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231 Commits
Author SHA1 Message Date
Martin Cech fe37996de3 rename the config option to enable_gdpr_beta 
to reflect the information that we do not guarantee compliance
 2018-05-16 12:38:46 -05:00
Martin Cech 3a9a46f772 Merge pull request #6069 from erasche/gdpr 
[18.05] GDPR Compliance Mode
 2018-05-15 20:40:20 -05:00
Martin Cech f8bfb82169 fix what 🦅 👀 spotted 2018-05-15 20:23:37 -05:00
Martin Cech 1dc4749846 iteration of gdpr compliance docs 2018-05-14 20:30:22 -05:00
Helena Rasche 41e6910df2 document more gdpr stuff :( 2018-05-14 16:15:57 +02:00
Helena Rasche 2f351bf3a7 rebuild configuratoin 2018-05-14 15:33:34 +02:00
Helena Rasche c122b3f573 better docs 2018-05-14 15:28:09 +02:00
Helena Rasche 6cc20f2634 start writing compliance documentation 2018-05-14 14:02:00 +02:00
Helena Rasche ee985e6bbc Update documentation 2018-05-14 11:51:10 +02:00
Helena Rasche b4bd972b71 update documentation 2018-05-10 17:44:11 +02:00
Nicola Soranzo 916078beb0 Merge branch 'release_18.01' into release_18.05 2018-04-27 19:22:24 +01:00
Nate Coraor cbaff1dca2 Correct uWSGI UNIX domain socket syntax. 2018-04-27 10:49:07 -04:00
Nicola Soranzo 7ce49394c3 Merge branch 'release_18.01' into release_18.05 2018-04-26 19:05:38 +01:00
Nicola Soranzo a3e6963666 Merge branch 'release_17.09' into release_18.01 2018-04-26 19:01:48 +01:00
Nicola Soranzo 7d81d2cfcb Fix 2 typos in the docs 2018-04-26 10:23:14 +01:00
Nicola Soranzo c41c84eec6 Merge branch 'release_18.01' into release_18.05 2018-04-25 18:36:11 +01:00
Nate Coraor e58034b987 Correct examples in dynamic job conf doc, remove handlers section from 
basic sample job config (defining a single default handler is no longer
needed). Fixes #5976.
 2018-04-25 13:10:04 -04:00
Nicola Soranzo 284795b94f Merge branch 'release_18.01' into dev 2018-04-23 15:21:12 +01:00
John Chilton 393f055a23 Merge pull request #5928 from erasche/document-gh-reporter 
[18.01] forgot to document github bug reporter
 2018-04-19 11:57:53 -04:00
E Rasche fe0a4853b9 forgot to document github bug reporter 2018-04-19 17:13:32 +02:00
E Rasche 3182dfa70e correct signal num 2018-04-19 13:20:17 +02:00
John Chilton 2829a1f164 Merge pull request #5854 from natefoo/run-scripts-conda 
Improve startup interoperability with Conda
 2018-04-18 16:08:13 -04:00
Vahid 1009047626 Add OIDC and OAuth2.0 config to authentication docs 2018-04-17 13:33:41 -07:00
Oleksandr Moskalenko 2cec29c043 Update cluster config docs for virtualenv issue for drmaa real user jobs. 2018-04-12 12:13:32 -04:00
E Rasche 4a6eb37b47 Add config option 2018-04-10 11:36:11 +02:00
vjalili 259daf1749 Merge remote-tracking branch 'upstream/dev' into oauth2-after-rebase 
# Conflicts:
#	lib/galaxy/dependencies/pinned-requirements.txt
#	lib/galaxy/dependencies/requirements.txt
 2018-04-06 11:15:27 -07:00
Nate Coraor 8261a2398a Make the startup scripts play just as nicely with Conda as they do with 
virtualenv.
