Dannon Baker
370ea25d2c
Minor refactoring, comments.
2018-06-15 12:48:02 -04:00
Dannon Baker
e110489cc5
Call plugin static dir regeneration in the event client isn't being built (which also does this, albeit slightly differently)
2018-06-15 11:46:08 -04:00
Dannon Baker
fc47618f67
Initial python-based plugin staging. to be used from common startup.
2018-06-15 11:41:06 -04:00
Martin Cech
36fcb5c1b7
Merge pull request #6301 from martenson/grt-config
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[18.05] add the canonical url to grt config
2018-06-07 15:01:03 -05:00
Martin Cech
ed56454ca0
add the canonical url to grt config
2018-06-07 09:15:47 -04:00
Helena Rasche
acb4cdf584
Merge pull request #6285 from martenson/grt-defensive
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[18.05] telescope export: change to a more defensive approach
2018-06-06 15:15:27 +00:00
Nicola Soranzo
2b8beb69c4
Merge branch 'release_18.01' into release_18.05
2018-06-06 15:58:08 +01:00
Martin Cech
e767438afc
add spaces before inline comment
2018-06-05 16:38:56 -04:00
Martin Cech
b62099f418
change to a more defensive approach, clarify varnames
2018-06-05 16:19:04 -04:00
Anastasia Tyryshkina
c37e384454
style fix
2018-06-05 12:47:19 -04:00
Anastasia Tyryshkina
dd4de3f3b2
catch dataset_id=None
2018-06-05 12:23:02 -04:00
Anastasia Tyryshkina
6db9fd3d51
style fix
2018-06-04 16:01:32 -04:00
Anastasia Tyryshkina
191a134bbc
got rid of things that are no longer necessary
2018-06-04 15:57:22 -04:00
Anastasia Tyryshkina
948d0767eb
more style fixes
2018-06-04 14:34:09 -04:00
Anastasia Tyryshkina
ba45c15fff
tried to fix some of stylization fails
2018-06-04 14:27:24 -04:00
Anastasia Tyryshkina
4630994fd0
get output datasets as well
2018-06-04 13:33:59 -04:00
Anastasia Tyryshkina
5b7055fc6f
respect blacklisted tools
2018-06-04 12:56:47 -04:00
Anastasia Tyryshkina
0c852257bb
delete comment thats no longer necessary
2018-06-04 12:39:55 -04:00
Anastasia Tyryshkina
aa062f8546
fixed the issues with the last pull
2018-06-04 11:53:14 -04:00
Nicola Soranzo
aaff474142
Use consistent preference order for config files
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1) galaxy.yml
2) galaxy.ini
3) universe_wsgi.ini
Also:
- properly quote variables which may contain spaces
- no need to pass the config file to `./scripts/manage_tool_dependencies.py`
- simplify `scripts/maintenance.sh` by moving the `cd` up and reusing
functions from `scripts/common_startup_functions.sh`
2018-06-02 03:28:54 +01:00
Nicola Soranzo
c9daa60e91
Look for config file inside galaxy.dependencies.optional()
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Also don't fail if no config file is found, just print a message on
stderr.
This allows the removal of the code to set `GALAXY_CONFIG_FILE` from
`scripts/common_startup.sh` .
2018-06-02 03:14:38 +01:00
Nicola Soranzo
0ea8107191
Use separate pid_log_paster_args variable
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to store --pid-file and --log-file options of `./scripts/paster.py` .
https://github.com/galaxyproject/galaxy/pull/6239 fixed 3 bugs:
- `GALAXY_RUN_ALL=1 ./run.sh` was reusing the same pid and log files for
all Galaxy processes;
- `./run.sh restart` was always using `paster.pid` and `paster.log` instead
of the configured files
- `./run.sh status` was always using `paster.pid`
but also introduced a regression, i.e. the plain `./run.sh` started
writing to the log file instead of the standard output (console).
This fixes the regression by using a separate variable for these options
instead of conflating them in `paster_args` or `server_args`.
2018-06-02 01:09:10 +01:00
Anastasia Tyryshkina
11575132dc
exports a dataset tsv
2018-06-01 16:47:57 -04:00
Anastasia Tyryshkina
6dee708ae8
export another tsv file named datasets.tsv
2018-06-01 16:43:45 -04:00
Dannon Baker
44b42e7e7e
Merge remote-tracking branch 'upstream/release_18.01' into release_18.05
2018-05-31 16:08:55 -04:00
Lance Parsons
88c94fc49b
Set pid and log file for paster in server_args
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This avoids setting log and pid file in paster_args so that with
GALAXY_RUN_ALL they can be set individually, but ensures they are set
when running paster otherwise.
