galaxy-config 25.0.1

Galaxy configuration

Overview

The Galaxy config module.

• Code: https://github.com/galaxyproject/galaxy

History

25.0.1 (2025-06-20)

Bug fixes

• Fix galaxy-config script, move install to galaxy-dependencies in app package by @natefoo in #20531

Other changes

• Fixes for static handling and the web_client package by @natefoo in #20516

25.0.0 (2025-06-18)

Bug fixes

• Use resource_path() to access datatypes_conf.xml.sample as a package resource by @nsoranzo in #19331

• Remove hgv_sift from tool_conf.xml.sample by @natefoo in #19972

• Add job config variable for singularity –contain by @bernt-matthias in #20400

Enhancements

• Isolate singularity containers more thoroughly for better reproducibility. by @rhpvorderman in #18628

• Implement tool markdown reports. by @jmchilton in #19054

• Calculate hash for new non-deferred datasets when finishing a job by @nsoranzo in #19181

• eLabFTW integration via Galaxy file source by @kysrpex in #19319

• Misc fixes 202412 by @nsoranzo in #19341

• Add Dataverse RDM repository integration by @KaiOnGitHub in #19367

• Clarify that extra_scopes is sometimes non-optional by @martenson in #19385

• Change galaxy system user uid for K8s image by @afgane in #19403

• Prevent users from reusing a banned email after account is purged by @jdavcs in #19413

• Add IGB display support for CRAM files by @paige-kulzer in #19428

• Add config options for tool dependency installs by @afgane in #19565

• Support setting masthead height in a theme by @ksuderman in #19581

• Add failed jobs working directory cleanup as a celery periodic task by @sanjaysrikakulam in #19594

• Enhance OpenAI Chat Integration by @uwwint in #19612

• Data-source tool for DICED database (https://diced.lerner.ccf.org/) added. by @jaidevjoshi83 in #19689

• Update RStudio IT by @afgane in #19711

• Add bigbed to bed converter and tests by @d-callan in #19787

• Decrease sentry_sdk.errors log level to INFO by @natefoo in #19951

• Allow different AI providers (as long as they are openai compatible) by @uwwint in #19989

• Add vitesscejson datatype by @guerler in #20027

• Add VTK Visualization Toolkit Plugin by @guerler in #20028

• Add docx datatype by @bgruening in #20055

• Add markdown datatype by @bgruening in #20056

• Add flac audio format by @bgruening in #20057

• Add rd datatype by @richard-burhans in #20060

• Enhance external login interface styling by @ahmedhamidawan in #20100

• Add specific datatypes for Cytoscape and Kepler.gl by @guerler in #20117

• Add more metadata, esp infer_from to datatypes configuration by @bgruening in #20142

• Add three AAI providers by @martenson in #20165

• Add replacement_dataset option to collection filter tools by @simonbray in #20166

• Visualization-First Display functionality by @dannon in #20190

• Deprecate enable_tool_document_cache by @nsoranzo in #20433

• Add Aladin as standard FITS viewer by @bgruening in #20465

• Add molstar as default viewer for some molecule formats by @bgruening in #20467

Other changes

• Make job cache generally available by @dannon in #19798

• Rename vitessce_json file_ext to vitessce.json by @mvdbeek in #20473

24.2.4 (2025-06-17)

Bug fixes

• Reduce default framework tool test timeout to 60 seconds by @mvdbeek in #19819

24.2.3 (2025-03-16)

Enhancements

• Add rDock prm datatype by @nsoranzo in #19783

24.2.2 (2025-03-08)

Bug fixes

• Fix conditional dependency path resolution by @mvdbeek in #19723

Enhancements

• Add bwa_mem2_index directory datatype, framework enhancements for testing directories by @mvdbeek in #19694

24.2.1 (2025-02-28)

Bug fixes

• Updated registration warning message by @dannon in #19598

Enhancements

• Add fastk_ktab_tar datatype required for fastk tool by @SaimMomin12 in #19615

24.2.0 (2025-02-11)

