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42,809 Commits 62 Branches 243 Tags
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Commit Graph
1407 Commits
Author SHA1 Message Date
Martin CechandMarius van den Beek fc8b832888 Apply suggestions from code review @mvdbeek 
Co-Authored-By: Marius van den Beek <m.vandenbeek@gmail.com>
 2019-11-19 09:32:15 -05:00
Martin Cech 0c075f73b4 set logging level according to the argument 
also report the run summary as 'info' level
 2019-11-18 12:05:02 -05:00
Martin Cech 8668441c9f use configured config file when using uwsgi directly 2019-11-18 12:01:26 -05:00
Martin Cech 5c495d6514 refactor logging 2019-11-18 11:25:47 -05:00
Martin Cech 19c56c725b add exec timer 2019-11-18 09:56:15 -05:00
Martin Cech 4725903b0f switch from every minute to every hour 2019-11-14 18:17:32 -05:00
Martin Cech dfc20759a7 use built-in uwsgi CRON-like feature to build shed search idnexes every hour 2019-11-14 18:07:48 -05:00
Martin Cech c9d9009299 refactor and modernize toolshed search indexes build script 
mainly so it can read yml config
 2019-11-14 18:07:06 -05:00
Sergey Golitsynskiy a855e2ca64 Fix TypeError in logging commands 
Fix the following exception:

```
TypeError: not all arguments converted during string formatting
```

Also, make other log format strings more consistent: %d for numeric object IDs.
 2019-11-03 21:35:07 +00:00
John Chilton 7620880a9b Release notes for 19.09. 2019-10-01 13:42:46 -04:00
John Chilton 4287bb787f Merge pull request #8621 from martenson/ux-ts-installer 
[19.09] allow the TS search API to bypass wildcard search
 2019-09-12 13:35:01 -04:00
Martin Cech 99ec4ecf75 adjust indexing and searching of special keywords to be case-insensitive 2019-09-11 16:39:14 -04:00
Martin Cech 02a3342bd6 regenerate ts search indexes in tmp directory 2019-09-10 16:06:21 -04:00
Dannon Baker 9d1e784868 Alternate approach to plugin building; this should be useful as a stepping stone towards moving these out of the repo completely, and it'll work *right now*. 2019-09-06 14:56:10 -04:00
Daniel BlankenbergandNicola Soranzo a2199ee575 Update scripts/interactivetools/key_type_token_mapping.py 
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2019-08-23 11:29:36 -04:00
Daniel Blankenberg 995fce6b9b Little more RealTimeTools cleanup. 2019-08-23 09:24:55 -04:00
mvdbeek a820e52f2a Fix missed control_worker->queue_worker rename 
Missed that one in 6b52f62fe4
 2019-08-22 10:58:01 +02:00
Daniel Blankenberg 55c929768c more realtime to interactivetools name changes 2019-08-20 16:58:55 -04:00
Daniel Blankenberg c3c4aefcbd Merge branch 'dev' of https://github.com/galaxyproject/galaxy into realtimetools 2019-08-20 13:44:44 -04:00
Dannon 053510678f Merge pull request #8474 from bgruening/node-conda 
Node is called nodejs in conda land.
 2019-08-20 11:36:38 -04:00
Marius van den Beek ce61509122 Merge pull request #8473 from nsoranzo/restore_mysql 
Fix MySQL database creation and migrations
 2019-08-19 16:52:59 +02:00
Nicola Soranzo ca226282f1 Fix startup checks when using a Conda env 
Unless `--skip-venv` is specified, Galaxy creates/activates a virtualenv
also when using a Conda environment.
