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1112 Commits
Author SHA1 Message Date
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
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
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
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
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 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
Nate Coraor c720af066b Attempt to log startup as late as possible 2018-03-22 21:43:26 -04:00
Nicola Soranzo 74d0bcb353 Merge branch 'release_17.09' into release_18.01 2018-03-19 17:50:57 +00:00
Nicola Soranzo 3b87dac780 Add Galaxy lib directory to Python path for 2 scripts 
Also fix check introduced in commit 0763cab37a .

Fix https://github.com/galaxyproject/galaxy/issues/5722 .
 2018-03-19 14:53:19 +00:00
E Rasche 6a20984c57 try harder to handle unexpected values 2018-02-27 18:06:52 +01:00
E Rasche 71c79fda32 File sizes were not being added 2018-02-27 17:56:31 +01:00
Nicola Soranzo eba3fb4b35 Fix common_startup.sh for galaxy tarballs 
Do not assume git is installed and the `.git` directory is present.

Fix https://github.com/galaxyproject/galaxy/issues/5466
 2018-02-08 11:52:24 -05:00
Nate Coraor 977bbf1481 Install node and yarn in common_startup.sh using nodeenv and the venv's 
npm.
 2018-02-08 11:33:55 -05:00
Nate Coraor fd96864bd6 Finish updates to framework dependencies doc 2018-01-25 12:36:11 -05:00
Dannon Baker dd88194e8f Merge pull request #5371 from jmchilton/environment_client_skip 
Environment variable to skip client build.
 2018-01-24 11:16:50 -05:00
John Chilton 6e865a3363 Environment variable to skip client build. 
Need to fix https://github.com/galaxyproject/planemo/issues/750 but I don't want to send along command-line arguments that will break older Galaxies, better just to set an environment variable that will be ignored for older Galaxies I think.
 2018-01-24 08:59:59 -05:00
John Chilton e14dde16fb Merge pull request #5346 from mvdbeek/fix_hda_parent_access 
Fix dataset purging, dataset cleanup script and db_shell script
 2018-01-21 14:10:32 -05:00
mvdbeek 991f79e630 Use print() function in common_startup.sh 2018-01-21 13:24:07 +01:00
Marius van den Beek 8f65cd46b0 Merge pull request #5180 from bgruening/bam_unsorted 
Add BamNative datatype
 2018-01-19 16:37:36 +01:00
mvdbeek 89d45416fb Import Registry directly 2018-01-19 15:27:55 +01:00
mvdbeek 654ed86b37 Setup a dummy registry to allow some more operations, e.g. accessing metadata 2018-01-19 15:09:38 +01:00
mvdbeek ca51898bc4 Fix cleanup datasets script 2018-01-19 14:50:08 +01:00
Marius van den Beek 33bd54079b Merge pull request #4916 from scholtalbers/add_maintenance_script 
Add maintenance script..
 2018-01-19 12:26:42 +01:00
Nate Coraor 44c291bc66 Merge remote-tracking branch 'origin/dev' into ini_to_yaml_config 2018-01-18 12:30:05 -05:00
mvdbeek aaaf7b50a7 Enable conda_auto_init and conda_auto_install for framework tests 2018-01-17 17:11:41 +01:00
Martin Cech 542a489079 Merge pull request #5294 from dannon/fix_skip_client_build 
Fixes the --no-client-build startup option
 2018-01-17 10:16:21 -05:00
anup kumar 6cb9d664de Fix Galaxy instance startup error 2018-01-14 11:42:15 +01:00
Nicola Soranzo a70ecd0147 Fix common_startup.sh bashisms 
Introduced in commit 45a25a1b8b .

This was causing this error on the `dev` branch on Ubuntu (which uses
`dash`):

```
$ ./run.sh
./scripts/common_startup.sh: 69: [: dev: unexpected operator
Activating virtualenv at .venv
...
```

instead of exiting with the "The Galaxy client build is out of date." message.
 2018-01-12 13:21:04 +01:00
Nate Coraor 1daa2ae6e5 Fix support for proxy prefix under uWSGI. 2018-01-11 13:56:05 -05:00
mvdbeek 5c4c25b63d Mention how to specify the config file location 
and how to do that when using ipython.
 2018-01-11 10:42:44 +01:00
Dannon Baker a5cef0fe68 Fixes the --no-client-build startup option (and renames it --skip-client-build, too) 2018-01-10 12:04:32 -05:00
Nate Coraor 542aa95fa4 uWSGI: Use --master when daemonizing (required when using http server w/ 
daemonization) and fix `run.sh --stop-daemon`
 2018-01-08 14:24:43 -05:00
Martin Cech bb29444edf Merge pull request #5128 from dannon/check_for_client_build 
Client build check
 2018-01-03 17:11:13 -05:00
Dannon Baker c8b454b532 More descriptive help for the dev client build check. 2017-12-20 10:47:06 -05:00
John Chilton f9969ee97a Remove API scripts for axed APIs. 2017-12-15 16:02:18 -05:00
Nicola Soranzo 18221ae931 paster.pid/log to galaxy.pid/log reference update 
Fix errors in `first_startup` jobs:
https://travis-ci.org/galaxyproject/galaxy/jobs/316342622#L1029

Introduced in https://github.com/galaxyproject/galaxy/pull/4475
 2017-12-15 15:34:47 +00:00
Nicola Soranzo 14259b11d9 Python3: finish first pass on whole codebase 2017-12-14 12:01:01 +00:00
Nate Coraor 33abb94252 Drop missing --safe-pidfile uWSGI arg until it is released. 2017-12-06 20:28:21 -05:00
Nate Coraor 8f69d17e86 Don't use uWSGI master mode by default. Fixes Ctrl+C on macOS and is 
really only important in production configs where you should be using a
config file anyway.
 2017-12-06 20:28:21 -05:00
John Chilton 7bae23e105 yaml_config - update code base for converting galaxy.ini.sample to YAML. 2017-12-06 20:28:20 -05:00
Dannon Baker b57af28c9b Elaborate on comment, todo 2017-12-05 07:04:21 -05:00