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1361 Commits
Author SHA1 Message Date
mvdbeek ea3f48a5ec Document metadata_strategy 2020-07-04 19:44:34 +02:00
Sergey Golitsynskiy c083c27c07 Run make config-rebuild 2020-07-02 03:07:31 -04:00
mvdbeek 46e0f2833c Merge branch 'release_20.05' into dev 2020-06-30 18:27:39 +02:00
Nicola Soranzo ba3a07a736 Small fixes 2020-06-30 16:23:13 +01:00
mvdbeek 93e02008a3 Update release notes with later PRs 2020-06-30 16:32:37 +02:00
Kaivan Kamali 072be091e2 Removed trailing whitespace 2020-06-25 15:31:39 -04:00
Kaivan Kamali 2f6063c1f8 Revised documentation per code review feedback. 2020-06-25 15:04:16 -04:00
Kaivan Kamali b2ad77340a Revised doc based on PR feedback. 2020-06-25 15:02:23 -04:00
Kaivan Kamali ed30e7b051 More small revision 2020-06-25 15:02:23 -04:00
Kaivan Kamali ef38ff5390 Minor revision 2020-06-25 15:02:23 -04:00
Kaivan Kamali 88a76cd65a Added page documenting steps that happen during Galaxy startup. 2020-06-25 15:02:23 -04:00
Gianmauro Cuccuru c8182b7e21 generated files from make config-rebuild 2020-06-24 10:11:43 +02:00
Nicola Soranzo 7ded4170ce Merge branch 'release_20.05' into dev 2020-06-23 10:25:25 +01:00
Nicola Soranzo e8466d002a Python 2.7 is officially unsupported on 20.05 2020-06-20 19:04:57 +01:00
Dannon Baker 0c3a81b0d2 Merge remote-tracking branch 'upstream/release_20.05' into dev 2020-06-17 12:05:55 -04:00
Martin Cech 7b99755029 include RN in index and add minor changes to them 2020-06-16 12:06:13 +02:00
Nate Coraor 06bded296b Change usage of whitelist/blacklist to allowlist/blocklist, attempt 
backwards compatibility.
 2020-06-11 13:37:43 -04:00
Marius van den BeekandNicola Soranzo e687b463f1 Typo fix 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-06-09 12:41:21 +02:00
mvdbeek ec55c42ae3 Update main announcement 2020-06-09 12:30:11 +02:00
Marius van den BeekandNicola Soranzo 9ba04d3aa5 IT announcement 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-06-09 11:23:11 +02:00
Alexander OSTROVSKY 45d71df053 blurb 2020-06-05 09:43:45 -07:00
Nicola Soranzo 1aa9163975 Fix ELIXIR 2020-06-05 16:49:59 +01:00
Juleen Graham c97e4135c2 Add note about Custos and CILogon 2020-06-05 02:05:17 -04:00
Marius van den Beek 87518d4f3f Fix quoting 2020-06-03 18:37:51 +02:00
Marius van den BeekandSergey Golitsynskiy c74510214e Scrolling typo fix 
Co-authored-by: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
 2020-06-03 18:35:31 +02:00
Helena Rasche 6c44718d51 add gif 2020-06-03 13:54:26 +02:00
Helena Rasche 7fa8f8392d Add images 2020-06-03 12:11:34 +02:00
Helena Rasche 521c3b0ce3 rewrite user-facing notes 2020-06-03 12:11:34 +02:00
Helena Rasche aced456c41 Missing link from main notes 2020-06-03 12:10:00 +02:00
Matthias Bernt b3933506ad added short paragraph on OpenMS datatypes 2020-06-03 12:00:26 +02:00
mvdbeek 9b82bb12ab Release notes for 20.05 2020-06-02 16:18:16 +02:00
Sergey Golitsynskiy ecf7cb7306 Edit option description in schema 
Do not explicitly warn about error if option is set but file is missing.
