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1288 Commits
Author SHA1 Message Date
John Chilton c122e74240 Fixes for core.galaxy_ui.yaml. 
Neither of these prevent the tour from working but I think they are bugs. The extra click isn't an elemment that is clickable at that point in the tour and the referenced id isn't available so nothing in particular is tagged in the UI at that point.
 2016-11-21 16:49:41 -05:00
Martin Cech 92105d99fa Merge pull request #2818 from erasche/rstudio-1610 
Return of RStudio
 2016-11-16 16:01:12 -05:00
Enis Afgan 45259b7f16 Fix typo 2016-11-16 11:47:38 -05:00
Nicola Soranzo ca4e8914ec Merge branch 'release_16.07' into dev 
Conflicts:
	lib/galaxy/tools/deps/conda_util.py
 2016-11-14 14:45:23 +00:00
John Chilton 04935ce94b Merge pull request #3105 from abretaud/patch-2 
Add doc for conda_copy_dependencies option
 2016-11-07 08:20:46 -05:00
Anthony Bretaudeau 8a972cc325 be stronger 2016-11-07 11:03:41 +01:00
peterjc ea717dd001 Add BLAST datatypes to datatypes_conf.xml.sample 2016-11-04 17:00:14 +00:00
peterjc 2e36fdb0bd Include all three BLAST .loc files in data table conf 2016-11-04 17:00:13 +00:00
mvdbeek a3ac57dbc5 Remove verbose_install_check option 
This option was introduced with #2554 and #2538, in reponse to a false
positive conda install.  This would have been caught by simply checking
the exit code, which we are doing by default now. The additional
verification is too strigent and not in line with the conda resolver.
Activating this option will report perfectly well installed conda
environments as having failed and will cause them to be uninstalled.
 2016-11-04 17:24:18 +01:00
Nicola Soranzo 8f89a04eae Fix job_working_directory commented default 
Follow-up to commit 0eab8346b3.
 2016-11-02 20:28:20 +00:00
Anthony Bretaudeau 69cda7ee10 clarify links 2016-10-28 12:21:32 +02:00
Anthony Bretaudeau 16866b5e80 add extra time problem 2016-10-28 12:13:33 +02:00
Anthony Bretaudeau 05fbef510c Add doc for conda_copy_dependencies option 
Discussed on IUC gitter, related to https://github.com/galaxyproject/galaxy/issues/3008
 2016-10-28 12:02:30 +02:00
guerler 0b1c171ebc Revise tab viewer, add test cases 2016-10-27 13:02:01 -04:00
guerler ec9ca3ffd1 Fix list view title 2016-10-27 08:38:36 -04:00
guerler d9dfc2cc78 Move thumbnail list view to shared ui elements 2016-10-27 08:37:49 -04:00
Martin Cech 541643d7fe Merge pull request #3073 from nturaga/add_cel_datatype 
Add CEL datatype
 2016-10-26 13:49:01 -04:00
Peter Cock fc027124e7 Fix BLAST database *.loc files inconsistency 
We should have all of the ``blast*.loc`` files in the sample configuration, or none of them.

Historically Galaxy included only the nucleotide BLAST database ``blastdb.loc`` file for use with mega-blast, with ``blastdb_p.loc`` later for protein databases added as part of the BLAST+ suite (which initially was in the main Galaxy repository).

In a3018feb02 the mega-blast tool was moved to the Tool Shed, and the ``blastdb.loc`` entry removed. Likewise the BLAST+ tools were moved to the Tool Shed, but the ``blastdb_p.loc`` entry remains.

