybot <https://github.com/galaxybot>`__).
|
||||
`Pull Request 16389`_
|
||||
* Update carbon emissions methodology page to match current feature specifications
|
||||
(thanks to `@Renni771 <https://github.com/Renni771>`__).
|
||||
`Pull Request 16392`_
|
||||
* Update Python dependencies
|
||||
(thanks to `@galaxybot <https://github.com/galaxybot>`__).
|
||||
`Pull Request 16409`_
|
||||
* Update Python dependencies
|
||||
(thanks to `@galaxybot <https://github.com/galaxybot>`__).
|
||||
`Pull Request 16436`_
|
||||
* Vueify Data Uploader
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 16472`_
|
||||
* Update Python dependencies
|
||||
(thanks to `@galaxybot <https://github.com/galaxybot>`__).
|
||||
`Pull Request 16485`_
|
||||
* Add support for CILogon deployments in different regions than the US
|
||||
(thanks to `@uwwint <https://github.com/uwwint>`__).
|
||||
`Pull Request 16490`_
|
||||
* Published Workflow Sharing page overhaul
|
||||
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
|
||||
`Pull Request 16510`_
|
||||
* Update Python dependencies
|
||||
(thanks to `@galaxybot <https://github.com/galaxybot>`__).
|
||||
`Pull Request 16521`_
|
||||
* Tweak tool memory use and optimize shared memory when using preload
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16536`_
|
||||
* Document that required text parameters need a validator
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 16538`_
|
||||
* Make tool id searchable in side panel search
|
||||
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
|
||||
`Pull Request 16543`_
|
||||
* Add uploader test cases, consolidate payload processing
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 16554`_
|
||||
* Implement datatype upload warnings
|
||||
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
|
||||
`Pull Request 16564`_
|
||||
* Update Python dependencies
|
||||
(thanks to `@galaxybot <https://github.com/galaxybot>`__).
|
||||
`Pull Request 16577`_
|
||||
* Vueify Tool Form Data Selector
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 16578`_
|
||||
* Run eslint autofix as a part of client format when using Makefile
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 16586`_
|
||||
* Add scroll pagination and username filter to `HistoryPublishedList`
|
||||
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
|
||||
`Pull Request 16642`_
|
||||
* Add GitHub CI workflow to test on Python 3.7 the packages needed by Pulsar
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 16649`_
|
||||
* cwl testing: use the proposed 1.2.1 CWL conformance tests
|
||||
(thanks to `@mr-c <https://github.com/mr-c>`__).
|
||||
`Pull Request 16658`_
|
||||
* Clarify documentation on how to build a job runner
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16665`_
|
||||
* Enhance disk quota usage summary
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16670`_
|
||||
* Include `regex` when linting validators
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16684`_
|
||||
* Change Sentry error reporting plug-in
|
||||
(thanks to `@kysrpex <https://github.com/kysrpex>`__).
|
||||
`Pull Request 16686`_
|
||||
* Use fs.onedatarestfs for Onedata files source plugin implementation
|
||||
(thanks to `@lopiola <https://github.com/lopiola>`__).
|
||||
`Pull Request 16690`_
|
||||
* Skip node installation for ``check_indexes`` tests
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 16694`_
|
||||
* Migrate `collection elements` store to Pinia
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16725`_
|
||||
* Update Python dependencies
|
||||
(thanks to `@galaxybot <https://github.com/galaxybot>`__).
|
||||
`Pull Request 16735`_
|
||||
* Improve collection items scrolling
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16738`_
|
||||
* Don't copy collection elements in ``test_dataset_collection_hide_originals``
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 16747`_
|
||||
* Selective bold text
|
||||
(thanks to `@hujambo-dunia <https://github.com/hujambo-dunia>`__).
|
||||
`Pull Request 16748`_
|
||||
* Workflow report enhancement: add time format to generated text
|
||||
(thanks to `@assuntad23 <https://github.com/assuntad23>`__).
|
||||
`Pull Request 16757`_
|
||||
* Workflow report enhancement: convert ISO to UTC for invocation date/time
|
||||
(thanks to `@assuntad23 <https://github.com/assuntad23>`__).
|
||||
`Pull Request 16758`_
|
||||
* Workflow report enhancement: expose workflow version as workflow checkpoint
|
||||
(thanks to `@assuntad23 <https://github.com/assuntad23>`__).
|
||||
`Pull Request 16760`_
|
||||
* Replace ELIXIR AAI button with Life Science login
|
||||
(thanks to `@sebastian-schaaf <https://github.com/sebastian-schaaf>`__).
|
||||
`Pull Request 16762`_
|
||||
* Update Python dependencies
|
||||
(thanks to `@galaxybot <https://github.com/galaxybot>`__).
|
||||
`Pull Request 16770`_
|
||||
* Add ClientSearchMiss Sentry capture
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 16789`_
|
||||
* Update Python dependencies
|
||||
(thanks to `@galaxybot <https://github.com/galaxybot>`__).
|
||||
`Pull Request 16807`_
|
||||
* Update Python dependencies
|
||||
(thanks to `@galaxybot <https://github.com/galaxybot>`__).
|
||||
`Pull Request 16853`_
|
||||
* Visually indicate currently viewed/edited dataset
|
||||
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
|
||||
`Pull Request 16859`_
|
||||
* Allow partial matches in workflow name tag search and search all tags for unquoted query
|
||||
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
|
||||
`Pull Request 16860`_
|
||||
* Vueify visualizations grid
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 16892`_
|
||||
* Update Python dependencies
|
||||
(thanks to `@galaxybot <https://github.com/galaxybot>`__).
|
||||
`Pull Request 16896`_
|
||||
* Remove record access handling for Invenio RDM plugin
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16900`_
|
||||
* Test link data with extended metadata
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16921`_
|
||||
* Publish Tool Shed frontend to npm
|
||||
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
|
||||
`Pull Request 16924`_
|
||||
* Update Python dependencies
|
||||
(thanks to `@galaxybot <https://github.com/galaxybot>`__).
|
||||
`Pull Request 16939`_
|
||||
* Adds `biii` as supported xref reference type
|
||||
(thanks to `@kostrykin <https://github.com/kostrykin>`__).
|
||||
`Pull Request 16952`_
|
||||
* Remove sentry.py from mypy exclusions
|
||||
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
|
||||
`Pull Request 16959`_
|
||||
* Enhance Invenio RDM integration
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16964`_
|
||||
* Allow non-optional integer/float params without value attribute
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 16966`_
|
||||
* Update Python dependencies
|
||||
(thanks to `@galaxybot <https://github.com/galaxybot>`__).
|
||||
`Pull Request 16978`_
|
||||
* Update API tool_panels route conditions
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 16991`_
|
||||
* Update Python dependencies
|
||||
(thanks to `@galaxybot <https://github.com/galaxybot>`__).
|
||||
`Pull Request 17011`_
|
||||
* Restyle Vue multiselect and adapt option order
|
||||
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
|
||||
`Pull Request 17015`_
|
||||
* Show current tool panel view name on top of tool panel
|
||||
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
|
||||
`Pull Request 17021`_
|
||||
* Change broadcast notifications style
|
||||
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
|
||||
`Pull Request 17032`_
|
||||
* Open `HistoryStorageOverview` in center panel from `HistoryPanel`
|
||||
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
|
||||
`Pull Request 17043`_
|
||||
* Update Python dependencies
|
||||
(thanks to `@galaxybot <https://github.com/galaxybot>`__).
|
||||
`Pull Request 17050`_
|
||||
* Enhance xsd schema and allow simpler assertion lists
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17134`_
|
||||
* Disable workflow report and generate PDF buttons unless workflow is successful
|
||||
(thanks to `@assuntad23 <https://github.com/assuntad23>`__).
|
||||
`Pull Request 17149`_
|
||||
* Add rerun and show details buttons in expanded collection
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17182`_
|
||||
.. small_enhancement
|
||||
|
||||
* Tool Shed client build separation
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 15000`_
|
||||
* Migrate cloud API to FastAPI
|
||||
(thanks to `@heisner-tillman <https://github.com/heisner-tillman>`__).
|
||||
`Pull Request 16296`_
|
||||
* Drop (admin only) userskeys controller
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 16318`_
|
||||
* Migrate some Remote Files Export components to composition API + TS
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16391`_
|
||||
* Standardize, lint vue component name casing
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 16398`_
|
||||
* Refactor FilesDialog services to use Fetcher
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16414`_
|
||||
* Refactor FilesDialog + Remote Files API schema improvements
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16420`_
|
||||
* Towards SQLAlchemy 2.0 (upgrades to SQLAlchemy ORM usage in /test)
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16431`_
|
||||
* SQLAlchemy 2.0 upgrades to ORM usage in /lib
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16434`_
|
||||
* Force makefile client targets to use .venv-shipped node if it exists
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 16462`_
|
||||
* Rename MetadataEqualsValidator
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 16489`_
|
||||
* Refactor/OIDC custos
|
||||
(thanks to `@uwwint <https://github.com/uwwint>`__).
|
||||
`Pull Request 16497`_
|
||||
* Migrate configuration store to Pinia
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16514`_
|
||||
* Scope Workflow Stores to Workflow ID
|
||||
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
|
||||
`Pull Request 16523`_
|
||||
* Move database access code out of ``galaxy.util``
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16526`_
|
||||
* Drop syncConfigToGalaxy
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16562`_
|
||||
* Switch out conditional requirement parser
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16636`_
|
||||
* Fix flaky test timing issue in DiskUsageSummary component
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16685`_
|
||||
* Enhance task monitor composable
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16695`_
|
||||
* Migrate `dataset` store to Pinia
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16709`_
|
||||
* Enhance Short Term Storage Composable
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16711`_
|
||||
* Misc. edits/refactorings to session handling
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16712`_
|
||||
* SQLAlchemy 2.0 upgrades (part 2)
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16724`_
|
||||
* Reset autocommit to False
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16745`_
|
||||
* Migrate `collection attributes` store to Pinia
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16752`_
|
||||
* Drop legacy server-side search
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16755`_
|
||||
* Optimize iteration in DatasetInstance model + SA2.0 fix
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16776`_
|
||||
* Migrate a part of the jobs API to FastAPI
|
||||
(thanks to `@heisner-tillman <https://github.com/heisner-tillman>`__).
|
||||
`Pull Request 16778`_
|
||||
* Replace file_name property with get_file_name function
|
||||
(thanks to `@SergeyYakubov <https://github.com/SergeyYakubov>`__).
|
||||
`Pull Request 16783`_
|
||||
* SQLAlchemy 2.0 fixes for TS2.0
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16791`_
|
||||
* Another batch of SQLAlchemy 2.0 edits in TS 2.0
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16799`_
|
||||
* Use vue modal instead of global backbone modal in user preferences
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 16830`_
|
||||
* Another batch of SQLAlchemy 2.0 edits in TS 2.0 (part 3)
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16833`_
|
||||
* Remove remaining legacy backbone form input elements
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 16834`_
|
||||
* Adjust tz inclusion in workflow reports
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 16835`_
|
||||
* Refactor dataset services
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16839`_
|
||||
* Refactor client API packages
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16847`_
|
||||
* SQLAlchemy 2.0 upgrades (part 4)
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16852`_
|
||||
* Update client dependencies
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 16867`_
|
||||
* Convert `historyItemsStore` to ts+composition
|
||||
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
|
||||
`Pull Request 16873`_
|
||||
* Drop unused HistoryContentManager code and related tests
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16882`_
|
||||
* Bump undici from 5.19.1 to 5.26.5 in /client
|
||||
(thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
|
||||
`Pull Request 16897`_
|
||||
* Enable some flake8-logging-format rules in ruff
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 16915`_
|
||||
* Fix import in historyItemsStore.ts
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16916`_
|
||||
* Change `api/tool_panel` to `api/tool_panels/...`
|
||||
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
|
||||
`Pull Request 16928`_
|
||||
* Standardize to W3C naming for color
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 16949`_
|
||||
* Add helper to get dataset or collection via ``src`` and ``id``
|
||||
(thanks to `@mr-c <https://github.com/mr-c>`__).