2018-05-31 12:07:02 -04:00
Lance Parsons
ce9b671bd4
Hack paster args to not duplicate pid file stuff for RUN_ALL.
2018-05-29 11:57:30 -04:00
Martin Cech
0cfac515b5
Merge branch 'release_18.01' into release_18.05
2018-05-07 12:34:08 -04:00
Martin Cech
8255d1ccc8
Merge pull request #5613 from erasche/fix-fraking-grt
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[18.01] File sizes not being annotated in GRT
2018-05-07 11:55:55 -04:00
John Chilton
a29770ca55
Pin the version of node we use in CI, etc....
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Our dependencies won't resolve under node 10 currently (because of upath at least https://github.com/anodynos/upath/blob/master/package.json#L43 but maybe other packages as well).
2018-04-27 08:09:51 -04:00
John Chilton
3dbcc7c83c
Pin the version of node we use in CI, etc....
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Our dependencies won't resolve under node 10 currently (because of upath at least https://github.com/anodynos/upath/blob/master/package.json#L43 but maybe other packages as well).
2018-04-24 16:57:43 -04:00
Nicola Soranzo
284795b94f
Merge branch 'release_18.01' into dev
2018-04-23 15:21:12 +01:00
Matthias Bernt
0c321cb86e
removed config.ini parameter from cleanup scripts
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fixes https://github.com/galaxyproject/galaxy/issues/5941
2018-04-23 14:58:48 +02:00
John Chilton
2829a1f164
Merge pull request #5854 from natefoo/run-scripts-conda
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Improve startup interoperability with Conda
2018-04-18 16:08:13 -04:00
Nate Coraor
564f7ecafe
Make the swarm manager recover on uncaught exceptions. It should do a
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better job of catching them in the application, but this is good enough
for the moment.
2018-04-13 12:34:55 -04:00
Nate Coraor
e651b34156
Remove swarm manager from lib
2018-04-12 16:52:10 -04:00
Nate Coraor
c5262e8971
Look for both base and root conda envs
2018-04-04 23:18:57 -04:00
Nate Coraor
b3eff87a1b
Clean up and useability enhancements
2018-04-04 21:03:08 -04:00
Nate Coraor
a88e19064a
Don't set uWSGI's virtualenv option when running from Conda
2018-04-04 16:47:36 -04:00
Nate Coraor
8261a2398a
Make the startup scripts play just as nicely with Conda as they do with
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virtualenv.
2018-04-04 16:38:01 -04:00
Nicola Soranzo
c9881fdc5c
Merge branch 'release_18.01' into dev
2018-04-03 10:54:48 +01:00
Dannon Baker
e7ecab7734
If psycopg2-binary is installed (as might be if switching between
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branches), uninstalling psycopg2 will leave psycopg2-binary installed
but in a broken state. If we're removing psycopg2, we need to remove
psycopg2-binary at the same time, leaving psycopg2-binary to be
correctly installed afterwards.
2018-04-02 14:14:23 -04:00
John Chilton
08c2c5b5ac
Merge pull request #5698 from dannon/psycopg2_bump
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Bump psycopg2 to 2.7.4;
2018-03-29 10:47:22 -04:00
Dannon Baker
60ca4d4cc9
Instead of using -q, send to /dev/null, since the early pipe exit blows up pip
2018-03-28 12:42:37 -04:00
Dannon Baker
8742614e52
Quieter grepping.
2018-03-28 12:13:23 -04:00
John Chilton
b4a30bcd82
Revise uwsgi defaults and display.
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In https://github.com/galaxyproject/galaxy/issues/1530 we realized that buffer-size needs to be increased for Galaxy requests. Also mention thunder-lock since that should frequently be enabled - https://github.com/galaxyproject/ansible-galaxy-extras/pull/195 .
2018-03-27 08:48:58 -04:00
John Chilton
bb90ae93d8
More grt fixes - spotted by @nsoranzo.
2018-03-23 16:14:50 -04:00
John Chilton
fea7953410
Remove two scripts - dataset purging hasn't worked this way for a very long time.
2018-03-23 16:14:49 -04:00
John Chilton
49fed72eea
Drop data library whoosh/lucene scripts.
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We don't set that config option in Galaxy anymore so these are broken anyway.
2018-03-23 16:14:49 -04:00
John Chilton
1911a55390
Remove unused and unuseful scripts.
2018-03-23 16:14:49 -04:00
Dannon Baker