Bug fixes

• Fix loading error for built in tool sift by @bernt-matthias in #18357

• Add gtf to auto_compressed_types by @mvdbeek in #19175

• Partial backport of #19331 by @nsoranzo in #19342

• Fix to only show ChatGXY when available. by @dannon in #19389

Enhancements

• Experimental galactic wizard by @dannon in #15860

• Improve usability of Directory datatype by @wm75 in #17614

• Add pod5 datatype by @TomHarrop in #18419

• Add onedata templates by @bwalkowi in #18457

• Support high-availability setups for the interactive tools proxy by @kysrpex in #18481

• Minor config documentation enhancements by @bgruening in #18499

• Add Tool-Centric APIs to the Tool Shed 2.0 by @jmchilton in #18524

• Bring your own file sources: Add the WebDAV template and configuration by @sanjaysrikakulam in #18598

• Add BlobToolkit to the list of interactive tools by @Delphine-L in #18630

• Remove defaults channel for conda usage by @bernt-matthias in #18757

• Workflow Landing Requests by @jmchilton in #18807

• Jupyter Interactive Tool 1.0.1/24.07 by @natefoo in #18861

• Allow setting a few global defaults for file source plugin types. by @jmchilton in #18909

• Add filter null collection operation tool by @mvdbeek in #18928

• Add hint to the tool schema about runtime conditional changes by @martenson in #18996

• Irods ssl connection by @pauldg in #19014

• Add some Zarr-based datatypes by @davelopez in #19040

• Run installed Galaxy with no config and a simplified entry point by @natefoo in #19050

• Add XML based vtk datatype by @tStehling in #19104

• Allow a posix file source to prefer linking. by @jmchilton in #19132

• Add bcsp datatype by @SantaMcCloud in #19365

• add MuData as subclass of H5 by @pavanvidem in #19416

24.1.4 (2024-12-11)

Bug fixes

• Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by @mvdbeek in #18428

• Strip whitespace when listifying admin users by @jdavcs in #18656

• Remove defaults channel for conda usage by @bernt-matthias in #18859

Enhancements

• Make default_panel_view a _by_host option by @natefoo in #18471

• More datatype deprecation warnings by @mvdbeek in #18612

• Implemented the generic OIDC backend from python-social-auth into Gal… by @Edmontosaurus in #18670

Other changes

• Backport pod5 datatype by @TomHarrop in #18507

• Backport PR 18630 “Add BlobToolkit to the list of interactive tools” to release_24.1 by @cat-bro in #18784

24.1.3 (2024-10-25)

Bug fixes

• Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by @mvdbeek in #18428

• Strip whitespace when listifying admin users by @jdavcs in #18656

• Remove defaults channel for conda usage by @bernt-matthias in #18859

Enhancements

• Make default_panel_view a _by_host option by @natefoo in #18471

• More datatype deprecation warnings by @mvdbeek in #18612

• Implemented the generic OIDC backend from python-social-auth into Gal… by @Edmontosaurus in #18670

Other changes

• Backport pod5 datatype by @TomHarrop in #18507

• Backport PR 18630 “Add BlobToolkit to the list of interactive tools” to release_24.1 by @cat-bro in #18784

24.1.2 (2024-09-25)

Bug fixes

• Strip whitespace when listifying admin users by @jdavcs in #18656

Enhancements

• Make default_panel_view a _by_host option by @natefoo in #18471

• More datatype deprecation warnings by @mvdbeek in #18612

• Implemented the generic OIDC backend from python-social-auth into Gal… by @Edmontosaurus in #18670

Other changes

• Backport pod5 datatype by @TomHarrop in #18507

• Backport PR 18630 “Add BlobToolkit to the list of interactive tools” to release_24.1 by @cat-bro in #18784

24.1.1 (2024-07-02)

Bug fixes

• Replace sample Celery result_backend in config by @davelopez in #17949

• Fix for unexpected OIDC XML validation error by @Edmontosaurus in #18106

• Fix various packages’ issues by @nsoranzo in #18301

• Rebuild Galaxy config by @bgruening in #18325

Enhancements

• Enable all-vs-all collection analysis patterns. by @jmchilton in #17366

• Add onedata objectstore by @bwalkowi in #17540

• Add colabfold tar file datatype by @astrovsky01 in #17567

• Update Python dependencies by @galaxybot in #17653

• SQLAlchemy 2.0 by @jdavcs in #17778

• Add email notifications channel by @davelopez in #17914

• Update config docs about Celery by @davelopez in #17918

• Make urgent notifications mandatory by @davelopez in #17975

• Enable warn_unused_ignores mypy option by @nsoranzo in #17991

• Add Zenodo integration by @davelopez in #18022

• Add support for additional media types by @arash77 in #18054

• Update Python dependencies by @galaxybot in #18063

• Add Net datatype by @martenson in #18080

• Empower users to bring their own storage and file sources by @jmchilton in #18127