|
||||
`Pull Request 16953`_
|
||||
* Move and re-use persist_extra_files
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16955`_
|
||||
* Upgrade job manager's index_query method to SA2.0
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 17020`_
|
||||
* Remove eventHub custom module, swap to appropriate alternatives
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 17037`_
|
||||
|
||||
|
||||
Fixes
|
||||
-------------------------------
|
||||
|
||||
.. major_bug
|
||||
|
||||
|
||||
.. bug_tag_viz
|
||||
|
||||
* Fix and update visualization plugins
|
||||
(thanks to `@mahendrapaipuri <https://github.com/mahendrapaipuri>`__).
|
||||
`Pull Request 16119`_
|
||||
* Allow the legacy DELETE dataset endpoint to accept any string for the history_id
|
||||
(thanks to `@assuntad23 <https://github.com/assuntad23>`__).
|
||||
`Pull Request 16593`_
|
||||
.. bug_tag_datatypes
|
||||
|
||||
* MINERVA display application: enable cors, add for tabular datasets
|
||||
(thanks to `@hexylena <https://github.com/hexylena>`__).
|
||||
`Pull Request 16737`_
|
||||
* Prep for updated h5py
|
||||
(thanks to `@mr-c <https://github.com/mr-c>`__).
|
||||
`Pull Request 16963`_
|
||||
* Update tar_to_directory dependency
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17009`_
|
||||
* Fix display application link generation
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17227`_
|
||||
* Display application fixes and tests
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17233`_
|
||||
.. bug_tag_tools
|
||||
|
||||
* Add missing requirements to perl tools
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16763`_
|
||||
* Fix typos across code base
|
||||
(thanks to `@afuetterer <https://github.com/afuetterer>`__).
|
||||
`Pull Request 16851`_
|
||||
* Fix missing grep input in sort1 tool
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16910`_
|
||||
* Fix maf_thread_for_species.py
|
||||
(thanks to `@lldelisle <https://github.com/lldelisle>`__).
|
||||
`Pull Request 16971`_
|
||||
* Fix duplicated tools in tool panel view section copying
|
||||
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
|
||||
`Pull Request 17036`_
|
||||
.. bug_tag_workflows
|
||||
|
||||
* Fix workflow output display without label
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16749`_
|
||||
* Fix up local tool version handling
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16836`_
|
||||
* Fix safe update version handling in run form
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16865`_
|
||||
* Fix workflow import losing tool_version
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16869`_
|
||||
* Remove more flushes in database operation tools
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16875`_
|
||||
* Include owner's annotation when exporting workflow
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 16930`_
|
||||
* Skip change_datatype things if we're not actually changing the extension
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16931`_
|
||||
* Add execute back to published workflows list
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 16934`_
|
||||
* Skip state filtering in ``__MERGE_COLLECTION__`` tool
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16937`_
|
||||
* Prevent workflow submission with missing input values
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17048`_
|
||||
.. bug_tag_ui
|
||||
|
||||
* Replace Persistedstate Pinia Plugin with User-Scoped Composable
|
||||
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
|
||||
`Pull Request 16371`_
|
||||
* Bump tough-cookie from 4.1.2 to 4.1.3 in /client
|
||||
(thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
|
||||
`Pull Request 16385`_
|
||||
* Bump semver from 5.7.1 to 5.7.2 in /client
|
||||
(thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
|
||||
`Pull Request 16388`_
|
||||
* Bump word-wrap from 1.2.3 to 1.2.4 in /client
|
||||
(thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
|
||||
`Pull Request 16417`_
|
||||
* Bump @babel/traverse from 7.18.11 to 7.23.2 in /client
|
||||
(thanks to `@dependabot[bot] <https://github.com/dependabot[bot]>`__).
|
||||
`Pull Request 16874`_
|
||||
* Client publication
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 16999`_
|
||||
* Upgrade axios to 1.6.2
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 17053`_
|
||||
* Ensure that plugin build hash actually has a git hash to compare with otherwise force rebuild
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 17104`_
|
||||
.. bug_tag_jobs
|
||||
|
||||
* Ensure Job belongs to current SQLAlchemy session
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16647`_
|
||||
* Fix and prevent persisting null file_size
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16855`_
|
||||
* Fix tag ownership check
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16877`_
|
||||
* Ruff and flake8 fixes
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 16884`_
|
||||
* Fix unbound ``runner`` variable when there is an error in the job config
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16906`_
|
||||
* Assert that ``DatasetCollectioElement`` has an associated object
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17071`_
|
||||
* Remove rollback from ``__check_jobs_at_startup``
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17085`_
|
||||
* Fix cardinality violation error: subquery returns multiple results
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 17224`_
|
||||
.. bug_tag_admin
|
||||
|
||||
* Fix: serialize `tool_shed_urls` directly from the API
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16561`_
|
||||
* Change log level for duplicate data table entries to warning
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16988`_
|
||||
* Quote singularity env parameters
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 17055`_
|
||||
.. bug
|
||||
|
||||
* Disable verbose parso logging in db_shell.py
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16410`_
|
||||
* Fix SQLAlchemy 2.0 syntax in scripts/helper.py, fix ancient bug
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16425`_
|
||||
* Pin fs.dropboxfs to >=1
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 16451`_
|
||||
* Fix labeler for UI UX labels
|
||||
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
|
||||
`Pull Request 16456`_
|
||||
* Never consider `_galaxy_` conda env as unused
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 16460`_
|
||||
* Adjust test_data_download method in GalaxyInteractorApi so an admin user is not required
|
||||
(thanks to `@simonbray <https://github.com/simonbray>`__).
|
||||
`Pull Request 16482`_
|
||||
* Test that object store cache file gets updated
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16493`_
|
||||
* Remove unnecessary check: item cannot be None
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16550`_
|
||||
* Rename to_dict to populate in FormDefintion to fix bug
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16553`_
|
||||
* Run poetry under Python 3.8
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 16638`_
|
||||
* Fix dependency update GitHub workflow
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 16639`_
|
||||
* Force `__DUPLICATE_FILE_TO_COLLECTION__` 'size' param to integer
|
||||
(thanks to `@simonbray <https://github.com/simonbray>`__).
|
||||
`Pull Request 16659`_
|
||||
* Update build_a_job_runner.rst
|
||||
(thanks to `@maikenp <https://github.com/maikenp>`__).
|
||||
`Pull Request 16673`_
|
||||
* Fix notifications icon not showing in Masthead
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16679`_
|
||||
* Fix package version handling for initial minor releases
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 16743`_
|
||||
* Account for shared usage between TS and galaxy apps
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16746`_
|
||||
* Fix large gap between labels and form elements
|
||||
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
|
||||
`Pull Request 16753`_
|
||||
* Add deprecation notice for api/search
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16756`_
|
||||
* Don't allow empty selection on required select field
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16759`_
|
||||
* Fix public archived histories not importable
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16766`_
|
||||
* Provide specific example for API docs - tags
|
||||
(thanks to `@martenson <https://github.com/martenson>`__).
|
||||
`Pull Request 16769`_
|
||||
* Fix ItemOwnerShipException in tag removal
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16773`_
|
||||
* Initial bug fixes for Tool Shed 2.0
|
||||
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
|
||||
`Pull Request 16787`_
|
||||
* Fix short ids in tool panel views.
|
||||
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
|
||||
`Pull Request 16800`_
|
||||
* Use AlignedSegment.to_string
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16803`_
|
||||
* Move the email and username redacting from the role loop
|
||||
(thanks to `@martenson <https://github.com/martenson>`__).
|
||||
`Pull Request 16805`_
|
||||
* Move history and tool panel tooltips out of the way
|
||||
(thanks to `@martenson <https://github.com/martenson>`__).
|
||||
`Pull Request 16808`_
|
||||
* Fix tool panel views for versionless tool ids
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16809`_
|
||||
* Fix duplicate key eslint error
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16810`_
|
||||
* Fix shed unit test
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16811`_
|
||||
* Fix collection drilling
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16819`_
|
||||
* Fix parameter display in job info page for tools with sections
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16821`_
|
||||
* Tool Shed 2.0 fixes
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 16825`_
|
||||
* Fix workflow preview display if tool state does not contain all parameter values
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16829`_
|
||||
* Specify uid for the k8s image
|
||||
(thanks to `@afgane <https://github.com/afgane>`__).
|
||||
`Pull Request 16844`_
|
||||
* Exclude on_opened and on_closed from watcher events
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16850`_
|
||||
* Allow referring to steps by label only in markdown editor
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16861`_
|
||||
* Restore ToolsApi and create new api route for new panel structure
|
||||
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
|
||||
`Pull Request 16872`_
|
||||
* Fix delete collection + elements
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16879`_
|
||||
* Fix join condition for nested collection query
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16880`_
|
||||
* Fix bug in SQLAlchemy statement
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16881`_
|
||||
* Fix bug in SQLAlchemy statement: desc() applied to column, not statement
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16887`_
|
||||
* Update help in relabel_from_file.xml
|
||||
(thanks to `@lldelisle <https://github.com/lldelisle>`__).
|
||||
`Pull Request 16891`_
|
||||
* Fix link to mercurial tip in Tool Shed 2.0
|
||||
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
|
||||
`Pull Request 16895`_
|
||||
* Fix type annotation of ``lib/tool_shed/test/functional/``
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 16901`_
|
||||
* Fix navigation error in Tool Shed tests
|
||||
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
|
||||
`Pull Request 16902`_
|
||||
* Fix subtle bug in listify function + simplify list munging
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 16904`_
|
||||
* Provide error message instead of internal server error
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16905`_
|
||||
* Fix selenium selector for Workflow Run warnings
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16908`_
|
||||
* Fix GQL infinite scrolling in Tool Shed
|
||||
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
|
||||
`Pull Request 16914`_
|
||||
* Fix library import from path linking files
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16919`_
|
||||
* Fix discarded dataset ordering in Storage Dashboard
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 16929`_
|
||||
* Fix select parameter doesn't show parameter name in UI
|
||||
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
|
||||
`Pull Request 16942`_
|
||||
* Backport Fix select parameter doesn't show parameter name in UI
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16943`_
|
||||
* Don't store job in JobIO instance attributes
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16965`_
|
||||
* Workaround issue in Routes
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 16981`_
|
||||
* Fix rendering of an empty page
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 16985`_
|
||||
* Empty page render fix - backport
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 16992`_
|
||||
* Fixes for job metrics Galaxy markdown component
|
||||
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
|
||||
`Pull Request 16994`_
|
||||
* Fix copying metadata to copied job outputs
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17007`_
|
||||
* Upgrade minimum conda to be compatible with latest conda-build
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 17013`_
|
||||
* Fix filtering of active broadcasts for admins
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 17049`_
|
||||
* Use debounce instead of timeout utility
|
||||
(thanks to `@guerler <https://github.com/guerler>`__).
