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Commit Graph
1288 Commits
Author SHA1 Message Date
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instead of exiting with the "The Galaxy client build is out of date."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
Nate Coraor 418fd53739 Merge remote-tracking branch 'origin/dev' into job-handler-mules 2017-11-15 12:42:20 -05:00
Nate Coraor c340d4ebec Fix tool migrations with config file changes, do everything from 
manage_db.sh.
 2017-11-15 12:37:22 -05:00
Nicola Soranzo bbd96c435b Merge pull request #4903 from jmchilton/dev_at_same_time 
Install dev and regular dependencies at the same time.
 2017-11-15 11:47:40 +00:00
Nicola Soranzo 2cd95c48f6 Fix import order everywhere 
- Add flake8-import-order to flake8 Pipfile and remove py27-lint-imports
  and py27-lint-imports-include-list tox envs
- Fix most E201 and E202 errors reported by flake8-import-order v0.15,
  but pin flake8-import-order to v0.14.3 until
  https://github.com/PyCQA/flake8-import-order/issues/123
  is fixed

This let us drop 2 jobs on Travis per each job.
 2017-11-14 19:42:39 +00:00
Nate Coraor f5ee540df1 To avoid duplication, move common utilities used by external scripts to 
galaxy.util.script. Update one such script to use the new module.
 2017-11-13 12:18:09 -05:00
Nate Coraor 806438edc9 Revert script changes unrelated to uWSGI mule work. Includes 
galaxy.util.script so that get_uwsgi_args.py still works, but that will
be PR'd separately and merged later.
 2017-11-13 12:08:28 -05:00
Nate Coraor b75583ea26 Fix post-merge lint issues 2017-11-09 14:00:46 -05:00
Nate Coraor 30266c5221 Merge remote-tracking branch 'origin/dev' into job-handler-mules 2017-11-09 13:11:46 -05:00
John Chilton a1e91231aa If installing dev dependencies, do so along side regular dependencies. 
Catch conflicts and works faster.
 2017-11-02 09:49:08 -04:00
Jelle Scholtalbers b372c3b4b9 fix location of cleanup_datasets.py if executed outside of the root 2017-11-02 12:37:39 +01:00
Jelle Scholtalbers 1fedf7e680 add maintenance.sh to simplify setting up a cleanup cron job or run the cleanup scripts in general 2017-11-02 11:06:26 +01:00
Nicola Soranzo 07d11c6d0b Merge pull request #4876 from jmchilton/update_linting_deps 
Absolute pins on linting dependencies.
 2017-10-31 21:12:58 +00:00
Nicola Soranzo aacdf8d939 Merge branch 'release_17.09' into dev 
Conflicts:
	static/style/blue/base.css
 2017-10-30 19:15:50 +00:00
Nicola Soranzo 45d4fefe63 Merge pull request #4898 from jmchilton/fix_extra_index 
[17.09] Fix extra index URL call in common startup.
 2017-10-30 15:52:41 +00:00
John Chilton 09fdac513d Fix extra index URL call in common startup. 
- Use it for dev requirements also.
- Use more correct API target that supports older versions of dependencies on PyPI.

xref https://gist.github.com/jmchilton/ad8f180f5ac1eb5f689f815b04f603fa
 2017-10-30 10:49:29 -04:00
John Chilton ccb5f61845 Absolute pins on linting dependencies. 
- Use completely pinned and hashed dependencies for more consistent, reproducible linting.
- Leverage the awesomeness of pipenv to automate updating these.
- These will always be locked now so builds don't break randomly on other people updating their software. When we finally have the bot up and running that forward merges fixes for Galaxy we can add another if statement that runs this check against dev once a day and opens a PR if needed.
 2017-10-26 15:53:25 -04:00