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Commit Graph
404 Commits
Author SHA1 Message Date
Martin Cech 8e4ca7b74c clarify that shed_data_manager is auto created 2019-10-10 16:18:14 -04:00
Martin Cech cf48ba33c3 Merge pull request #8610 from natefoo/autocreate-shed-tool-conf-fix 
[19.09] Fix autocreation of shed_*_conf.xml
 2019-09-17 13:52:09 -04:00
Nicola Soranzo f593b14641 Change MySQL from deprecated to unsupported 
Follow-up on https://github.com/galaxyproject/galaxy/pull/8407
 2019-09-13 10:16:03 +01:00
Nate Coraor be5aafd34b - Document and correct usage of shed_tool_config_file 
- Fix automatic creation of shed_*_conf.xml, migrated_tools_conf.xml
- Don't look in cwd for configs
 2019-09-10 15:54:53 -04:00
Nicola Soranzo 10e1945f36 Replaces tabs with spaces in apache.md 2019-09-09 11:38:20 +01:00
John Chilton 6264871fe8 Merge pull request #8574 from bgruening/it_cleanups 
Interactive tools cleanup
 2019-09-06 15:09:32 -04:00
John Chilton c8c34fa2f7 Enable mulled containers by default for 19.09. 2019-09-04 10:12:49 -04:00
Bjoern Gruening b5559e1a2e remove condor note 2019-08-31 14:01:59 +02:00
Bjoern Gruening c575bd8c2c RT to IT 2019-08-31 13:36:51 +02:00
Sergey Golitsynskiy 2270dace26 Run make config-rebuild to reflect latest edits 2019-08-28 15:49:09 -04:00
John Chilton 6a1279e702 Merge pull request #8475 from ic4f/dev_config_reload 
Enable dynamic reloading of select config options
 2019-08-22 15:32:57 -04:00
Sergey Golitsynskiy e73e024ade Merge remote-tracking branch 'upstream/dev' into dev_config_reload 2019-08-20 17:00:08 -04:00
Daniel Blankenberg 4bda4c92bd Make InteractiveTools enable-able. 2019-08-20 14:57:45 -04:00
Daniel Blankenberg c3c4aefcbd Merge branch 'dev' of https://github.com/galaxyproject/galaxy into realtimetools 2019-08-20 13:44:44 -04:00
Sergey Golitsynskiy 05b1965365 Make edits based on code review (part 2) 
- Use default event handler instead of SimpleFileModifiedEventHandler
- Edit wording in galaxy/config_schema.yml
 2019-08-19 13:49:54 -04:00
Marius van den Beek 9eabc9c65f Merge pull request #8315 from natefoo/installable-config 
Config updates for installable Galaxy
 2019-08-19 16:54:37 +02:00
Sergey Golitsynskiy ac5538beec Make misc. edits based on code review 
- setting reloadable options simplified
- admin_users treated as special case; handled w/property + setter
- watch_config option changed to watch_core_config
- minor cosmetic changes
 2019-08-18 12:30:34 -04:00
Sergey Golitsynskiy 5188a42336 Enable dynamic reloading of select config options 2019-08-17 02:09:32 -04:00
Daniel Blankenberg 5ed5ff6d49 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into realtimetools 2019-08-13 14:47:53 -04:00
guerler 626fbdd5b3 Fix comment in config schema for visualization visibility option 2019-08-12 15:22:47 -04:00
guerler 40ea2f695f Add configuration option to hide visualizations from masthead 2019-08-12 15:12:19 -04:00
John Chilton 19134aeece Merge remote-tracking branch 'galaxyproject/dev' into installable-config 2019-08-09 13:52:29 -04:00
Helena Rasche af5ecc487d rewrite 2019-08-09 16:14:32 +02:00
Helena Rasche 82c417d6e4 document workflow_schedulers_config_file 2019-08-09 15:19:43 +02:00
John Chilton 6b3fec0a92 Merge pull request #8404 from martenson/nginx-docs 
mention IGB in the docs
 2019-08-05 10:26:58 -04:00
Martin Cech 8c01ae716d change mysql support to deprecated 
until we fix migrations at least
 2019-08-02 11:12:44 -04:00
Martin Cech cb3c5b7a5e mention IGB in the docs 2019-08-02 09:36:37 -04:00
Daniel Blankenberg 8aebb64ae4 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into realtimetools 2019-07-25 14:59:53 -04:00
Nicola Soranzo e565ef043c Merge branch 'release_19.05' into dev 2019-07-20 01:33:10 +01:00
Nate Coraor a914200965 Correct uWSGI socket path in nginx/Apache docs 2019-07-15 15:43:26 -04:00
Daniel Blankenberg 56aab88923 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into realtimetools 2019-07-11 17:04:17 -04:00
Marius van den Beek ef9698895a Merge pull request #8319 from nsoranzo/lowercase_boolean_yaml 
Use lowercase true/false in config_schema.yml
 2019-07-10 11:18:19 +02:00
Nicola Soranzo d0c28f669b Use lowercase true/false in config_schema.yml 
since these are the only allowed values for booleans in YAML 1.2:
https://yaml.org/spec/1.2/spec.html#id2803629

make config-rebuild
 2019-07-09 18:58:51 +01:00
Nate Coraor b099ea34cf Update galaxy config to include config_dir and data_dir options 2019-07-08 18:14:53 +02:00
Daniel Blankenberg f231e42c48 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into realtimetools 2019-07-05 16:43:01 +02:00
guerler d8e089308a Merge branch 'dev' into activate_toolshed 2019-07-05 14:09:08 +02:00
Sergey Golitsynskiy 6f167a2e8d Run make config-rebuild to update config/docs 
This is to update galaxy.yml.sample and galaxy_options.rst to be
consistent with the latest update to config_schema.yml (#5651edc)

(generated with make config-rebuild)
 2019-06-25 00:18:21 -04:00
Daniel Blankenberg ccc4fc482f Merge branch 'dev' of https://github.com/galaxyproject/galaxy into realtimetools 2019-06-06 17:39:45 -04:00
Enis Afgan 90f56ebc40 Fix link formats for mulled_containers.rst, minor rewording 2019-05-31 15:32:23 -04:00
Daniel Blankenberg 138e90413a More doc formatting 2019-05-15 08:29:03 -04:00
Daniel Blankenberg 1c12c74576 update docs 2019-05-14 23:23:25 -04:00
Daniel Blankenberg b0baaabf2c notes on resource consumption; and condor 2019-05-14 08:04:55 -04:00
Daniel Blankenberg 5ee6e65d12 More doc info 2019-05-14 07:10:07 -04:00
Daniel Blankenberg 6cc43da9b7 Doc formatting 2019-05-13 17:03:00 -04:00
Daniel Blankenberg 2866b5ff13 Update docs 2019-05-13 16:01:18 -04:00
Daniel Blankenberg 7376cc9fd7 Add docs and example job config. 2019-05-13 14:36:31 -04:00
Nicola Soranzo c82749688e Merge branch 'release_19.05' into dev 2019-05-11 14:05:55 +01:00
Dannon Baker 349ac80412 Include suggestion from Marius to make port specification more clear. 2019-05-10 10:12:27 -04:00
Dannon Baker a1487d733a Fix a few more random typos in config, rebuild 2019-05-10 10:09:10 -04:00
Dannon Baker 6bc802307f Document the modern docker networking special DNS 'host.docker.internal' for use with GIES. Fix another typo I saw. 2019-05-10 10:04:12 -04:00