opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
34,987 Commits 69 Branches 243 Tags
191a134bbc511c508d9ee0636030da2e2e68ea44
Commit Graph
1161 Commits
Author SHA1 Message Date
Anastasia Tyryshkina 191a134bbc got rid of things that are no longer necessary 2018-06-04 15:57:22 -04:00
Anastasia Tyryshkina 948d0767eb more style fixes 2018-06-04 14:34:09 -04:00
Anastasia Tyryshkina ba45c15fff tried to fix some of stylization fails 2018-06-04 14:27:24 -04:00
Anastasia Tyryshkina 4630994fd0 get output datasets as well 2018-06-04 13:33:59 -04:00
Anastasia Tyryshkina 5b7055fc6f respect blacklisted tools 2018-06-04 12:56:47 -04:00
Anastasia Tyryshkina 0c852257bb delete comment thats no longer necessary 2018-06-04 12:39:55 -04:00
Anastasia Tyryshkina aa062f8546 fixed the issues with the last pull 2018-06-04 11:53:14 -04:00
Anastasia Tyryshkina 11575132dc exports a dataset tsv 2018-06-01 16:47:57 -04:00
Anastasia Tyryshkina 6dee708ae8 export another tsv file named datasets.tsv 2018-06-01 16:43:45 -04:00
Dannon Baker 44b42e7e7e Merge remote-tracking branch 'upstream/release_18.01' into release_18.05 2018-05-31 16:08:55 -04:00
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 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