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 Beek and Nicola 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
mvdbeek