Later (on the Tool Shed only?) ``blastdb_d.loc``was added for protein domain databases.
 2016-10-26 10:45:33 +01:00
nturaga f891034390 Lowercase the datatypes, add edam_data, thanks @nsoranzo 2016-10-25 15:18:14 -04:00
Dannon Baker a6d52cdbdc Merge remote-tracking branch 'bgruening/feature/plugin-system' into dev 2016-10-23 19:00:43 +02:00
nturaga 7e2725d125 add CEL datatypes to datatypes conf sample 2016-10-19 12:11:57 -04:00
guerler bdc8829dd2 Dataset metadata should not be cached when building chart visualizations 2016-10-17 15:20:25 -04:00
John Chilton 1dc2d6a4ea Merge pull request #2875 from guerler/remote_chart_plugins 
Link charts to external repo, adjust interface
 2016-10-17 13:33:33 -04:00
John Chilton 448a27a4a1 Merge remote-tracking branch 'jmchilton/dev' into collection_tools 2016-10-16 09:49:31 -04:00
Evgeny Anatskiy ebaffa2e0d fix failing Travis tests #2 (TOX_ENV=py27-lint) and #6 (TOX_ENV=py27-lint-imports) 2016-10-14 22:29:55 +02:00
guerler f053f9bb3d Merge branch 'dev' into remote_chart_plugins 2016-10-14 16:24:39 -04:00
Bjoern Gruening 3d4f302c47 change default settings in galaxy.ini.sample 2016-10-14 02:02:57 +02:00
Evgeny Anatskiy 3770239281 Merge branch 'feature/plugin-system' of github.com:bgruening/galaxy into feature/plugin-system 2016-10-14 00:29:39 +02:00
Bjoern Gruening 3cb8189e1f Merge branch 'dev' into feature/plugin-system 2016-10-13 23:33:25 +02:00
Bjoern Gruening 3aadd84b80 add case where no user is logged in 2016-10-13 23:28:02 +02:00
Evgeny Anatskiy 2703ba1a0c activate all demo plugins in testing purposes 2016-10-13 22:37:02 +02:00
Bjoern Gruening f4dc38a54d activate all plugins in the demo folder 2016-10-13 22:31:41 +02:00
Evgeny Anatskiy 6894df3dcb Merge branch 'feature/plugin-system' of github.com:bgruening/galaxy into feature/plugin-system 2016-10-13 20:52:43 +02:00
Bjoern Gruening 773d85453f move all plugins into a demo folder 2016-10-13 19:28:18 +02:00
Bjoern Gruening 6a62dbc91a Merge branch 'dev' into feature/plugin-system 2016-10-13 19:18:13 +02:00
Eric Rasche 6c17d1a823 Remove outdated warning 
After digging through the code I am not finding evidence that this
was ever possible to do, at least not since sometime pre-2010.
 2016-10-13 16:21:12 +00:00
Evgeny Anatskiy 0a15289d31 added missing dependencies check 2016-10-12 22:22:59 +02:00
guerler fe73009db5 Fix default options for storing request 2016-10-11 23:36:30 -04:00
guerler f467384fdd Use fixed repository path 2016-10-11 20:58:31 -04:00
guerler 1805ac8b59 Add chart plugins back to plugins directory of visualization framework 2016-10-11 20:27:37 -04:00
Nicola Soranzo 1156006733 Merge branch 'release_16.07' into dev 
Conflicts:
	lib/galaxy/tools/deps/__init__.py
 2016-10-11 16:50:37 +01:00
guerler bf5cc30b84 Remove tabular file from repo, fix comments 2016-10-11 09:08:41 -04:00
Martin Cech 20dcc4d693 remove duplicated option from config sample 2016-10-10 19:19:51 -04:00
Evgeny Anatskiy 69a9344c52 - show Webhook on a workflow page 
- fix merge errors
 2016-10-09 22:18:15 +02:00
Evgeny Anatskiy ce346b6ad4 pass trans object into the helper function 2016-10-09 21:32:08 +02:00
Evgeny Anatskiy 8b5716ddfd fix bugs after previous commit 2016-10-09 21:32:01 +02:00
Evgeny Anatskiy e58fe7ca49 bug fixes and improvements 2016-10-09 21:31:49 +02:00
anatskiy 29a57ba0fd - add new entry point (Workflow) 
- temporarily hide masthead webhook (due to instability)
 2016-10-09 21:31:17 +02:00
anatskiy 27e0302ea3 renamings and fixes 2016-10-09 21:30:22 +02:00
anatskiy 060df24ff5 add one more plugin 2016-10-09 21:30:12 +02:00