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Commit Graph
624 Commits
Author SHA1 Message Date
John Chilton b8c11ab21a Link in MQ docs stub. 2021-01-12 09:34:28 -05:00
John Chilton 6c79073eb4 Mark some Sphinx as orphans - they seem to be not linked to TOC for reasons. 2021-01-12 09:29:54 -05:00
John Chilton e643c09806 Fixup more sphinx warning in config option doc generation. 2021-01-12 09:29:53 -05:00
John Chilton f5648e2025 Fixup some linking between documents in sphinx. 2021-01-12 09:29:53 -05:00
John Chilton 6fd6100285 Various sphinx warning fixes. 2021-01-11 12:58:45 -05:00
John Chilton 0482543402 Merge pull request #10822 from jmchilton/conda_readonly_2 
Implement read-only conda resolver (alternative)
 2021-01-10 12:43:59 -05:00
Marius van den Beek af4d041dc9 Merge pull request #10592 from hexylena/edam-tool-panel 
EDAM tool panel
 2021-01-08 18:56:28 +01:00
John Chilton 22aa23e1db Implement read-only conda resolver. 2021-01-08 11:09:10 -05:00
Dannon 02f6e028bb Merge pull request #10960 from astrovsky01/new_version_tab 
Add version tab which links to release notes to help tab
 2021-01-08 11:08:38 -05:00
Dannon c0b45fde61 Merge pull request #10701 from linnil1/fix-ftp-doc 
Update ftp document for rounds=100000
 2021-01-07 19:20:12 -05:00
Helena Rasche f5a3545541 Merge branch 'dev' into edam-tool-panel 2021-01-07 19:54:12 +01:00
John Chilton b7cb74c600 Merge pull request #11067 from nsoranzo/clarify_master_api_key 
Clarify `master_api_key` intended use
 2021-01-06 22:21:50 -05:00
Marius van den Beek 683bb54183 Merge pull request #10347 from brinkmanlab/mq_doc 
Stub MQ docs
 2021-01-06 22:12:22 +01:00
Nicola Soranzo 967ad305dc Clarify master_api_key intended use 
xref. https://github.com/galaxyproject/galaxy/issues/11065
 2021-01-06 20:26:44 +00:00
John Chilton 9b5526a998 Merge pull request #10959 from ic4f/dev_issue10607 
Add custom activation email message
 2021-01-04 10:51:27 -05:00
John Chilton c7d6f286e5 Merge pull request #10919 from mvdbeek/zipstream_replace_tarball 
Replace StreamBall, replace tarballs with zip
 2020-12-21 10:27:51 -05:00
Marius van den Beek 1501fa9a65 Merge pull request #10497 from natefoo/gxit-stop 
Support stopping Interactive Tools without deleting their outputs
 2020-12-21 10:06:07 +01:00
mvdbeek 64b75e074c Restore upstream_gzip option, rename upstream_zip to upstream_mod_zip 2020-12-19 19:03:53 +01:00
Alexander OSTROVSKY b6891f9f99 different return if running a dev instance 2020-12-18 14:21:48 -08:00
Alexander OSTROVSKY 249e8744eb updated config name 2020-12-18 09:06:16 -08:00
Marius van den BeekandNicola Soranzo f3bf548da5 Improve mod-zip documentation 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-12-18 17:04:00 +01:00
mvdbeek ad655b9e52 Fix grammar and clarify internal statement 2020-12-18 16:45:37 +01:00
mvdbeek d4552d31cb Enable archive creating via mod-zip 2020-12-18 14:09:31 +01:00
Nicola Soranzo 925fa216d2 Fix link in mulled containers docs 2020-12-18 02:23:21 +00:00
Nicola Soranzo acc20994f4 Update minimum Python version in admin docs 2020-12-18 02:20:11 +00:00
Alexander OSTROVSKY 588438f6b4 lint and docs 
rst and yml docs
 2020-12-17 16:28:28 -08:00
Sergey Golitsynskiy 6b7db9fd99 Add custom activation email message 2020-12-17 15:55:06 -05:00
Sergey Golitsynskiy f14f72547f Set from email in tool error reports 2020-12-17 12:16:39 -05:00
Nate Coraor b47da22cae Add option to retry setting GxIT metadata internally. 2020-12-11 17:15:59 +01:00
John Chilton b03e9c8d04 Drop legacy_eager_objectstore_initialization option. 
Reduce branching/complexity around when/where objectstore is getting set for downstream work.
 2020-11-30 12:28:09 -05:00
Nicola Soranzo f09d0a7d03 Remove extra / and galaxy-dist 2020-11-19 13:39:21 +00:00
Richard James Acton f497fd6849 Fix Example links 
Example config file links were broken in https://github.com/galaxyproject/galaxy/commit/e75f2b089528e362a6587eb41ce4cd9c3d883ff0
 2020-11-19 12:39:13 +01:00
Marius van den Beek 641b7e9f73 Merge pull request #10608 from bernt-matthias/topic/drop-iuc-channel 
Remove IUC conda channel from default configuration
 2020-11-18 12:09:54 +01:00
linnil1 e87b14136f Update ftp document for rounds=100000 2020-11-12 13:08:02 +08:00
M Bernt 963fb994dd fix link to job config sample in docs 2020-11-10 11:34:31 +01:00
mvdbeek 7df17504bf Merge branch 'release_20.09' into dev 2020-11-05 19:03:01 +01:00
Sergey Golitsynskiy 4890ba17d5 Update docs to reflect uuid/id, file_path updates 
Run `make config-rebuild`
 2020-11-03 16:07:30 -05:00
Matthias Bernt ec8643bf05 drop IUC conda channel 2020-11-03 10:44:30 +01:00
Helena Rasche e506ebf10c Remove option for url 2020-10-30 18:00:04 +01:00
Helena Rasche 646b133bb3 Add EDAM topics to unannotated tools 2020-10-30 17:59:45 +01:00
Helena Rasche 1733f462dd Parse EDAM ontology to decode names 2020-10-30 12:37:23 +01:00
Helena Rasche 5728189085 Implement simple edam toolbox using non-readable ids 2020-10-30 10:25:14 +01:00
Enis Afgan 1afb79d2b5 Merge pull request #10540 from guerler/enable_custom_logo 
Allow admins to add an additional custom logo to the masthead
 2020-10-29 09:40:35 -04:00
Sergey Golitsynskiy 31b908226a Set uwsgi's honor-stdin when in debug mode 2020-10-28 14:08:25 -04:00
John Chilton ddcaddd40e Merge pull request #10537 from ic4f/dev_config_doc_path 
Generate path resolution note for sample file, docs
 2020-10-27 14:55:28 -04:00
mvdbeek d0047c1085 Merge branch 'release_20.09' into dev 2020-10-24 16:21:52 +02:00
guerler 2928b5256c Allow admins to add custom logo to the masthead 2020-10-23 11:54:36 -04:00
Sergey Golitsynskiy 066a9bc78a Generate path resolution note for sample file, docs 2020-10-22 22:00:10 -04:00
Dannon Baker 434d406bde Cleanout communication server. 
I don't think anyone's actively using this anymore, and most
communication has moved to (also embeddable) things like Gitter, etc.
 2020-10-22 09:58:34 -04:00
Dannon Baker d0ad39a909 Rebuild config for 20.09, including missing option in galaxy_options doc 2020-10-22 09:42:01 -04:00