 2020-05-20 09:28:44 -04:00
Sergey Golitsynskiy af3cad6497 Make config-rebuild 2020-05-20 00:02:33 -04:00
John Chilton f62bca7a7c Merge pull request #9742 from bernt-matthias/doc/dynamic_dest_id 
doc: dynamic destinations better set the id in JobDestination
 2020-05-13 16:32:37 -04:00
Dannon Baker c8ecc4e249 Merge remote-tracking branch 'upstream/release_20.05' into dev 2020-05-11 06:43:16 -04:00
Nuwan Goonasekera ce2e709379 Minor fixes to docs on how to build a job runner 2020-05-09 22:14:00 +05:30
Dannon Baker 9077ee389f Make config-rebuild. 2020-05-08 14:32:38 -04:00
Anup Kumar e728ccbedd Remove usused code 2020-05-08 16:44:10 +02:00
Anup Kumar 7f2fd69ba6 Update config 2020-05-08 16:44:10 +02:00
Matthias Bernt 63c11fc37f doc: better set the id in JobDestination 
otherwise it looks odd in the logs (None)
 2020-05-08 12:12:39 +02:00
mvdbeek 8be1ac07e6 Merge branch 'release_20.01' into dev 2020-05-05 21:04:03 +02:00
Daniel Blankenberg 79d4b1a8c0 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into refgenie 
and remake dependencies
 2020-05-04 14:56:15 -04:00
mvdbeek f6a79f6341 Rename galaxy.util.logging to galaxy.util.custom_logging 
Otherwise there may be import issues:
```
==================================== ERRORS ====================================

________________________ ERROR collecting test session _________________________

.tox/py27-unit/lib/python2.7/site-packages/py/_path/common.py:383: in visit

    for x in Visitor(fil, rec, ignore, bf, sort).gen(self):

.tox/py27-unit/lib/python2.7/site-packages/py/_path/common.py:425: in gen

    if p.check(dir=1) and (rec is None or rec(p))])

.tox/py27-unit/lib/python2.7/site-packages/_pytest/main.py:667: in _recurse

    ihook = self.gethookproxy(dirpath)

.tox/py27-unit/lib/python2.7/site-packages/_pytest/main.py:482: in gethookproxy

    my_conftestmodules = pm._getconftestmodules(fspath)

.tox/py27-unit/lib/python2.7/site-packages/_pytest/config/__init__.py:424: in _getconftestmodules

    mod = self._importconftest(conftestpath.realpath())

.tox/py27-unit/lib/python2.7/site-packages/_pytest/config/__init__.py:463: in _importconftest

    raise ConftestImportFailure(conftestpath, sys.exc_info())

E   ConftestImportFailure: (local('/home/circleci/repo/test/unit/queue_worker/conftest.py'), (<type 'exceptions.AttributeError'>, AttributeError("'module' object has no attribute 'getLogger'",), <traceback object at 0x7fabd96b7eb0>))

----- generated html file: file:///home/circleci/repo/run_unit_tests.html ------

!!!!!!!!!!!!!!!!!!! Interrupted: 1 errors during collection !!!!!!!!!!!!!!!!!!!!

=========================== 1 error in 1.83 seconds ============================

```
 2020-05-03 21:50:12 +02:00
Nicola Soranzo addb73c1c4 Update documentation 
- Fixes for `interactivetools.rst`
- Run `make updaterst`
 2020-05-01 01:20:06 +01:00
Martin Cech 4161883caa Merge pull request #9632 from nsoranzo/update_procedures 
[PROCEDURES] Officially allow adding new datatypes to the latest tagged release
 2020-04-28 15:31:00 +02:00
Martin Cech d11aca39f4 Merge pull request #9668 from dannon/minor-it-doc-clarification 
Minor IT doc clarification
 2020-04-28 15:27:56 +02:00
Dannon ec40ffd2ba Merge pull request #9664 from kxk302/dev 
Added documentation for debugging Galaxy and unit/integration tests
 2020-04-27 18:12:08 -04:00
kxk302andNicola Soranzo 5a9410bdc6 Apply suggestions from code review 
Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-04-27 16:08:48 -04:00
Dannon Baker 493c24bdf3 Minor IT doc clarification 2020-04-27 15:25:19 -04:00
Dannon 2ec991a3ab Merge pull request #9650 from astrovsky01/it_docs 
It docs additional info
 2020-04-27 15:05:25 -04:00