 2018-04-04 16:38:01 -04:00
Dannon Baker 412ff1e16a Add config rebuild left out of migration of options from 18.01 (I think) 2018-03-27 08:43:05 -04:00
Dannon Baker 39d5ec89f8 Merge branch 'release_18.01' into dev 2018-03-27 08:42:09 -04:00
Dannon Baker cacef65139 Merge pull request #5742 from erasche/statsd-influxdb 
Allow formatting statsd data for influxdb
 2018-03-23 11:08:41 -04:00
Dannon Baker bf59e0da04 Fix (again) the typo I previously fixed and then I rebuilt over. D'oh. 2018-03-22 09:39:08 -04:00
Dannon Baker a2398a28ea Annotate statsd_influxdb in new config schema, rebuild. 2018-03-22 09:27:23 -04:00
vjalili f634c40ad4 Merge remote-tracking branch 'upstream/dev' into oauth2-after-rebase 
# Conflicts:
#	static/style/blue/base.css
 2018-03-21 13:15:26 -07:00
Nicola Soranzo c99c7b4d84 Fix type of some options in config_schema.yml 
Also:
- drop unused `nginx_x_archive_files_base` option, last use removed in
commit fe5983aafc
- rebuild config samples and docs.
 2018-03-21 02:59:30 +00:00
Nicola Soranzo 03f5f5310e Fix typos 2018-03-21 02:35:29 +00:00
John Chilton 5f23f5da72 Merge pull request #5625 from bernt-matthias/topic/memperslot 
added GALAXY_MEMORY_MB_PER_SLOT variable
 2018-03-20 09:34:59 -04:00
vjalili 730b931b87 OIDC config in galaxy.yml.sample is now set via config_schema. 2018-03-19 17:45:16 -07:00
Nicola Soranzo 0cf88623ee Merge branch 'release_18.01' into dev 2018-03-19 17:52:05 +00:00
mvdbeek d5d1e4b80d Clarfify that nginx-extras needs to be install for the upload_store directive to work 2018-03-19 11:41:48 +01:00
guerler 8d1e0fccc2 Add chunk size config option to schema 2018-03-13 17:25:51 -04:00
Nicola Soranzo b92a5e1b47 Small doc fixes 2018-03-13 16:51:17 +00:00
Matthias Bernt 4a59f30209 added cluster admin docs for the new variables 2018-03-13 17:22:05 +01:00
John Chilton e7f7759cc2 Better default configuration of Galaxy test data directory. 2018-03-06 20:07:52 -05:00
John Chilton b84da7a07a Allow per-request SQL debugging via URL parameter. 
This has been super helpful in debugging the SQL generated by Galaxy for recent PRs.

To use this simply enable the middleware, use your browser's network logger to find the URL of interest, copy the URL into the browser address bar and add ``?debug_sql=1`` to it. You will then see the sql in the logs only for that request and for every statement in that request.

Simply turning all logging on results in a deluge of logging I've never been able to grok and that is very hard to ping to particular request. Slow request logging is great but it doesn't make this kind of per-query full profile of the SQL generated as easy as this approach and isn't great at debugging performance problems when the result from a large number of small requests (you'd have to set a very low threshold to make sure you are logging every query and then it is no different from the full log).
 2018-02-18 13:37:19 -05:00
Nicola Soranzo 6f2a0cceb0 Unify config-rebuild Makefile targets 
Rebuild reports sample and RST from schema with the new Makefile target.
 2018-02-08 10:16:58 -05:00
Dannon Baker 8ce7f96353 Rebuild rst for new configuration options 2018-02-08 08:16:46 -05:00
Anthony Bretaudeau 4dbfd50f06 Merge branch 'dev' into i18n 2018-02-07 09:40:19 +01:00
Nicola Soranzo 245394acb6 Merge branch 'release_18.01' into dev 2018-02-02 22:19:02 +00:00
Martin Cech f24043e8a7 Merge pull request #5441 from natefoo/framework-dependencies-doc-update-18.01 
[18.01] Admin doc corrections
 2018-02-01 16:38:50 -05:00
Nate Coraor 6d8edce331 Admin doc corrections 2018-02-01 16:25:12 -05:00