• More unit testing for object store stuff. by @jmchilton in #18136

• Tighten axt sniffer by @martenson in #18204

• More structured indexing for user data objects. by @jmchilton in #18291

• Onedada object store and files source stability fixes by @bwalkowi in #18372

Other changes

• Chore: remove repetitive words by @tianzedavid in #18076

• Fix the link to the carbon config by @bgruening in #18314

24.0.3 (2024-06-28)

Bug fixes

• Backport OIDC schema fix by @mvdbeek in #18111

• Minor fix to enable external hgweb process by @mvdbeek in #18256

Other changes

• Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by @mvdbeek in #18428

24.0.2 (2024-05-07)

No recorded changes since last release

24.0.1 (2024-05-02)

Bug fixes

• Invenio plugin fixes by @davelopez in #17997

• clarify the object store relocate functionality by @martenson in #18033

• Updated the datatypes name for FASTK tool by @SaimMomin12 in #18053

Enhancements

• Added 4dn_pairs and 4dn_pairsam datatypes by @SaimMomin12 in #17875

• Add middleware for logging start and end of request by @mvdbeek in #18046

Other changes

• Rebuild config samples by @davelopez in #17911

• Backport colabfold tar file datatype by @mvdbeek in #18029

24.0.0 (2024-04-02)

Bug fixes

• Follow-up on #17274 and #17262 by @nsoranzo in #17302

• Fix minor oidc_backends_config comment bug by @ahmedhamidawan in #17385

Enhancements

• Add harmonize collections tool (or whatever other name) by @lldelisle in #16662

• Python 3.8 as minimum by @mr-c in #16954

• Support for OIDC API Auth and OIDC integration tests by @nuwang in #16977

• Add support for (fast5.tar).xz binary compressed files by @tuncK in #17106

• Add a3m datatype by @astrovsky01 in #17217

• Convert sample object store configuration to YAML and support configuring inline by @natefoo in #17222

• Allow job files to consume TUS uploads by @jmchilton in #17242

• Add OIDC backend configuration schema and validation by @uwwint in #17274

• Update to black 2024 stable style by @nsoranzo in #17391

• Allow using tool data bundles as inputs to reference data select parameters by @mvdbeek in #17435

• Use short link for TPV shared database by @nuwang in #17467

• Feature SBOL datatypes by @guillaume-gricourt in #17482

• Add documentation on how to use vault keys in file sources by @bernt-matthias in #17498

• add npy datatype by @astrovsky01 in #17517

• Enhance Avivator display app to support regular Tiffs by @davelopez in #17554

• Allow admin to sharpen language about selected object stores. by @jmchilton in #17806

23.2.1 (2024-02-21)

Bug fixes

• pin fs.dropboxfs to >=1 by @bernt-matthias in #16451

• MINERVA display application: enable cors, add for tabular by @hexylena in #16737

• chore: fix typos by @afuetterer in #16851

• Add back 1.1.0 version of Filtering1 tool by @mvdbeek in #16883

• Set webdav file source to use temp files by default by @davelopez in #17388

Enhancements

• Update cellxgene interactive tool to 1.1.1 by @pcm32 in #15313

• Tool Shed 2.0 by @jmchilton in #15639

• Limit number of celery task executions per second per user by @claudiofr in #16232

• Add carbon emissions admin configuration options by @Renni771 in #16307

• Add Invenio RDM repository integration by @davelopez in #16381

• Add new datatype: STL by @TanguyGen in #16478

• add new tabular file formats cns,cnr and cnn to datatypes_conf.xml.sample file as they are neaded for cnvkit galaxy tools by @khaled196 in #16503

• Tweak tool memory use and optimize shared memory when using preload by @mvdbeek in #16536

