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a29770ca554b5aaf8ea6533ee413fed77042a0ea
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1104 Commits
Author SHA1 Message Date
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
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
Dannon Baker 45a25a1b8b Rudimentary build checking for -dev only. 2017-12-04 18:03:27 -05:00
Nicola Soranzo 48aca7dce8 Update to flake8-import-order 0.16 2017-12-01 11:09:57 +00:00
John Chilton d69962e7f4 Implement model abstraction for `ImplicitCollectionJobs`. 
These aggregate all the jobs contributing to an implicitly created HistoryDatasetCollectionAssociation.

- Model enhancements that allow this.
- API endpoint for jobs summary of history content (somewhat uniform across HDAs and HDCAs just for consistency).
- Test cases.
- Rework history contents API a bit to eliminate more costly state summary checks by default.
 2017-11-30 10:02:02 -05:00
Nate Coraor 49158ba38b Add multi-farm support to the main script 2017-11-17 17:09:36 -05:00
Nate Coraor e858ceb84a Do not autostart uWSGI mules 2017-11-17 17:05:43 -05:00
Nate Coraor b4863b2df8 Fix lint errors 2017-11-17 13:59:25 -05:00
Nate Coraor 1ec960bcf6 Improve shutdown cleanliness under uWSGI. 2017-11-17 13:52:24 -05:00
Nate Coraor c18521d7f7 Move signal handling from uWSGI stack to main 2017-11-17 13:51:13 -05:00