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1619 Commits
Author SHA1 Message Date
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 
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() 
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 
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
Martin Cech 53d2664b0b Merge pull request #6200 from erasche/grt-asdf 
Permit numeric values of GRT instance ID in config
 2018-05-31 15:31:59 -05:00
Dannon Baker 06d0fcc0de Merge remote-tracking branch 'upstream/release_18.05' into dev 2018-05-31 16:09:26 -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 
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
Helena Rasche 94ae2e6a95 permit actual numbers in conf file 2018-05-23 16:31:40 +02:00
Martin Cech c67c4b4b82 Merge branch 'release_18.05' into dev 2018-05-07 12:34:46 -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 
[18.01] File sizes not being annotated in GRT
 2018-05-07 11:55:55 -04:00
Nicola Soranzo 479e76ff13 Add closing old milestone to release issue 2018-04-30 16:13:08 +01:00
John Chilton 74939a3f11 Update release process - do not require merge PRs to have milestones. 2018-04-27 11:17:36 -04:00
John Chilton a29770ca55 Pin the version of node we use in CI, etc.... 
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.... 
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 
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 
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 
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 
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 
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 
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. 
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. 
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
John Chilton 16d821e12e Mark scripts/* that don't work with YAML configuraiton options as deprecated. 2018-03-23 16:14:49 -04:00
John Chilton 5f3f792f6f Unification of Galaxy configuration parsing for scripts/* 2018-03-23 16:14:49 -04:00
John Chilton 8fa8660b25 Small improvements to scripts/grt/export.py for testing. 
- Don't rely on external sha256sum, use Python hashing (add utility to hash_util to enable this).
- Drop unused galaxy_config from grt.yml.sample - it isn't used anywhere as far as I can tell.
 2018-03-23 16:14:49 -04:00
Nicola Soranzo 88e6e94a81 Merge branch 'release_18.01' into dev 2018-03-23 17:14:22 +00:00
Dannon Baker d44b47741b Specify format to squelch deprecation warning about columns/legacy 2018-03-23 12:05:29 -04:00
Dannon Baker 30c2ea0c3e Make psycopg2 grep a little more robust 2018-03-23 12:02:41 -04:00
Dannon Baker e84dd5db6b Rudimentary check for old psycopg2==2.4.3, which we clean up before installing psycopg2-binary. 2018-03-23 11:59:56 -04:00
Nate Coraor c720af066b Attempt to log startup as late as possible 2018-03-22 21:43:26 -04:00
John Chilton 6422955a22 Merge pull request #5669 from bgruening/propagate_tags_script 
Add script for propagating hashtags in a Galaxy history
 2018-03-20 15:43:28 -04:00
John Chilton 8316cb64b2 Merge pull request #5731 from martenson/botstrapdev 
improve galaxy update commands, update some bootstrap checkpoints
 2018-03-20 09:16:03 -04:00
Nicola Soranzo b2d7ca40d3 Fix typo 2018-03-19 18:10:04 +00:00