|
||||
`Pull Request 17057`_
|
||||
* Disable conda_auto_init in embedded pulsar test cases
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17061`_
|
||||
* Fix testing of the galaxy-tool-shed package
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 17062`_
|
||||
* Make job state param optional again
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17077`_
|
||||
* Fix input dates in notifications: consider timezone offset
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 17088`_
|
||||
* Allow relative URLs in broadcasts action links
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 17093`_
|
||||
* Fix web_apps dependencies
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17099`_
|
||||
* Implement missing upload for S3 file sources
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 17100`_
|
||||
* Set correct tool_path for packaged galaxy
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17102`_
|
||||
* Expose file_name property in DatasetFilenameWrapper
|
||||
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
|
||||
`Pull Request 17107`_
|
||||
* Fix hid/elementindex for collection displays
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 17110`_
|
||||
* Tool panel views overflow bug
|
||||
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
|
||||
`Pull Request 17112`_
|
||||
* Disable admin notifications management if notifications are disabled in config
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 17114`_
|
||||
* Add missing optional description field, fixes ephemeris data library example
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17116`_
|
||||
* Fix CSS issue affecting all dropdown menus
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 17124`_
|
||||
* Fix job search when ``command_version`` is None
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 17129`_
|
||||
* Assert that tus uploader instance has URL
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17133`_
|
||||
* Make payload optional again for create tag API
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 17144`_
|
||||
* Fix select option appears for single select
|
||||
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
|
||||
`Pull Request 17146`_
|
||||
* Add support for Cgroupsv2
|
||||
(thanks to `@natefoo <https://github.com/natefoo>`__).
|
||||
`Pull Request 17169`_
|
||||
* Fix workflow index total matches counting
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 17176`_
|
||||
* Fix job destination extra params
|
||||
(thanks to `@dannon <https://github.com/dannon>`__).
|
||||
`Pull Request 17186`_
|
||||
* Fix tools missing in panel bug
|
||||
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
|
||||
`Pull Request 17192`_
|
||||
* Fix Multiselect in BModal overflows out of view bug
|
||||
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
|
||||
`Pull Request 17197`_
|
||||
* Remove `SingleItemSelector` deselect label, fix history filters hidden on smaller screen
|
||||
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
|
||||
`Pull Request 17199`_
|
||||
* Fix `url_for` in tool error reports
|
||||
(thanks to `@davelopez <https://github.com/davelopez>`__).
|
||||
`Pull Request 17210`_
|
||||
* Fix `ToolSearch` bug for `StaticToolPanelView`s
|
||||
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
|
||||
`Pull Request 17213`_
|
||||
* Fix categories in ToolShed repo create API
|
||||
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
|
||||
`Pull Request 17218`_
|
||||
* Fix job parameter display
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17226`_
|
||||
* Fix User.current_galaxy_session
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17232`_
|
||||
* Separate collection and non-collection data element
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17236`_
|
||||
|
||||
.. include:: 23.2_prs.rst
|
||||
|
||||
@@ -1,12 +1,202 @@
|
||||
|
||||
:orphan:
|
||||
|
||||
===========================================================
|
||||
October 2023 Galaxy Release (v 23.2)
|
||||
Late 2023 Galaxy Release (v 23.2)
|
||||
===========================================================
|
||||
|
||||
.. include:: _header.rst
|
||||
|
||||
Schedule
|
||||
Highlights
|
||||
===========================================================
|
||||
* Planned Freeze Date: 2023-10-02
|
||||
* Planned Release Date: 2023-10-23
|
||||
|
||||
**Workflow comments** are a brand new feature of the Galaxy Workflow Editor. They add a suite of tools - such as text, markdown, freehand commenting and more - to help visually explain and structure Workflows. Workflow publishing and workflow sharing UI have received significant updates. A lot of work has been done on improving the page and workflow report editor options; a variety of new directives have been added to Galaxy Markdown.
|
||||
|
||||
**InvenioRDM** has been integrated into Galaxy. Users can now import files directly from InvenioRDM repositories into Galaxy, and publish records containing artifacts (Histories, datasets, etc.) from Galaxy to InvenioRDM.
|
||||
|
||||
**Miscellaneous improvements.** There have been numerous updates to the UI, including Galaxy Help forum integration, improved navigation and styling, helpful warnings, improvements to search, etc. Check out the `23.2 user release notes <23.2_announce_user.html>`__ for all the details.
|
||||
|
||||
Are you an admin? See the Administration Notes below, and check out `some admin relevant PRs <https://github.com/galaxyproject/galaxy/pulls?q=label%3Ahighlight%2Fadmin+milestone%3A23.2+is%3Aclosed+is%3Apr>`__.
|
||||
|
||||
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_23.2 https://github.com/galaxyproject/galaxy.git
|
||||
|
||||
To update an existing Galaxy repository run:
|
||||
.. code-block:: shell
|
||||
|
||||
$ git fetch origin && git checkout release_23.2 && git pull --ff-only origin release_23.2
|
||||
|
||||
See the `community hub <https://galaxyproject.org/develop/source-code/>`__ for additional details on source code locations.
|
||||
|
||||
Administration Notes
|
||||
===========================================================
|
||||
|
||||
* A lot of work has been done on path-based interactive tools, including major additions to documentation and configuration. (`#16795 <https://github.com/galaxyproject/galaxy/pull/16795>`__)
|
||||
* It is now possible to configure per-user limits for celery task execution (`#16232 <https://github.com/galaxyproject/galaxy/pull/16232>`__)
|
||||
* An admin panel for managing notifications and broadcasts has been added. Admins will be able to schedule/update/delete a broadcast and send message notifications to selected users, roles or groups. (`#16278 <https://github.com/galaxyproject/galaxy/pull/16278>`__)
|
||||
* Configuration options are now available for carbon emissions reporting. (`#16307 <https://github.com/galaxyproject/galaxy/pull/16307>`__)
|
||||
* The pgcleanup script has been modified to allow periodically deleting old datasets; operations can now be restricted to specific object store ids. (`#16340 <https://github.com/galaxyproject/galaxy/pull/16340>`__)
|
||||
* Tool memory usage has been improved. (`#16536 <https://github.com/galaxyproject/galaxy/pull/16536>`__)
|
||||
* Documentation added for tool panel and panel view administration. (`#17078 <https://github.com/galaxyproject/galaxy/pull/17078>`__)
|
||||
* Support added for cgroups-v2 (`#17169 <https://github.com/galaxyproject/galaxy/pull/17169>`__)
|
||||
* Support added for configuring job metrics inline; documentation improved (`#17178 <https://github.com/galaxyproject/galaxy/pull/17178>`__)
|
||||
|
||||
Configuration Changes
|
||||
===========================================================
|
||||
|
||||
Added
|
||||
-----
|
||||
|
||||
The following configuration options are new
|
||||
|
||||
config/user_preferences_extra_conf.yml.sample
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
- preferences.invenio
|
||||
- preferences.onedata
|
||||
|
||||
config/galaxy.yml.sample:galaxy
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
- mapping.tool_shed.mapping.config_hg_for_dev
|
||||
- mapping.tool_shed.mapping.ga4gh_service_environment
|
||||
- mapping.tool_shed.mapping.ga4gh_service_id
|
||||
- mapping.tool_shed.mapping.organization_name
|
||||
- mapping.tool_shed.mapping.organization_url
|
||||
|
||||
|
||||
Changed
|
||||
-------
|
||||
|
||||
The following configuration options have been changed
|
||||
|
||||
config/file_sources_conf.yml.sample
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
- has changed from
|
||||
|
||||
::
|
||||
|
||||
{'type': 'dropbox', 'id': 'dropbox1', 'label': 'Dropbox files (configure access in user preferences)', 'doc': 'Your Dropbox files - configure an access token via the user preferences', 'accessToken': "${user.preferences['dropbox|access_token']}"}
|
||||
{'type': 'webdav', 'id': 'owncloud1', 'label': 'OwnCloud', 'doc': 'External OwnCloud files (configure access in user preferences)', 'url': "${user.preferences['owncloud|url']}", 'root': "${user.preferences['owncloud|root']}", 'login': "${user.preferences['owncloud|username']}", 'password': "${user.preferences['owncloud|password']}"}
|
||||
{'type': 'posix', 'root': '/data/5/galaxy_import/galaxy_user_data/covid-19/data/sequences/', 'id': 'covid19-raw-sequences', 'label': 'COVID-19 FASTQ', 'doc': 'COVID-19 RAW sequences in FASTQ format'}
|
||||
{'type': 'posix', 'root': '/data/db/databases/pdb/pdb/', 'id': 'pdb-gzip', 'doc': 'Protein Data Bank (PDB)', 'label': 'PDB'}
|
||||
{'type': 'ftp', 'id': 'ebi-ftp', 'label': 'EBI FTP server', 'doc': 'European Bioinformatic Institute FTP server', 'host': 'ftp.ebi.ac.uk', 'user': 'anonymous', 'passwd': '', 'timeout': 10, 'port': 21}
|
||||
{'type': 'ftp', 'id': 'ncbi-ftp', 'label': 'NCBI FTP server', 'doc': 'NCBI FTP server', 'host': 'ftp.ncbi.nlm.nih.gov', 'user': 'anonymous', 'passwd': '', 'timeout': 10, 'port': 21}
|
||||
{'type': 'ftp', 'id': 'ensembl-ftp', 'label': 'ENSEMBL FTP server', 'doc': 'ENSEMBL FTP server', 'host': 'ftp.ensemblgenomes.org/vol1/pub/', 'user': 'anonymous', 'passwd': '', 'timeout': 10, 'port': 21}
|
||||
{'type': 'ssh', 'id': 'writeable-ssh-dir', 'requires_roles': 'writeable-galaxy-role', 'writable': True, 'label': 'Push your files to me', 'doc': 'This is an example of a writeable SSH dir', 'host': 'coolhost', 'user': 'user', 'passwd': 'passwd', 'timeout': 10, 'path': '/home/cooluser/', 'config_path': '', 'port': 2222}
|
||||
{'type': 's3fs', 'label': 'My MinIO storage', 'endpoint_url': 'https://minio.usegalaxy.eu', 'id': 'galaxy-minio-storage', 'doc': 'Galaxy MinIO S3 storage', 'anon': False, 'secret': 'UHAJ6asd6asdhasd', 'key': 'MCJU76agdt98GGFAROIP7'}
|
||||
{'type': 's3fs', 'label': 'Genome Ark', 'id': 'genomeark', 'doc': 'Access to Genome Ark open data on AWS.', 'bucket': 'genomeark', 'anon': True}
|
||||
{'type': 's3fs', 'label': '1000 Genomes', 'id': '1000genomes', 'doc': 'Access to the 1000 Genomes Project with human genetic variation, including SNPs, structural variants, and their haplotype context.', 'bucket': '1000genomes', 'anon': True}
|
||||
{'type': 's3fs', 'label': 'The Cancer Genome Atlas', 'id': 'tcga-2-open', 'doc': 'Access to the Cancer Genome Atlas (TCGA)', 'bucket': 'tcga-2-open', 'anon': True}
|
||||
