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648 Commits
Author SHA1 Message Date
mvdbeek 2f22a31a15 Update documentation for new defaults and recommendations 2021-04-13 10:13:42 +02:00
Helena e5000e24c8 Merge pull request #11351 from selten/analytics 2021-04-08 16:45:34 +00:00
John Chilton 0b0b8c48b9 Merge pull request #11557 from VJalili/two_container 
Add documentation on how to setup Pulsar's two-container job runner
 2021-04-07 10:33:32 -04:00
Nicola Soranzo e1014acc9d Merge branch 'release_21.01' into dev 2021-04-07 13:13:29 +01:00
Nicola Soranzo 13d91da1f4 Fix typo in upstream_mod_zip admin docs 2021-04-06 20:04:19 +01:00
mvdbeek 8bda8d4110 Add enable_celery_tasks config option 2021-03-29 09:29:25 -04:00
mvdbeek f5800bed50 Break up dynamic dataset collection into chunks 
Addresses https://github.com/galaxyproject/galaxy/issues/11488.

One drawback here is that if multiple jobs are concurrently creating
datasets in a history the HID is not guaranteed to be sequential
between chunks. We can address this, but this is also a problem
when breaking workflow executions at
``maximum_workflow_jobs_per_scheduling_iteration``.
If we consider this to be a problem (personally I don't think it is, but
I could be convinved otherwise) I would work on this in a different PR.

On the upside the history panel will display an increasing amount of
datasets created during the dataset discovery.
 2021-03-23 10:15:41 +01:00
Ruben Vorderman 684978bc4f Add missing ssl keyword in nginx example 
Otherwise it will use the http protocol instead of https.
 2021-03-16 11:57:26 +01:00
vjalili 5d68570a85 Make docs on setting galaxy_infrastructure_url more generic. 2021-03-10 17:49:30 -08:00
Dannon Baker 7942402bd3 Merge remote-tracking branch 'upstream/dev' into proftpd 2021-03-09 09:46:22 -05:00
vjalili 9e7c1386a4 Add documentation on how to setup Pulsar's two-container job runner. 2021-03-05 12:21:21 -08:00
Nate Coraor a2d1625780 Merge remote-tracking branch 'upstream/release_21.01' into dev 2021-03-01 16:52:02 -05:00
Marius van den BeekandNicola Soranzo d61321d872 Improve enable_tool_cache option description 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-02-23 10:22:52 +01:00
mvdbeek 82f26d40ac Disable tool document cache by default 
It's kind of brittle, and https://github.com/galaxyproject/galaxy/pull/10804
has improved the parsing so much that it doesn't add much benefit.
Instances on Anvil start up in ~ 32 seconds, with all of main's toolbox.
 2021-02-23 08:53:45 +01:00
Helena 85fafd5a06 Merge pull request #11384 from martenson/auth-docs 
fix broken docs links
 2021-02-16 11:20:28 +01:00
Martin Cech 99d0fae2fe fix broken links, clarify 2021-02-16 11:13:53 +01:00
setlen 4677cf9e0d Make sure the options are all documented, remove some logging. 2021-02-12 21:23:52 +01:00
mvdbeek dd7aa6ec38 Merge branch 'release_21.01' into dev 2021-02-08 16:01:53 +01:00
mvdbeek 7d0ec29fa0 Drop legacy metadata mode 
And always serialize input dataset metadata using the model exports.
This means we don't have to pickle anymore, which breaks with weakrefs
used by sqlalchemy-json's Mutable class.
 2021-02-05 11:38:50 +01:00
Nicola Soranzo 352c488aaf Merge pull request #11238 from mvdbeek/drop_unused_transfer_manager 
Drop unused transfer_manager.py
 2021-01-27 17:57:48 +00:00
mvdbeek c1b0fab1e8 Drop unused transfer_manager.py 
scripts/transfer_manager.py had been deleted previously, so this can't
be functional.
 2021-01-27 17:29:00 +01:00
Sergey Golitsynskiy 6b2220e1ac Add cache_dir to schema, rebuild 2021-01-21 10:30:12 -05:00
mvdbeek 4d984c5132 Add setting that lets admins enable/disable the tool document cache 
Closes https://github.com/galaxyproject/galaxy/issues/11082
 2021-01-20 10:12:07 +01:00
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