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
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[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 Blankenberg and Nicola Soranzo
a2199ee575
Update scripts/interactivetools/key_type_token_mapping.py
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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
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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
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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
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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
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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
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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
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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
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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
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`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
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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
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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
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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.
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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
John Chilton
d194520fdf
Merge pull request #8152 from jmchilton/tool_deps_serialize
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Re-try dependency manager serialization and embedded config.
2019-07-07 12:44:35 +02:00
Sergey Golitsynskiy
1694b79185
Update import paths for loader_directory
2019-07-06 00:52:45 +02:00
Daniel Blankenberg
f231e42c48
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into realtimetools
2019-07-05 16:43:01 +02:00
Nate Coraor
37522f5e8e
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into installable
2019-07-05 16:05:17 +02:00
Nate Coraor
cdb9040e26
Merge remote-tracking branch 'origin/dev' into installable
2019-07-05 15:51:15 +02:00
John Chilton
584c117df3
Refactor to cleanup dependencies around galaxy.web.stack.
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Move galaxy.web.stack.database_heartbeat into galaxy.model - since it was the only thing in galaxy.web.stack that used galaxy.model at all and it didn't import anything else from galaxy.web.stack.
Once that was done, I refactored this whole package (galaxy.web.stack) into galaxy.web_stack. It doesn't use the framework setup or exported by the base galaxy.web package so it wouldn't seem to belong there. It also has very different dependencies than the rest of that. And finally and most importantly, this elimiantes almost all dependency from galaxy.jobs and galaxy.tools and galaxy.workflows to anything in galaxy.web.
2019-06-26 18:54:52 -04:00
John Chilton
450ae76ddb
Re-try dependency manager serialization and embedded config.
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PR #8118 - adding to_dict to the dependency manager and an embedded loading of dependency resolution options from galaxy.yml - was really quite poorly thought through.
Certain options could be embedded - but only the resolvers and the actual dictified representation of the DependencyManager couldn't be actually embedded properly in the app config - but this is exactly what I wanted to do on the Pulsar side and it would make no sense to have the exact same options in both apps and configured differently.
So now the actual dictified representation of the whole DependencyManager can be directly embedded in galaxy.yml as the ``dependency_resolution:`` parameter. All the parameters can still be configured at the top level of the YAML file but with 'dependency' in the config option name (some prefixes, some suffixes, etc... a hodgepodge that has grown organically). Give the messiness of the existing options might be better to encourage using ``dependency_resolution:`` in the future.
2019-06-20 14:36:40 -04:00
Daniel Blankenberg
540b2b386b
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into realtimetools
2019-06-17 09:02:21 -04:00
Nicola Soranzo
90a6c6d46b
Fix issues reported by ShellCheck
2019-06-13 12:53:26 +01:00
John Chilton