{'type': 's3fs', 'label': 'COVID-19 Data Lake', 'id': 'covid19-lake', 'doc': 'A centralized repository of up-to-date and curated datasets on or related to the spread and characteristics of the novel corona virus (SARS-CoV-2) and its associated illness, COVID-19', 'bucket': 'covid19-lake', 'anon': True}
|
||||
{'type': 's3fs', 'label': 'Encyclopedia of DNA Elements (ENCODE)', 'id': 'encode-public', 'doc': 'The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI)', 'bucket': 'encode-public', 'anon': True}
|
||||
{'type': 's3fs', 'label': 'Sentinel-3', 'id': 'meeo-s3-nrt', 'doc': 'European Commission’s Copernicus Earth Observation Programme. Sentinel-3 is a polar orbiting satellite that completes 14 orbits of the Earth a day.', 'bucket': 'meeo-s3/NRT/', 'anon': True}
|
||||
{'type': 's3fs', 'label': 'Sentinel-5P Level 2', 'id': 'meeo-s5p-nrti', 'doc': 'Observations from the Sentinel-5 Precursor satellite of the Copernicus Earth Observation Programme. It contains a polar orbiting satellite that completes 14 orbits of the Earth a day.', 'bucket': 'meeo-s5p/RPRO/', 'anon': True}
|
||||
{'type': 's3fs', 'label': 'Coupled Model Intercomparison Project 6', 'id': 'esgf-world', 'doc': 'The sixth phase of global coupled ocean-atmosphere general circulation model ensemble', 'bucket': 'esgf-world', 'anon': True} {'type': 's3fs', 'label': 'CMIP6 GCMs downscaled using WRF', 'id': 'wrf-cmip6-noversioning', 'doc': 'High-resolution historical and future climate simulations from 1980-2100', 'bucket': 'wrf-cmip6-noversioning', 'anon': True}
|
||||
{'type': 's3fs', 'label': 'NOAA Global Forecast System (GFS)', 'id': 'noaa-gfs-bdp-pds', 'doc': 'The Global Forecast System (GFS) is a weather forecast model produced by the National Centers for Environmental Prediction (NCEP).', 'bucket': 'noaa-gfs-bdp-pds', 'anon': True}
|
||||
{'type': 's3fs', 'label': 'NOAA Unified Forecast System Subseasonal to Seasonal Prototype 5', 'id': 'noaa-ufs-prototype5-pds', 'doc': 'The Unified Forecast System Subseasonal to Seasonal prototype 5 (UFS S2Sp5) dataset is reforecast data from the UFS atmosphere-ocean.', 'bucket': 'noaa-ufs-prototype5-pds', 'anon': True}
|
||||
{'type': 's3fs', 'label': 'Copernicus Digital Elevation Model (DEM)', 'id': 'copernicus-dem-30m', 'doc': 'The Copernicus DEM is a Digital Surface Model (DSM) which represents the surface of the Earth including buildings, infrastructure and vegetation.', 'bucket': 'copernicus-dem-30m', 'anon': True}
|
||||
{'type': 'http', 'label': 'Custom http filesource', 'id': 'httpcustom', 'url_regex': '^https?://myprotectedsite.org/', 'http_headers': {'Authorization': '#import base64\nBasic ${base64.b64encode(str.encode(user.preferences[\'myprotectedsite|username\'] + ":" + user.preferences[\'myprotectedsite|password\'])).decode()}'}, 'doc': 'Only define this if you want custom control over http downloads. You should also define a stock http source (below) or only downloads from this site will be allowed.'}
|
||||
{'type': 'http', 'label': 'Stock http filesource', 'id': 'httpstock', 'doc': 'Make sure to define this generic http file source if you have defined any other http file sources, or stock http download capability will be disabled.'}
|
||||
{'type': 'drs', 'label': 'Custom DRS filesource', 'id': 'drscustom', 'url_regex': '^drs://mydrssite.org/', 'http_headers': {'Authorization': '#import base64\nBasic ${base64.b64encode(str.encode(user.preferences[\'mydrssite|username\'] + ":" + user.preferences[\'mydrssite|password\'])).decode()}'}, 'doc': 'Define this if you want custom control over drs downloads. You should also define a stock drs source (below) or only downloads from this drs server will be allowed.'}
|
||||
{'type': 'drs', 'label': 'Stock DRS filesource', 'id': 'drsstock', 'doc': 'Make sure to define this generic drs file source if you have defined any other drs file sources, or stock drs download capability will be disabled.'}
|
||||
|
||||
to
|
||||
|
||||
::
|
||||
|
||||
{'type': 'dropbox', 'id': 'dropbox1', 'label': 'Dropbox files (configure access in user preferences)', 'doc': 'Your Dropbox files - configure an access token via the user preferences', 'access_token': "${user.preferences['dropbox|access_token']}"}
|
||||
{'type': 'webdav', 'id': 'owncloud1', 'label': 'OwnCloud', 'doc': 'External OwnCloud files (configure access in user preferences)', 'url': "${user.preferences['owncloud|url']}", 'root': "${user.preferences['owncloud|root']}", 'login': "${user.preferences['owncloud|username']}", 'password': "${user.preferences['owncloud|password']}"}
|
||||
{'type': 'posix', 'root': '/data/5/galaxy_import/galaxy_user_data/covid-19/data/sequences/', 'id': 'covid19-raw-sequences', 'label': 'COVID-19 FASTQ', 'doc': 'COVID-19 RAW sequences in FASTQ format'}
|
||||
{'type': 'posix', 'root': '/data/db/databases/pdb/pdb/', 'id': 'pdb-gzip', 'doc': 'Protein Data Bank (PDB)', 'label': 'PDB'}
|
||||
{'type': 'ftp', 'id': 'ebi-ftp', 'label': 'EBI FTP server', 'doc': 'European Bioinformatic Institute FTP server', 'host': 'ftp.ebi.ac.uk', 'user': 'anonymous', 'passwd': '', 'timeout': 10, 'port': 21}
|
||||
{'type': 'ftp', 'id': 'ncbi-ftp', 'label': 'NCBI FTP server', 'doc': 'NCBI FTP server', 'host': 'ftp.ncbi.nlm.nih.gov', 'user': 'anonymous', 'passwd': '', 'timeout': 10, 'port': 21}
|
||||
{'type': 'ftp', 'id': 'ensembl-ftp', 'label': 'ENSEMBL FTP server', 'doc': 'ENSEMBL FTP server', 'host': 'ftp.ensemblgenomes.org/vol1/pub/', 'user': 'anonymous', 'passwd': '', 'timeout': 10, 'port': 21}
|
||||
{'type': 'ssh', 'id': 'writeable-ssh-dir', 'requires_roles': 'writeable-galaxy-role', 'writable': True, 'label': 'Push your files to me', 'doc': 'This is an example of a writeable SSH dir', 'host': 'coolhost', 'user': 'user', 'passwd': 'passwd', 'timeout': 10, 'path': '/home/cooluser/', 'config_path': '', 'port': 2222}
|
||||
{'type': 's3fs', 'label': 'My MinIO storage', 'endpoint_url': 'https://minio.usegalaxy.eu', 'id': 'galaxy-minio-storage', 'doc': 'Galaxy MinIO S3 storage', 'anon': False, 'secret': 'UHAJ6asd6asdhasd', 'key': 'MCJU76agdt98GGFAROIP7'}
|
||||
{'type': 's3fs', 'label': 'Genome Ark', 'id': 'genomeark', 'doc': 'Access to Genome Ark open data on AWS.', 'bucket': 'genomeark', 'anon': True}
|
||||
{'type': 's3fs', 'label': '1000 Genomes', 'id': '1000genomes', 'doc': 'Access to the 1000 Genomes Project with human genetic variation, including SNPs, structural variants, and their haplotype context.', 'bucket': '1000genomes', 'anon': True}
|
||||
{'type': 's3fs', 'label': 'The Cancer Genome Atlas', 'id': 'tcga-2-open', 'doc': 'Access to the Cancer Genome Atlas (TCGA)', 'bucket': 'tcga-2-open', 'anon': True}
|
||||
{'type': 's3fs', 'label': 'COVID-19 Data Lake', 'id': 'covid19-lake', 'doc': 'A centralized repository of up-to-date and curated datasets on or related to the spread and characteristics of the novel corona virus (SARS-CoV-2) and its associated illness, COVID-19', 'bucket': 'covid19-lake', 'anon': True}
|
||||
{'type': 's3fs', 'label': 'Encyclopedia of DNA Elements (ENCODE)', 'id': 'encode-public', 'doc': 'The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI)', 'bucket': 'encode-public', 'anon': True}
|
||||
{'type': 's3fs', 'label': 'Sentinel-3', 'id': 'meeo-s3-nrt', 'doc': 'European Commission’s Copernicus Earth Observation Programme. Sentinel-3 is a polar orbiting satellite that completes 14 orbits of the Earth a day.', 'bucket': 'meeo-s3/NRT/', 'anon': True}
|
||||
{'type': 's3fs', 'label': 'Sentinel-5P Level 2', 'id': 'meeo-s5p-nrti', 'doc': 'Observations from the Sentinel-5 Precursor satellite of the Copernicus Earth Observation Programme. It contains a polar orbiting satellite that completes 14 orbits of the Earth a day.', 'bucket': 'meeo-s5p/RPRO/', 'anon': True}
|
||||
{'type': 's3fs', 'label': 'Coupled Model Intercomparison Project 6', 'id': 'esgf-world', 'doc': 'The sixth phase of global coupled ocean-atmosphere general circulation model ensemble', 'bucket': 'esgf-world', 'anon': True} {'type': 's3fs', 'label': 'CMIP6 GCMs downscaled using WRF', 'id': 'wrf-cmip6-noversioning', 'doc': 'High-resolution historical and future climate simulations from 1980-2100', 'bucket': 'wrf-cmip6-noversioning', 'anon': True}
|
||||
{'type': 's3fs', 'label': 'NOAA Global Forecast System (GFS)', 'id': 'noaa-gfs-bdp-pds', 'doc': 'The Global Forecast System (GFS) is a weather forecast model produced by the National Centers for Environmental Prediction (NCEP).', 'bucket': 'noaa-gfs-bdp-pds', 'anon': True}
|
||||
{'type': 's3fs', 'label': 'NOAA Unified Forecast System Subseasonal to Seasonal Prototype 5', 'id': 'noaa-ufs-prototype5-pds', 'doc': 'The Unified Forecast System Subseasonal to Seasonal prototype 5 (UFS S2Sp5) dataset is reforecast data from the UFS atmosphere-ocean.', 'bucket': 'noaa-ufs-prototype5-pds', 'anon': True}
|
||||
{'type': 's3fs', 'label': 'Copernicus Digital Elevation Model (DEM)', 'id': 'copernicus-dem-30m', 'doc': 'The Copernicus DEM is a Digital Surface Model (DSM) which represents the surface of the Earth including buildings, infrastructure and vegetation.', 'bucket': 'copernicus-dem-30m', 'anon': True}
|
||||
{'type': 'http', 'label': 'Custom http filesource', 'id': 'httpcustom', 'url_regex': '^https?://myprotectedsite.org/', 'http_headers': {'Authorization': '#import base64\nBasic ${base64.b64encode(str.encode(user.preferences[\'myprotectedsite|username\'] + ":" + user.preferences[\'myprotectedsite|password\'])).decode()}'}, 'doc': 'Only define this if you want custom control over http downloads. You should also define a stock http source (below) or only downloads from this site will be allowed.'}
|
||||
{'type': 'http', 'label': 'Stock http filesource', 'id': 'httpstock', 'doc': 'Make sure to define this generic http file source if you have defined any other http file sources, or stock http download capability will be disabled.'}
|
||||
{'type': 'drs', 'label': 'Custom DRS filesource', 'id': 'drscustom', 'url_regex': '^drs://mydrssite.org/', 'http_headers': {'Authorization': '#import base64\nBasic ${base64.b64encode(str.encode(user.preferences[\'mydrssite|username\'] + ":" + user.preferences[\'mydrssite|password\'])).decode()}'}, 'doc': 'Define this if you want custom control over drs downloads. You should also define a stock drs source (below) or only downloads from this drs server will be allowed.'}
|
||||
{'type': 'drs', 'label': 'Stock DRS filesource', 'id': 'drsstock', 'doc': 'Make sure to define this generic drs file source if you have defined any other drs file sources, or stock drs download capability will be disabled.'}
|
||||
{'type': 'inveniordm', 'id': 'invenio', 'doc': 'Invenio RDM turn-key research data management repository', 'label': 'Invenio RDM Demo Repository', 'url': 'https://inveniordm.web.cern.ch/'}
|
||||
{'type': 'onedata', 'id': 'onedata1', 'label': 'Onedata', 'doc': 'Your Onedata files - configure an access token via user preferences', 'accessToken': "${user.preferences['onedata|access_token']}", 'onezoneDomain': "${user.preferences['onedata|onezone_domain']}"}
|
||||
|
||||
|
||||
|
||||
config/galaxy.yml.sample:galaxy
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
- mapping.galaxy.mapping.instance_resource_url.desc has changed from
|
||||
|
||||
::
|
||||
|
||||
URL of the support resource for the galaxy instance. Used in activation
|
||||
emails.
