galaxy-config 24.0.0

Galaxy configuration

Overview

The Galaxy config module.

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

History

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