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1149 Commits
Author SHA1 Message Date
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
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
Nicola Soranzo 0cf88623ee Merge branch 'release_18.01' into dev 2018-03-19 17:52:05 +00:00
Nicola Soranzo 74d0bcb353 Merge branch 'release_17.09' into release_18.01 2018-03-19 17:50:57 +00:00
Martin Cech e310d7a1f0 improve galaxy update commands, update some checkpoints 2018-03-19 13:38:11 -04:00
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 1dfaa476c0 Rebuild client only if there are changes 
in the client/ directory since the last build.
 2018-03-13 01:40:06 +00:00
anup kumar 122384f33e Add print statements with brackets 2018-03-09 08:01:56 +01:00
anup kumar 81e971af1d Fix python lint errors 2018-03-09 07:45:22 +01:00
anup kumar 3b6f6b803e Merge branch 'dev' of https://github.com/bgruening/galaxy into propagate_tags_script 2018-03-08 21:38:46 +01:00
anup kumar ade6727fda Add script to propagate hashtags in history 2018-03-08 21:37:52 +01:00
John Chilton 1c6cc02415 Hierarchical upload API optimized for folders & collections. 
Allows describing hierarchical data in JSON or inferring structure from archives or directories.

Datasets or archive sources can be specified via uploads, URLs, paths (if admin && allow_path_paste), library_import_dir/user_library_import_dir, and/or FTP imports. Unlike existing API endpoints, a mix of these on a per file basis is allowed and they work seemlessly between libraries and histories.

Supported "archives" include gzip, zip, bagit directories, bagit achives (with fetching and validations of downloads).

The existing upload API endpoint is quite rough to work with both in terms of adding parameters (e.g. the file type and dbkey hanlding in 4563 was difficult to implement, terribly hacky, and should seemingly have been trivial) and in terms of building requests (one needs to build a tool form - not describe sensible inputs in JSON). This API is built to be intelligable from an API standpoint instead of being constrained to the older style tool form. Additionally it built with hierarchical data in mind in a way that would not be easy at all enhancing the tool form components we don't even render.

This implements 5159 though much simpler YAML descriptions of data libraries should be possible basically as the API descriptions. We can replace the data library script in Ephemeris https://github.com/galaxyproject/ephemeris/blob/master/ephemeris/setup_data_libraries.py with one that converts a simple YAML file into an API call and allows many new options for free.

In future PRs I'll add filtering options to this and it will serve as the backend to 4733.
 2018-03-08 10:33:36 -05:00
Nicola Soranzo 326a564eb9 Stop shipping old BeautifulSoup library 2018-03-07 01:19:55 +00:00
Nicola Soranzo e8b78cb62b Fix typos 2018-03-05 09:44:26 +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 10ff797ac7 Merge branch 'release_18.01' into dev 
Conflicts:
	scripts/common_startup.sh
 2018-02-08 13:38:22 -05:00
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