|
||||
|
||||
Example value 'https://galaxyproject.org/'
|
||||
|
||||
to
|
||||
|
||||
::
|
||||
|
||||
URL of the support resource for the galaxy instance. Used outside of web contexts
|
||||
such as in activation emails and in Galaxy markdown report generation.
|
||||
|
||||
Example value 'https://galaxyproject.org/'
|
||||
|
||||
|
||||
- mapping.galaxy.mapping.job_metrics_config_file.desc has changed from
|
||||
|
||||
::
|
||||
|
||||
XML config file that contains the job metric collection configuration.
|
||||
|
||||
to
|
||||
|
||||
::
|
||||
|
||||
YAML or XML config file that contains the job metric collection configuration.
|
||||
|
||||
|
||||
|
||||
|
||||
Removed
|
||||
-------
|
||||
|
||||
The following configuration options have been completely removed
|
||||
|
||||
config/galaxy.yml.sample:galaxy
|
||||
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||
|
||||
- mapping.galaxy.mapping.ga4gh_service_organization_name
|
||||
- mapping.galaxy.mapping.ga4gh_service_organization_url
|
||||
- mapping.galaxy.mapping.interactivetools_shorten_url
|
||||
|
||||
Deprecation Notices
|
||||
===========================================================
|
||||
Add content or drop section.
|
||||
|
||||
Release Notes
|
||||
===========================================================
|
||||
|
||||
.. include:: 23.2.rst
|
||||
:start-after: announce_start
|
||||
|
||||
.. include:: _thanks.rst
|
||||
|
||||
@@ -0,0 +1,208 @@
|
||||
|
||||
===========================================================
|
||||
Late 2023 Galaxy Release (v 23.2)
|
||||
===========================================================
|
||||
|
||||
.. include:: _header.rst
|
||||
|
||||
Highlights
|
||||
===========================================================
|
||||
|
||||
Workflow Updates
|
||||
-----------------------------------------------------------
|
||||
|
||||
Workflow comments
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
Workflow comments are a brand new feature of the Galaxy Workflow Editor. They add a suite of tools to help you visually explain and structure your Workflows. Comments are saved on your workflow, so they can be shared with other workflow contributors, help guide workflow users, or just help you keep track of your work and sort your thoughts, while developing a workflow. They can also help you with teaching, live demos, and providing feedback on a workflow, all directly inside the workflow editor!
|
||||
|
||||
.. figure:: images/23.2-wf-comments-1.png
|
||||
:alt: In the menu that pops up, when a comment is selected, it can be styled in multiple ways, making the whole text italic, bold, coloured, or larger/smaller.
|
||||
|
||||
Workflow comments tools are made available as part of the Editor Toolbar - a new UI element in the workflow editor. They include:
|
||||
|
||||
* a snapping tool that makes it very easy to align your steps and comments to the workflow grid;
|
||||
* a text comment tool that comes with rich styling options;
|
||||
* a markdown comment tool for longer, rich-text, explanations or notes;
|
||||
* a frame comments tool that allows you to visually group parts of your workflow together, steps and comments alike;
|
||||
* freehand comments tools - a pen and an eraser that enable drawing directly on your Workflow, making them perfect for showing what you are referring to in live demos, leaving quick marks when reviewing or debugging a Workflow, drawing arrows to show what your markdown comment is referring to, etc.
|
||||
|
||||
.. figure:: images/23.2-wf-comments-2.png
|
||||
:alt: Example of a structured workflow.
|
||||
|
||||
.. raw:: html
|
||||
|
||||
<iframe width="560" height="315" src="https://www.youtube.com/embed/ndPeBov5O0s" title="Galaxy 23.2 - Workflow Comments - Placing Text Comments" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
|
||||
|
|
||||
|
||||
.. raw:: html
|
||||
|
||||
<iframe width="560" height="315" src="https://www.youtube.com/embed/lAOvpGRxTk4" title="Galaxy 23.2 - Workflow Comments - Placing Frame Comments" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
|
||||
|
|
||||
Workflow sharing
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
The Published Workflow Sharing page UI has been overhauled to make the page more informative, visually appealing, and easier to navigate. Some of the key improvements include adding a new read-only mode to the workflow editor, embedding an interactive view of the workflow editor, adding more information about the workflow, adding a run button, etc. The page is now responsive, which makes it usable on smaller screens.
|
||||
|
||||
.. figure:: images/23.2-pub-wf-sharing.png
|
||||
:alt: The new Workflow Sharing page.
|
||||
|
||||
Workflow publishing
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
Workflow Publishing now has a configurable iframe embed:
|
||||
|
||||
.. figure:: images/23.2-wf-pub-iframe.png
|
||||
:alt: iframe embed with copy url button and options.
|
||||
|
||||
Workflow reports
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
In response to user feedback and suggestions, a lot of work went into improving the page and workflow report editor options. Workflow image and license information have been added to Galaxy markdown capabilities. Workflow version is now included in the report; time is displayed in UTC time format. A variety of minor issues including invocation report and the job metrics markdown component have been fixed. To address requests to add citation information for the Galaxy instance on which the workflow has been executed, several new directives have been added to Galaxy Markdown: Galaxy URL, organization URL, citation URL, support URL, help URL, terms URL, and resources URL - alongside new configuration options to support them.
|
||||
|
||||
InvenioRDM Integrated into Galaxy
|
||||
---------------------------------
|
||||
|
||||
InvenioRDM has been integrated into Galaxy. Users can now import files directly from InvenioRDM repositories into Galaxy, and publish records containing artifacts (Histories, datasets, etc.) from Galaxy to InvenioRDM.
|
||||
|
||||
Importing data
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
To import from InvenioRDM, you simply select the InvenioRDM repository as a remote file source in the *Upload* tool and then select the records or individual files you want to import into your history, just like you would do with any other remote file source in Galaxy:
|
||||
|
||||
.. raw:: html
|
||||
|
||||
<iframe width="560" height="315" src="https://www.youtube.com/embed/GzN6heU70j4" title="Galaxy 23.2 - Invenio - Importing Datasets" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
|
||||
|
|
||||
Exporting data
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
To export your data to InvenioRDM, you need to set up your InvenioRDM API personal token. You can create a new personal token in your InvenioRDM account settings if you don't have one. In Galaxy, you need to add that personal token to your account (go to *User > Preferences > Manage Information*).
|
||||
|
||||
Exporting your Histories
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
Once you have set your personal token, you can publish your histories by selecting the InvenioRDM repository as a remote file source in the *Export History to File* menu option. You will be able to select an existing draft record or create a new one, and the files will be uploaded to it. Once exported, you will be able to import the history snapshot from the published record at any time.
|
||||
|
||||
.. raw:: html
|
||||
|
||||
<iframe width="560" height="315" src="https://www.youtube.com/embed/Qoy-buGb26Y" title="Galaxy 23.2 - Invenio - Exporting Histories" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
|
||||
|
|
||||
Archiving your Histories
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
When you are completely happy with your history, you can archive it, taking it out of your active histories and freeing up some disk quota. You can do so by selecting the *Archive History* menu option. The process will be similar to exporting a history; however, your history will be purged from Galaxy once the process is completed. You will be able to import the history as a copy from the published record at any time.
|
||||
|
||||
.. raw:: html
|
||||
|
||||
<iframe width="560" height="315" src="https://www.youtube.com/embed/CNXQphjW6LE" title="Galaxy 23.2 - Invenio - Archiving Histories" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
|
||||
|
|
||||
Exporting your Datasets
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
You can also publish individual datasets to InvenioRDM by selecting the InvenioRDM repository as a remote file source using the *Export Datasets* tool. Since the tool interface is a bit limited, you will need to create your draft record manually in advance, and then you can select it when exporting the datasets.
|
||||
|
||||
.. raw:: html
|
||||
|
||||
<iframe width="560" height="315" src="https://www.youtube.com/embed/t3baif6JFfA" title="Galaxy 23.2 - Invenio - Exporting Datasets" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
|
||||
|
|
||||
Miscellaneous Improvements
|
||||
--------------------------
|
||||
|
||||
The 23.2 release includes many other improvements to user experience. Following are a few examples:
|
||||
|
||||
* Galaxy Help forum has been integrated into the tool form: relevant posts are now part of the form; pressing the *Ask a New Question* button pre-fills the title and tags with the tools name and id respectively.
|
||||
* To encourage best practices and steer users away from problematic datatypes, datatype upload warnings have been added to the Upload tool.
|
||||
* Form repeat blocks are now reorderable: new UI additions include *Move Up/Move Down* buttons, as well as focus highlighting, so the active repeat block can be followed visually when moved.
|
||||
* Scroll pagination and username filter have been added to the list of published histories.
|
||||
* Currently viewed/edited datasets are now visually indicated in the list of datasets on the right sidebar.
|
||||
* A new button allows easy switching to a history from the Histories Storage Overview in Storage Dashboard Visualizations.
|
||||
* Broadcast Notifications have received a facelift, making them more readable and less intrusive.
|
||||
* Tool IDs are now searchable in the side panel search box with queries "id:sample_id" or "tool_id:sample_id".
|
||||
* You can now search for partial matches in workflow #name tags; all tags will be search in unquoted queries.
|
||||
* When a user clicks on the "eye" button for a binary dataset or a dataset with an unknown type, Galaxy will no longer attempt to download the entire file, which is not what the user wants for large files. Instead, Galaxy displays a descriptive warning message, as well as first 100K of the data as ASCII text.
|
||||
* Galaxy caching policies have been tightened: displaying a datasets's filename no longer pulls the entire file into cache; pulling the data is now postponed until that data is really needed.
|
||||
* Canceling an active workflow run will now cancel all of the running jobs of that workflow run.
|
||||
* Work is underway on an all new Tool Shed 2.0 - a major upgrade that cuts ties to old technologies and old concepts. The new tool shed is built on FastAPI, Typescript, Vue 3.2, Vite, Pinia, Quasar, and GraphQL, with Planemo and Ephemeris integrated into the UX.
|
||||
|
||||
Datatypes
|
||||
===========================================================
|
||||
|
||||
.. datatypes
|
||||
* Implement display function for all datatypes
|
||||
(thanks to `@SergeyYakubov <https://github.com/SergeyYakubov>`__).
|
||||
`Pull Request 15447`_
|
||||
* Add stl datatype
|
||||
(thanks to `@TanguyGen <https://github.com/TanguyGen>`__).
|
||||
`Pull Request 16478`_
|
||||
* Add new cns, cnr and cnn datatypes (cnvkit tools)
|
||||
(thanks to `@khaled196 <https://github.com/khaled196>`__).
|
||||
`Pull Request 16503`_
|
||||
* Support new genome browser chain file format
|
||||
(thanks to `@claudiofr <https://github.com/claudiofr>`__).
|
||||
`Pull Request 16576`_
|
||||
* Bump samtools converters
|
||||
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
|
||||
`Pull Request 16668`_
|
||||
* Add docx datatype
|
||||
(thanks to `@yvanlebras <https://github.com/yvanlebras>`__).
