Nicola Soranzo
303f9ec871
Merge pull request #8908 from bernt-matthias/topic/pgcleanup-also-delete
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make pgcleanup also delete HDAs
2019-11-04 10:21:04 +00:00
Nicola Soranzo
3e64bbb460
Merge branch 'release_19.09' into dev
2019-11-04 09:50:29 +00:00
Sergey Golitsynskiy
a855e2ca64
Fix TypeError in logging commands
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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
M Bernt
6f010bd49c
make pgcleanup also delete HDAs
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follow up to https://github.com/galaxyproject/galaxy/pull/3572
2019-10-30 13:42:31 +01:00
Nicola Soranzo
85f7f91206
Fix script shebangs
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Improve tools.
2019-10-26 20:20:01 +01:00
Martin Cech
fd6142f6ce
Merge branch 'release_19.09' into merge-1909
2019-10-07 10:24:12 -04:00
John Chilton
7620880a9b
Release notes for 19.09.
2019-10-01 13:42:46 -04:00
Nicola Soranzo
f659c2f86c
Merge pull request #8712 from erasche/grt-fixes-n
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GRT: Ensure correct encoding, no partial lines
2019-09-27 12:19:39 +01:00
Helena Rasche and Nicola Soranzo
584dbb28df
Apply suggestions from code review
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Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com >
2019-09-26 14:36:43 +02:00
Helena Rasche
f56cc13699
two spaces
2019-09-26 14:35:49 +02:00
Helena Rasche
e75a9f67b0
swap to io.open
2019-09-26 13:42:41 +02:00
Helena Rasche
f200835445
Ensure correct encoding, no partial lines
2019-09-26 12:12:22 +02:00
will
009611cf04
add .gitattributes file and normalize line endings to use LF instead of CLRF
2019-09-18 22:03:37 -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
Nicola Soranzo