• Implement datatype upload warnings by @jmchilton in #16564

• Support new genome browser chain file format by @claudiofr in #16576

• Update Python dependencies by @galaxybot in #16577

• Implement instance URLs in Galaxy markdown. by @jmchilton in #16675

• Use fs.onedatarestfs for Onedata files source plugin implementation by @lopiola in #16690

• Update datatypes_conf.xml.sample with docx type by @yvanlebras in #16713

• Replace ELIXIR AAI button with Life Science login by @sebastian-schaaf in #16762

• Add EGI Check-in as OIDC authentication option by @enolfc in #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 by @sveinugu in #16795

• Galaxy help forum integration by @ElectronicBlueberry in #16798

• Remove record access handling for Invenio RDM plugin by @davelopez in #16900

• optimize object store cache operations by @SergeyYakubov in #17025

• Support configuring job metrics inline, update documentation by @natefoo in #17178

• Add binary datatypes for intermediate output of fastk tools by @astrovsky01 in #17265

• Add magres datatype by @martenson in #17499

Other changes

• Merge 23.1 into dev by @mvdbeek in #16534

• Remove xml remnant in sample yml job conf by @bernt-matthias in #16609

23.1.4 (2024-01-04)

No recorded changes since last release

23.1.3 (2023-12-01)

No recorded changes since last release

23.1.2 (2023-11-29)

Bug fixes

• Prevent Singular external auth users from disconnecting identity by @ahmedhamidawan in #16961

• Set correct tool_path for packaged galaxy by @mvdbeek in #17102

Enhancements

• Add support for larch datatypes by @patrick-austin in #17080

23.1.1 (2023-10-23)

Bug fixes

• Fix some drs handling issues by @nuwang in #15777

• Improve container resolver documentation by @mvdbeek in #16280

• Limit tool document cache to tool configs with explicit cache path by @mvdbeek in #16537

• Backport tool mem fixes by @mvdbeek in #16601

• Fix allowlist deserialization in file sources by @mvdbeek in #16729

Enhancements

• External Login Flow: Redirect users if account already exists by @ahmedhamidawan in #15019

• Add slack error reporting plugin by @hexylena in #15025

• Documents use of k8s_extra_job_envs in job_conf sample advanced by @pcm32 in #15110

• Expose additional beaker caching backends by @claudiofr in #15349

• Unify url handling with filesources by @nuwang in #15497

• Handle “email_from” config option consistently, as per schema description by @jdavcs in #15557

• Drop workflow exports to myexperiment.org by @dannon in #15576

• Container resolvers: add docs, typing and tests by @bernt-matthias in #15614

• Add suggested Training material to Tool Form by @ElectronicBlueberry in #15628

• Deprecate tools/evolution by @bernt-matthias in #15656

• Add Galaxy Notification System by @davelopez in #15663

• More object store documentation. by @jmchilton in #15707

• Drop use_legacy_history from config by @dannon in #15861

• FITS data format by @volodymyrss in #15905

• Export tool citations configurable message by @minh-biocommons in #15998

• Rename object stores in config. by @jmchilton in #16029

• Add hdf4 datatype by @TheoMathurin in #16105

• Improved Cache Monitoring for Object Stores by @jmchilton in #16110

• Refactor caching object stores ahead of adding task-based store. by @jmchilton in #16144

• Add zipped mongodb and genenotebook datatypes by @abretaud in #16173

• Add Visium datatype for squidpy and spatialomics tools by @astrovsky01 in #16255

Other changes

• Implement some initial object store selection end-to-end tests. by @jmchilton in #15785

23.0.6 (2023-10-23)

No recorded changes since last release

23.0.5 (2023-07-29)

Bug fixes

• Minor bug fix for default mail templates by @neoformit in #16362

23.0.4 (2023-06-30)

No recorded changes since last release

23.0.3 (2023-06-26)

No recorded changes since last release

23.0.2 (2023-06-13)

No recorded changes since last release

23.0.1 (2023-06-08)

Bug fixes

• Change default watchdog inotify_buffer log level to info by @mvdbeek in #15967

Enhancements

• Add ca_certs option for sentry client by @mvdbeek in #15943

22.1.1 (2022-08-22)

• Initial release