|
||||
`Pull Request 16713`_
|
||||
* MINERVA display application: enable cors, add for tabular datasets
|
||||
(thanks to `@hexylena <https://github.com/hexylena>`__).
|
||||
`Pull Request 16737`_
|
||||
* Prep for updated h5py
|
||||
(thanks to `@mr-c <https://github.com/mr-c>`__).
|
||||
`Pull Request 16963`_
|
||||
* Update tar_to_directory dependency
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17009`_
|
||||
* Optimize object store cache operations
|
||||
(thanks to `@SergeyYakubov <https://github.com/SergeyYakubov>`__).
|
||||
`Pull Request 17025`_
|
||||
* Add support for larch datatypes
|
||||
(thanks to `@patrick-austin <https://github.com/patrick-austin>`__).
|
||||
`Pull Request 17080`_
|
||||
* Fix Display Application link generation
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17227`_
|
||||
* Display application fixes and tests
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 17233`_
|
||||
|
||||
Builtin Tool Updates
|
||||
===========================================================
|
||||
|
||||
.. tools
|
||||
* Update cellxgene interactive tool to 1.1.1
|
||||
(thanks to `@pcm32 <https://github.com/pcm32>`__).
|
||||
`Pull Request 15313`_
|
||||
* Update interactivetool_mgnify_notebook to v1.2.2
|
||||
(thanks to `@SandyRogers <https://github.com/SandyRogers>`__).
|
||||
`Pull Request 16517`_
|
||||
* Refactor Tool Panel views structures and combine ToolBox and ToolBoxWorkflow into one component
|
||||
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
|
||||
`Pull Request 16739`_
|
||||
* Add missing requirements to perl tools
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16763`_
|
||||
* Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including
|
||||
Podman job_conf
|
||||
(thanks to `@sveinugu <https://github.com/sveinugu>`__).
|
||||
`Pull Request 16795`_
|
||||
* Fix missing grep input in sort1 tool
|
||||
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
|
||||
`Pull Request 16910`_
|
||||
* Fix maf_thread_for_species.py
|
||||
(thanks to `@lldelisle <https://github.com/lldelisle>`__).
|
||||
`Pull Request 16971`_
|
||||
* Fix duplicated tools in tool panel view section copying
|
||||
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
|
||||
`Pull Request 17036`_
|
||||
|
||||
Release Notes
|
||||
===========================================================
|
||||
|
||||
Please see the :doc:`full release notes <23.2_announce>` for more details.
|
||||
|
||||
.. include:: 23.2_prs.rst
|
||||
|
||||
.. include:: _thanks.rst
|
||||
@@ -0,0 +1,316 @@
|
||||
|
||||
.. github_links
|
||||
.. _Pull Request 14892: https://github.com/galaxyproject/galaxy/pull/14892
|
||||
.. _Pull Request 14955: https://github.com/galaxyproject/galaxy/pull/14955
|
||||
.. _Pull Request 15000: https://github.com/galaxyproject/galaxy/pull/15000
|
||||
.. _Pull Request 15313: https://github.com/galaxyproject/galaxy/pull/15313
|
||||
.. _Pull Request 15440: https://github.com/galaxyproject/galaxy/pull/15440
|
||||
.. _Pull Request 15447: https://github.com/galaxyproject/galaxy/pull/15447
|
||||
.. _Pull Request 15482: https://github.com/galaxyproject/galaxy/pull/15482
|
||||
.. _Pull Request 15639: https://github.com/galaxyproject/galaxy/pull/15639
|
||||
.. _Pull Request 15825: https://github.com/galaxyproject/galaxy/pull/15825
|
||||
.. _Pull Request 16119: https://github.com/galaxyproject/galaxy/pull/16119
|
||||
.. _Pull Request 16232: https://github.com/galaxyproject/galaxy/pull/16232
|
||||
.. _Pull Request 16236: https://github.com/galaxyproject/galaxy/pull/16236
|
||||
.. _Pull Request 16252: https://github.com/galaxyproject/galaxy/pull/16252
|
||||
.. _Pull Request 16264: https://github.com/galaxyproject/galaxy/pull/16264
|
||||
.. _Pull Request 16278: https://github.com/galaxyproject/galaxy/pull/16278
|
||||
.. _Pull Request 16292: https://github.com/galaxyproject/galaxy/pull/16292
|
||||
.. _Pull Request 16293: https://github.com/galaxyproject/galaxy/pull/16293
|
||||
.. _Pull Request 16296: https://github.com/galaxyproject/galaxy/pull/16296
|
||||
.. _Pull Request 16305: https://github.com/galaxyproject/galaxy/pull/16305
|
||||
.. _Pull Request 16307: https://github.com/galaxyproject/galaxy/pull/16307
|
||||
.. _Pull Request 16312: https://github.com/galaxyproject/galaxy/pull/16312
|
||||
.. _Pull Request 16318: https://github.com/galaxyproject/galaxy/pull/16318
|
||||
.. _Pull Request 16340: https://github.com/galaxyproject/galaxy/pull/16340
|
||||
.. _Pull Request 16341: https://github.com/galaxyproject/galaxy/pull/16341
|
||||
.. _Pull Request 16345: https://github.com/galaxyproject/galaxy/pull/16345
|
||||
.. _Pull Request 16360: https://github.com/galaxyproject/galaxy/pull/16360
|
||||
.. _Pull Request 16361: https://github.com/galaxyproject/galaxy/pull/16361
|
||||
.. _Pull Request 16371: https://github.com/galaxyproject/galaxy/pull/16371
|
||||
.. _Pull Request 16378: https://github.com/galaxyproject/galaxy/pull/16378
|
||||
.. _Pull Request 16381: https://github.com/galaxyproject/galaxy/pull/16381
|
||||
.. _Pull Request 16385: https://github.com/galaxyproject/galaxy/pull/16385
|
||||
.. _Pull Request 16388: https://github.com/galaxyproject/galaxy/pull/16388
|
||||
.. _Pull Request 16389: https://github.com/galaxyproject/galaxy/pull/16389
|
||||
.. _Pull Request 16391: https://github.com/galaxyproject/galaxy/pull/16391
|
||||
.. _Pull Request 16392: https://github.com/galaxyproject/galaxy/pull/16392
|
||||
.. _Pull Request 16393: https://github.com/galaxyproject/galaxy/pull/16393
|
||||
.. _Pull Request 16398: https://github.com/galaxyproject/galaxy/pull/16398
|
||||
.. _Pull Request 16409: https://github.com/galaxyproject/galaxy/pull/16409
|
||||
.. _Pull Request 16410: https://github.com/galaxyproject/galaxy/pull/16410
|
||||
.. _Pull Request 16414: https://github.com/galaxyproject/galaxy/pull/16414
|
||||
.. _Pull Request 16417: https://github.com/galaxyproject/galaxy/pull/16417
|
||||
.. _Pull Request 16420: https://github.com/galaxyproject/galaxy/pull/16420
|
||||
.. _Pull Request 16425: https://github.com/galaxyproject/galaxy/pull/16425
|
||||
.. _Pull Request 16430: https://github.com/galaxyproject/galaxy/pull/16430
|
||||
.. _Pull Request 16431: https://github.com/galaxyproject/galaxy/pull/16431
|
||||
.. _Pull Request 16434: https://github.com/galaxyproject/galaxy/pull/16434
|
||||
.. _Pull Request 16436: https://github.com/galaxyproject/galaxy/pull/16436
|
||||
.. _Pull Request 16451: https://github.com/galaxyproject/galaxy/pull/16451
|
||||
.. _Pull Request 16456: https://github.com/galaxyproject/galaxy/pull/16456
|
||||
.. _Pull Request 16460: https://github.com/galaxyproject/galaxy/pull/16460
|
||||
.. _Pull Request 16462: https://github.com/galaxyproject/galaxy/pull/16462
|
||||
.. _Pull Request 16472: https://github.com/galaxyproject/galaxy/pull/16472
|
||||
.. _Pull Request 16478: https://github.com/galaxyproject/galaxy/pull/16478
|
||||
.. _Pull Request 16482: https://github.com/galaxyproject/galaxy/pull/16482
|
||||
.. _Pull Request 16485: https://github.com/galaxyproject/galaxy/pull/16485
|
||||
.. _Pull Request 16486: https://github.com/galaxyproject/galaxy/pull/16486
|
||||
.. _Pull Request 16489: https://github.com/galaxyproject/galaxy/pull/16489
|
||||
.. _Pull Request 16490: https://github.com/galaxyproject/galaxy/pull/16490
|
||||
.. _Pull Request 16493: https://github.com/galaxyproject/galaxy/pull/16493
|
||||
.. _Pull Request 16497: https://github.com/galaxyproject/galaxy/pull/16497
|
||||
.. _Pull Request 16503: https://github.com/galaxyproject/galaxy/pull/16503
|
||||
.. _Pull Request 16507: https://github.com/galaxyproject/galaxy/pull/16507
|
||||
.. _Pull Request 16510: https://github.com/galaxyproject/galaxy/pull/16510
|
||||
.. _Pull Request 16514: https://github.com/galaxyproject/galaxy/pull/16514
|
||||
.. _Pull Request 16517: https://github.com/galaxyproject/galaxy/pull/16517
|
||||
.. _Pull Request 16521: https://github.com/galaxyproject/galaxy/pull/16521
|
||||
.. _Pull Request 16522: https://github.com/galaxyproject/galaxy/pull/16522
|
||||
.. _Pull Request 16523: https://github.com/galaxyproject/galaxy/pull/16523
|
||||
.. _Pull Request 16526: https://github.com/galaxyproject/galaxy/pull/16526
|
||||
.. _Pull Request 16536: https://github.com/galaxyproject/galaxy/pull/16536
|
||||
.. _Pull Request 16538: https://github.com/galaxyproject/galaxy/pull/16538
|
||||
.. _Pull Request 16543: https://github.com/galaxyproject/galaxy/pull/16543
|
||||
.. _Pull Request 16550: https://github.com/galaxyproject/galaxy/pull/16550
|
||||
.. _Pull Request 16553: https://github.com/galaxyproject/galaxy/pull/16553
|
||||
.. _Pull Request 16554: https://github.com/galaxyproject/galaxy/pull/16554
|
||||
.. _Pull Request 16561: https://github.com/galaxyproject/galaxy/pull/16561
|
||||
.. _Pull Request 16562: https://github.com/galaxyproject/galaxy/pull/16562
|
||||
.. _Pull Request 16564: https://github.com/galaxyproject/galaxy/pull/16564
|
||||
.. _Pull Request 16576: https://github.com/galaxyproject/galaxy/pull/16576
|
||||
.. _Pull Request 16577: https://github.com/galaxyproject/galaxy/pull/16577
|
||||
.. _Pull Request 16578: https://github.com/galaxyproject/galaxy/pull/16578
|
||||
.. _Pull Request 16586: https://github.com/galaxyproject/galaxy/pull/16586
|
||||
.. _Pull Request 16593: https://github.com/galaxyproject/galaxy/pull/16593
|
||||
.. _Pull Request 16609: https://github.com/galaxyproject/galaxy/pull/16609
|
||||
.. _Pull Request 16612: https://github.com/galaxyproject/galaxy/pull/16612
|
||||
.. _Pull Request 16622: https://github.com/galaxyproject/galaxy/pull/16622
|
||||