 2019-08-19 01:28:35 +01:00
Nicola Soranzo d5633f6285 Enable on-screen logging for create_db.py and manage_db.py 2019-08-18 11:17:34 +01:00
Björn Grüning 4a2c316cfe node is called nodejs in conda-land 2019-08-17 15:42:38 +02:00
John Chilton e611797a77 Merge pull request #8470 from erasche/fix-975 
Fix #975
 2019-08-16 14:42:24 -04:00
Helena Rasche 5f615168bc Fix #975 2019-08-16 15:11:15 +02:00
Helena Rasche b316bab722 Remove scripts deprecated since 1 year 2019-08-15 14:30:53 +02:00
John Chilton 47d46c626e Merge pull request #8452 from erasche/faster-quota 
Replace in-python quota calc with a SQL query
 2019-08-14 14:40:12 -04:00
Helena Rasche 887aae2ab3 Refactor into model 2019-08-14 16:15:49 +02:00
Helena Rasche 58f4f65a4a new method 2019-08-14 16:08:04 +02:00
Dannon Baker 877bd322d6 Add pointer to client/README.md to address 'https://github.com/galaxyproject/galaxy/commit/8bb2b6bfbcac89910ec6b5cc58e23243571ab879#commitcomment-34259049' 2019-08-14 09:59:55 -04:00
Daniel Blankenberg 5ed5ff6d49 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into realtimetools 2019-08-13 14:47:53 -04:00
Nate Coraor 395d98857b Fix config file finding for the manage_db script 2019-08-07 16:33:40 -04:00
M Bernt f6ff679d63 cleanup: use logging instead of print 2019-08-01 09:25:13 +02:00
Daniel Blankenberg 8aebb64ae4 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into realtimetools 2019-07-25 14:59:53 -04:00
Martin Cech 00600e4006 Merge pull request #8298 from jmchilton/selenium_package 
Create galaxy-selenium package.
 2019-07-18 15:17:42 -04:00
Nicola Soranzo e7165c37e3 Fix issues reported by shellcheck 2019-07-17 12:46:46 +01:00
Nicola Soranzo 8e8c64308a Fix use of `PIP_PROGRESS_BAR` env variable 
`PIP_PROGRESS_BAR` environment variable is used by `pip` to set the value
for the `--progress-bar` option. It seems that specifying it also only the
command line does not override it in some configurations, e.g. on TravisCI
Linux builds of BioBlend, see e.g.

https://travis-ci.org/galaxyproject/bioblend/jobs/558857557
 2019-07-16 17:17:32 +01:00
Martin Cech e45d7959a7 Merge pull request #8308 from jmchilton/push_scripts_into_subpackages 
Push galaxy-meta scripts into appropiate subpackages.
 2019-07-15 18:45:13 -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 d22d7beaf4 Merge pull request #8305 from jmchilton/axe_log_tempfile 
Remove log_tempfile.
 2019-07-09 14:42:43 +02:00
Marius van den Beek 64c71ca7e1 Merge pull request #8290 from natefoo/remove-ci-pip-progress-bar 
Don't show the pip progress bar when installing under CI
 2019-07-09 12:17:49 +02:00
John Chilton 9b287ef06c Push scripts into subpackages. 2019-07-08 16:38:10 +02:00
John Chilton 753a151c76 Add dump tour script to galaxy-selenium package. 2019-07-08 15:48:19 +02:00
John Chilton 8a327db74d Remove log_tempfile. 
Simplify packaging - @natefoo said I could.
 2019-07-08 14:52:13 +02:00
Nate Coraor 906413d07b Rework config locating logic (it was reading the sample again). 2019-07-08 11:28:31 +02:00
Nate Coraor d65e3c904e Fix galaxy-main running from source now that setup,py is no longer in the root 2019-07-07 18:23:49 +02:00
Daniel Blankenberg e4dd821d7f Merge branch 'dev' of https://github.com/galaxyproject/galaxy into realtimetools 2019-07-07 17:54:48 +02:00
Nate Coraor 118e01f796 Don't show the pip progress bar when installing under CI 2019-07-07 14:22:07 +02:00
Nate Coraor 2034980b77 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into installable 2019-07-07 13:50:41 +02:00