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1092 Commits
Author SHA1 Message Date
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
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