.. _Pull Request 16625: https://github.com/galaxyproject/galaxy/pull/16625
|
||||
.. _Pull Request 16636: https://github.com/galaxyproject/galaxy/pull/16636
|
||||
.. _Pull Request 16638: https://github.com/galaxyproject/galaxy/pull/16638
|
||||
.. _Pull Request 16639: https://github.com/galaxyproject/galaxy/pull/16639
|
||||
.. _Pull Request 16642: https://github.com/galaxyproject/galaxy/pull/16642
|
||||
.. _Pull Request 16644: https://github.com/galaxyproject/galaxy/pull/16644
|
||||
.. _Pull Request 16647: https://github.com/galaxyproject/galaxy/pull/16647
|
||||
.. _Pull Request 16649: https://github.com/galaxyproject/galaxy/pull/16649
|
||||
.. _Pull Request 16657: https://github.com/galaxyproject/galaxy/pull/16657
|
||||
.. _Pull Request 16658: https://github.com/galaxyproject/galaxy/pull/16658
|
||||
.. _Pull Request 16659: https://github.com/galaxyproject/galaxy/pull/16659
|
||||
.. _Pull Request 16665: https://github.com/galaxyproject/galaxy/pull/16665
|
||||
.. _Pull Request 16668: https://github.com/galaxyproject/galaxy/pull/16668
|
||||
.. _Pull Request 16670: https://github.com/galaxyproject/galaxy/pull/16670
|
||||
.. _Pull Request 16672: https://github.com/galaxyproject/galaxy/pull/16672
|
||||
.. _Pull Request 16673: https://github.com/galaxyproject/galaxy/pull/16673
|
||||
.. _Pull Request 16675: https://github.com/galaxyproject/galaxy/pull/16675
|
||||
.. _Pull Request 16679: https://github.com/galaxyproject/galaxy/pull/16679
|
||||
.. _Pull Request 16684: https://github.com/galaxyproject/galaxy/pull/16684
|
||||
.. _Pull Request 16685: https://github.com/galaxyproject/galaxy/pull/16685
|
||||
.. _Pull Request 16686: https://github.com/galaxyproject/galaxy/pull/16686
|
||||
.. _Pull Request 16690: https://github.com/galaxyproject/galaxy/pull/16690
|
||||
.. _Pull Request 16691: https://github.com/galaxyproject/galaxy/pull/16691
|
||||
.. _Pull Request 16692: https://github.com/galaxyproject/galaxy/pull/16692
|
||||
.. _Pull Request 16694: https://github.com/galaxyproject/galaxy/pull/16694
|
||||
.. _Pull Request 16695: https://github.com/galaxyproject/galaxy/pull/16695
|
||||
.. _Pull Request 16709: https://github.com/galaxyproject/galaxy/pull/16709
|
||||
.. _Pull Request 16711: https://github.com/galaxyproject/galaxy/pull/16711
|
||||
.. _Pull Request 16712: https://github.com/galaxyproject/galaxy/pull/16712
|
||||
.. _Pull Request 16713: https://github.com/galaxyproject/galaxy/pull/16713
|
||||
.. _Pull Request 16724: https://github.com/galaxyproject/galaxy/pull/16724
|
||||
.. _Pull Request 16725: https://github.com/galaxyproject/galaxy/pull/16725
|
||||
.. _Pull Request 16735: https://github.com/galaxyproject/galaxy/pull/16735
|
||||
.. _Pull Request 16737: https://github.com/galaxyproject/galaxy/pull/16737
|
||||
.. _Pull Request 16738: https://github.com/galaxyproject/galaxy/pull/16738
|
||||
.. _Pull Request 16739: https://github.com/galaxyproject/galaxy/pull/16739
|
||||
.. _Pull Request 16743: https://github.com/galaxyproject/galaxy/pull/16743
|
||||
.. _Pull Request 16745: https://github.com/galaxyproject/galaxy/pull/16745
|
||||
.. _Pull Request 16746: https://github.com/galaxyproject/galaxy/pull/16746
|
||||
.. _Pull Request 16747: https://github.com/galaxyproject/galaxy/pull/16747
|
||||
.. _Pull Request 16748: https://github.com/galaxyproject/galaxy/pull/16748
|
||||
.. _Pull Request 16749: https://github.com/galaxyproject/galaxy/pull/16749
|
||||
.. _Pull Request 16752: https://github.com/galaxyproject/galaxy/pull/16752
|
||||
.. _Pull Request 16753: https://github.com/galaxyproject/galaxy/pull/16753
|
||||
.. _Pull Request 16754: https://github.com/galaxyproject/galaxy/pull/16754
|
||||
.. _Pull Request 16755: https://github.com/galaxyproject/galaxy/pull/16755
|
||||
.. _Pull Request 16756: https://github.com/galaxyproject/galaxy/pull/16756
|
||||
.. _Pull Request 16757: https://github.com/galaxyproject/galaxy/pull/16757
|
||||
.. _Pull Request 16758: https://github.com/galaxyproject/galaxy/pull/16758
|
||||
.. _Pull Request 16759: https://github.com/galaxyproject/galaxy/pull/16759
|
||||
.. _Pull Request 16760: https://github.com/galaxyproject/galaxy/pull/16760
|
||||
.. _Pull Request 16762: https://github.com/galaxyproject/galaxy/pull/16762
|
||||
.. _Pull Request 16763: https://github.com/galaxyproject/galaxy/pull/16763
|
||||
.. _Pull Request 16766: https://github.com/galaxyproject/galaxy/pull/16766
|
||||
.. _Pull Request 16769: https://github.com/galaxyproject/galaxy/pull/16769
|
||||
.. _Pull Request 16770: https://github.com/galaxyproject/galaxy/pull/16770
|
||||
.. _Pull Request 16773: https://github.com/galaxyproject/galaxy/pull/16773
|
||||
.. _Pull Request 16776: https://github.com/galaxyproject/galaxy/pull/16776
|
||||
.. _Pull Request 16778: https://github.com/galaxyproject/galaxy/pull/16778
|
||||
.. _Pull Request 16782: https://github.com/galaxyproject/galaxy/pull/16782
|
||||
.. _Pull Request 16783: https://github.com/galaxyproject/galaxy/pull/16783
|
||||
.. _Pull Request 16787: https://github.com/galaxyproject/galaxy/pull/16787
|
||||
.. _Pull Request 16789: https://github.com/galaxyproject/galaxy/pull/16789
|
||||
.. _Pull Request 16791: https://github.com/galaxyproject/galaxy/pull/16791
|
||||
.. _Pull Request 16795: https://github.com/galaxyproject/galaxy/pull/16795
|
||||
.. _Pull Request 16798: https://github.com/galaxyproject/galaxy/pull/16798
|
||||
.. _Pull Request 16799: https://github.com/galaxyproject/galaxy/pull/16799
|
||||
.. _Pull Request 16800: https://github.com/galaxyproject/galaxy/pull/16800
|
||||
.. _Pull Request 16803: https://github.com/galaxyproject/galaxy/pull/16803
|
||||
.. _Pull Request 16805: https://github.com/galaxyproject/galaxy/pull/16805
|
||||
.. _Pull Request 16807: https://github.com/galaxyproject/galaxy/pull/16807
|
||||
.. _Pull Request 16808: https://github.com/galaxyproject/galaxy/pull/16808
|
||||
.. _Pull Request 16809: https://github.com/galaxyproject/galaxy/pull/16809
|
||||
.. _Pull Request 16810: https://github.com/galaxyproject/galaxy/pull/16810
|
||||
.. _Pull Request 16811: https://github.com/galaxyproject/galaxy/pull/16811
|
||||
.. _Pull Request 16819: https://github.com/galaxyproject/galaxy/pull/16819
|
||||
.. _Pull Request 16821: https://github.com/galaxyproject/galaxy/pull/16821
|
||||
.. _Pull Request 16825: https://github.com/galaxyproject/galaxy/pull/16825
|
||||
.. _Pull Request 16829: https://github.com/galaxyproject/galaxy/pull/16829
|
||||
.. _Pull Request 16830: https://github.com/galaxyproject/galaxy/pull/16830
|
||||
.. _Pull Request 16833: https://github.com/galaxyproject/galaxy/pull/16833
|
||||
.. _Pull Request 16834: https://github.com/galaxyproject/galaxy/pull/16834
|
||||
.. _Pull Request 16835: https://github.com/galaxyproject/galaxy/pull/16835
|
||||
.. _Pull Request 16836: https://github.com/galaxyproject/galaxy/pull/16836
|
||||
.. _Pull Request 16838: https://github.com/galaxyproject/galaxy/pull/16838
|
||||
.. _Pull Request 16839: https://github.com/galaxyproject/galaxy/pull/16839
|
||||
.. _Pull Request 16844: https://github.com/galaxyproject/galaxy/pull/16844
|
||||
.. _Pull Request 16847: https://github.com/galaxyproject/galaxy/pull/16847
|
||||
.. _Pull Request 16848: https://github.com/galaxyproject/galaxy/pull/16848
|
||||
.. _Pull Request 16850: https://github.com/galaxyproject/galaxy/pull/16850
|
||||
.. _Pull Request 16851: https://github.com/galaxyproject/galaxy/pull/16851
|
||||
.. _Pull Request 16852: https://github.com/galaxyproject/galaxy/pull/16852
|
||||
.. _Pull Request 16853: https://github.com/galaxyproject/galaxy/pull/16853
|
||||
.. _Pull Request 16855: https://github.com/galaxyproject/galaxy/pull/16855
|
||||
.. _Pull Request 16859: https://github.com/galaxyproject/galaxy/pull/16859
|
||||
.. _Pull Request 16860: https://github.com/galaxyproject/galaxy/pull/16860
|
||||
.. _Pull Request 16861: https://github.com/galaxyproject/galaxy/pull/16861
|
||||
.. _Pull Request 16865: https://github.com/galaxyproject/galaxy/pull/16865
|
||||
.. _Pull Request 16867: https://github.com/galaxyproject/galaxy/pull/16867
|
||||
.. _Pull Request 16869: https://github.com/galaxyproject/galaxy/pull/16869
|
||||
.. _Pull Request 16872: https://github.com/galaxyproject/galaxy/pull/16872
|
||||
.. _Pull Request 16873: https://github.com/galaxyproject/galaxy/pull/16873
|
||||
.. _Pull Request 16874: https://github.com/galaxyproject/galaxy/pull/16874
|
||||
.. _Pull Request 16875: https://github.com/galaxyproject/galaxy/pull/16875
|
||||
.. _Pull Request 16877: https://github.com/galaxyproject/galaxy/pull/16877
|
||||
.. _Pull Request 16879: https://github.com/galaxyproject/galaxy/pull/16879
|
||||
.. _Pull Request 16880: https://github.com/galaxyproject/galaxy/pull/16880
|
||||
.. _Pull Request 16881: https://github.com/galaxyproject/galaxy/pull/16881
|
||||
.. _Pull Request 16882: https://github.com/galaxyproject/galaxy/pull/16882
|
||||
.. _Pull Request 16884: https://github.com/galaxyproject/galaxy/pull/16884
|
||||
.. _Pull Request 16887: https://github.com/galaxyproject/galaxy/pull/16887
|
||||
.. _Pull Request 16891: https://github.com/galaxyproject/galaxy/pull/16891
|
||||
.. _Pull Request 16892: https://github.com/galaxyproject/galaxy/pull/16892
|
||||
.. _Pull Request 16895: https://github.com/galaxyproject/galaxy/pull/16895
|
||||
.. _Pull Request 16896: https://github.com/galaxyproject/galaxy/pull/16896
|
||||
.. _Pull Request 16897: https://github.com/galaxyproject/galaxy/pull/16897
|
||||
.. _Pull Request 16900: https://github.com/galaxyproject/galaxy/pull/16900
|
||||
.. _Pull Request 16901: https://github.com/galaxyproject/galaxy/pull/16901
|
||||
