Galaxy configuration
Project description
Overview
The Galaxy config module.
History
24.0.3 (2024-06-28)
Bug fixes
Other changes
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
24.0.0 (2024-04-02)
Bug fixes
Fix minor oidc_backends_config comment bug by @ahmedhamidawan in #17385
Enhancements
Add harmonize collections tool (or whatever other name) by @lldelisle in #16662
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
Allow using tool data bundles as inputs to reference data select parameters by @mvdbeek in #17435
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
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
Enhancements
External Login Flow: Redirect users if account already exists by @ahmedhamidawan in #15019
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
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
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
Enhancements
22.1.1 (2022-08-22)
Initial release
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