.. _Pull Request 16902: https://github.com/galaxyproject/galaxy/pull/16902
|
||||
.. _Pull Request 16904: https://github.com/galaxyproject/galaxy/pull/16904
|
||||
.. _Pull Request 16905: https://github.com/galaxyproject/galaxy/pull/16905
|
||||
.. _Pull Request 16906: https://github.com/galaxyproject/galaxy/pull/16906
|
||||
.. _Pull Request 16908: https://github.com/galaxyproject/galaxy/pull/16908
|
||||
.. _Pull Request 16910: https://github.com/galaxyproject/galaxy/pull/16910
|
||||
.. _Pull Request 16914: https://github.com/galaxyproject/galaxy/pull/16914
|
||||
.. _Pull Request 16915: https://github.com/galaxyproject/galaxy/pull/16915
|
||||
.. _Pull Request 16916: https://github.com/galaxyproject/galaxy/pull/16916
|
||||
.. _Pull Request 16917: https://github.com/galaxyproject/galaxy/pull/16917
|
||||
.. _Pull Request 16919: https://github.com/galaxyproject/galaxy/pull/16919
|
||||
.. _Pull Request 16921: https://github.com/galaxyproject/galaxy/pull/16921
|
||||
.. _Pull Request 16924: https://github.com/galaxyproject/galaxy/pull/16924
|
||||
.. _Pull Request 16928: https://github.com/galaxyproject/galaxy/pull/16928
|
||||
.. _Pull Request 16929: https://github.com/galaxyproject/galaxy/pull/16929
|
||||
.. _Pull Request 16930: https://github.com/galaxyproject/galaxy/pull/16930
|
||||
.. _Pull Request 16931: https://github.com/galaxyproject/galaxy/pull/16931
|
||||
.. _Pull Request 16934: https://github.com/galaxyproject/galaxy/pull/16934
|
||||
.. _Pull Request 16937: https://github.com/galaxyproject/galaxy/pull/16937
|
||||
.. _Pull Request 16938: https://github.com/galaxyproject/galaxy/pull/16938
|
||||
.. _Pull Request 16939: https://github.com/galaxyproject/galaxy/pull/16939
|
||||
.. _Pull Request 16942: https://github.com/galaxyproject/galaxy/pull/16942
|
||||
.. _Pull Request 16943: https://github.com/galaxyproject/galaxy/pull/16943
|
||||
.. _Pull Request 16944: https://github.com/galaxyproject/galaxy/pull/16944
|
||||
.. _Pull Request 16945: https://github.com/galaxyproject/galaxy/pull/16945
|
||||
.. _Pull Request 16949: https://github.com/galaxyproject/galaxy/pull/16949
|
||||
.. _Pull Request 16952: https://github.com/galaxyproject/galaxy/pull/16952
|
||||
.. _Pull Request 16953: https://github.com/galaxyproject/galaxy/pull/16953
|
||||
.. _Pull Request 16955: https://github.com/galaxyproject/galaxy/pull/16955
|
||||
.. _Pull Request 16959: https://github.com/galaxyproject/galaxy/pull/16959
|
||||
.. _Pull Request 16963: https://github.com/galaxyproject/galaxy/pull/16963
|
||||
.. _Pull Request 16964: https://github.com/galaxyproject/galaxy/pull/16964
|
||||
.. _Pull Request 16965: https://github.com/galaxyproject/galaxy/pull/16965
|
||||
.. _Pull Request 16966: https://github.com/galaxyproject/galaxy/pull/16966
|
||||
.. _Pull Request 16971: https://github.com/galaxyproject/galaxy/pull/16971
|
||||
.. _Pull Request 16978: https://github.com/galaxyproject/galaxy/pull/16978
|
||||
.. _Pull Request 16981: https://github.com/galaxyproject/galaxy/pull/16981
|
||||
.. _Pull Request 16985: https://github.com/galaxyproject/galaxy/pull/16985
|
||||
.. _Pull Request 16988: https://github.com/galaxyproject/galaxy/pull/16988
|
||||
.. _Pull Request 16991: https://github.com/galaxyproject/galaxy/pull/16991
|
||||
.. _Pull Request 16992: https://github.com/galaxyproject/galaxy/pull/16992
|
||||
.. _Pull Request 16993: https://github.com/galaxyproject/galaxy/pull/16993
|
||||
.. _Pull Request 16994: https://github.com/galaxyproject/galaxy/pull/16994
|
||||
.. _Pull Request 16999: https://github.com/galaxyproject/galaxy/pull/16999
|
||||
.. _Pull Request 17007: https://github.com/galaxyproject/galaxy/pull/17007
|
||||
.. _Pull Request 17008: https://github.com/galaxyproject/galaxy/pull/17008
|
||||
.. _Pull Request 17009: https://github.com/galaxyproject/galaxy/pull/17009
|
||||
.. _Pull Request 17011: https://github.com/galaxyproject/galaxy/pull/17011
|
||||
.. _Pull Request 17013: https://github.com/galaxyproject/galaxy/pull/17013
|
||||
.. _Pull Request 17015: https://github.com/galaxyproject/galaxy/pull/17015
|
||||
.. _Pull Request 17020: https://github.com/galaxyproject/galaxy/pull/17020
|
||||
.. _Pull Request 17021: https://github.com/galaxyproject/galaxy/pull/17021
|
||||
.. _Pull Request 17025: https://github.com/galaxyproject/galaxy/pull/17025
|
||||
.. _Pull Request 17032: https://github.com/galaxyproject/galaxy/pull/17032
|
||||
.. _Pull Request 17036: https://github.com/galaxyproject/galaxy/pull/17036
|
||||
.. _Pull Request 17037: https://github.com/galaxyproject/galaxy/pull/17037
|
||||
.. _Pull Request 17038: https://github.com/galaxyproject/galaxy/pull/17038
|
||||
.. _Pull Request 17043: https://github.com/galaxyproject/galaxy/pull/17043
|
||||
.. _Pull Request 17048: https://github.com/galaxyproject/galaxy/pull/17048
|
||||
.. _Pull Request 17049: https://github.com/galaxyproject/galaxy/pull/17049
|
||||
.. _Pull Request 17050: https://github.com/galaxyproject/galaxy/pull/17050
|
||||
.. _Pull Request 17053: https://github.com/galaxyproject/galaxy/pull/17053
|
||||
.. _Pull Request 17055: https://github.com/galaxyproject/galaxy/pull/17055
|
||||
.. _Pull Request 17056: https://github.com/galaxyproject/galaxy/pull/17056
|
||||
.. _Pull Request 17057: https://github.com/galaxyproject/galaxy/pull/17057
|
||||
.. _Pull Request 17061: https://github.com/galaxyproject/galaxy/pull/17061
|
||||
.. _Pull Request 17062: https://github.com/galaxyproject/galaxy/pull/17062
|
||||
.. _Pull Request 17071: https://github.com/galaxyproject/galaxy/pull/17071
|
||||
.. _Pull Request 17072: https://github.com/galaxyproject/galaxy/pull/17072
|
||||
.. _Pull Request 17077: https://github.com/galaxyproject/galaxy/pull/17077
|
||||
.. _Pull Request 17080: https://github.com/galaxyproject/galaxy/pull/17080
|
||||
.. _Pull Request 17085: https://github.com/galaxyproject/galaxy/pull/17085
|
||||
.. _Pull Request 17088: https://github.com/galaxyproject/galaxy/pull/17088
|
||||
.. _Pull Request 17093: https://github.com/galaxyproject/galaxy/pull/17093
|
||||
.. _Pull Request 17095: https://github.com/galaxyproject/galaxy/pull/17095
|
||||
.. _Pull Request 17097: https://github.com/galaxyproject/galaxy/pull/17097
|
||||
.. _Pull Request 17099: https://github.com/galaxyproject/galaxy/pull/17099
|
||||
.. _Pull Request 17100: https://github.com/galaxyproject/galaxy/pull/17100
|
||||
.. _Pull Request 17102: https://github.com/galaxyproject/galaxy/pull/17102
|
||||
.. _Pull Request 17104: https://github.com/galaxyproject/galaxy/pull/17104
|
||||
.. _Pull Request 17107: https://github.com/galaxyproject/galaxy/pull/17107
|
||||
.. _Pull Request 17110: https://github.com/galaxyproject/galaxy/pull/17110
|
||||
.. _Pull Request 17111: https://github.com/galaxyproject/galaxy/pull/17111
|
||||
.. _Pull Request 17112: https://github.com/galaxyproject/galaxy/pull/17112
|
||||
.. _Pull Request 17114: https://github.com/galaxyproject/galaxy/pull/17114
|
||||
.. _Pull Request 17116: https://github.com/galaxyproject/galaxy/pull/17116
|
||||
.. _Pull Request 17124: https://github.com/galaxyproject/galaxy/pull/17124
|
||||
.. _Pull Request 17129: https://github.com/galaxyproject/galaxy/pull/17129
|
||||
.. _Pull Request 17133: https://github.com/galaxyproject/galaxy/pull/17133
|
||||
.. _Pull Request 17134: https://github.com/galaxyproject/galaxy/pull/17134
|
||||
.. _Pull Request 17144: https://github.com/galaxyproject/galaxy/pull/17144
|
||||
.. _Pull Request 17146: https://github.com/galaxyproject/galaxy/pull/17146
|
||||
.. _Pull Request 17149: https://github.com/galaxyproject/galaxy/pull/17149
|
||||
.. _Pull Request 17169: https://github.com/galaxyproject/galaxy/pull/17169
|
||||
.. _Pull Request 17176: https://github.com/galaxyproject/galaxy/pull/17176
|
||||
.. _Pull Request 17178: https://github.com/galaxyproject/galaxy/pull/17178
|
||||
.. _Pull Request 17182: https://github.com/galaxyproject/galaxy/pull/17182
|
||||
.. _Pull Request 17186: https://github.com/galaxyproject/galaxy/pull/17186
|
||||
.. _Pull Request 17192: https://github.com/galaxyproject/galaxy/pull/17192
|
||||
.. _Pull Request 17197: https://github.com/galaxyproject/galaxy/pull/17197
|
||||
.. _Pull Request 17199: https://github.com/galaxyproject/galaxy/pull/17199
|
||||
.. _Pull Request 17210: https://github.com/galaxyproject/galaxy/pull/17210
|
||||
.. _Pull Request 17213: https://github.com/galaxyproject/galaxy/pull/17213
|
||||
.. _Pull Request 17218: https://github.com/galaxyproject/galaxy/pull/17218
|
||||
.. _Pull Request 17224: https://github.com/galaxyproject/galaxy/pull/17224
|
||||
.. _Pull Request 17226: https://github.com/galaxyproject/galaxy/pull/17226
|
||||
.. _Pull Request 17227: https://github.com/galaxyproject/galaxy/pull/17227
|
||||
.. _Pull Request 17232: https://github.com/galaxyproject/galaxy/pull/17232
|
||||
.. _Pull Request 17233: https://github.com/galaxyproject/galaxy/pull/17233
|
||||
.. _Pull Request 17236: https://github.com/galaxyproject/galaxy/pull/17236
|
||||
@@ -0,0 +1,12 @@
|
||||
|
||||
:orphan:
|
||||
|
||||
===========================================================
|
||||
Early 2024 Galaxy Release (v 24.0)
|
||||
===========================================================
|
||||
|
||||
|
||||
Schedule
|
||||
===========================================================
|
||||
* Planned Freeze Date: 2024-02-05
|
||||
* Planned Release Date: 2024-02-26
|
||||
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@@ -4,6 +4,7 @@ Releases
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
|
||||
23.2_announce_user
|
||||
23.1_announce_user
|
||||
23.0_announce_user
|
||||
22.05_announce_user
|
||||
|
||||
Reference in New Issue
Block a user