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Author SHA1 Message Date
Dannon Baker c260e0b0c8 Sort tags for display (note, this is stupid to have in 3 places -- refactor) 2017-06-01 10:38:13 -04:00
Dannon Baker 75028ac1ee Merge pull request #4133 from guerler/escape_regex 
[17.05] Properly escape potential regex expression in workflow parameters
 2017-05-31 19:20:44 -04:00
Martin Cech f6ced00ef0 Merge pull request #4135 from blankenberg/17.05_zipfile 
[17.05] Fix for returning a fileobject in compression_utils.py when handling a zipfile.
 2017-05-31 18:48:01 -04:00
Daniel Blankenberg a9d0d3671a Fix for returning a fileobject in compression_utils.py when handling a zipfile. 
Will return the first named object in the archive. zipfile.os_zipfile does not exist...
 2017-05-31 16:55:32 -04:00
guerler c409572ef8 Handle potential regex expression in workflow parameter names 2017-05-31 16:28:18 -04:00
Martin Cech 42e274d334 Merge pull request #4122 from galaxyproject/release_17.01 
[17.05] merge Release 17.01
 2017-05-30 10:11:51 -04:00
Marius van den Beek 96e1cf58f4 Merge pull request #4117 from jmchilton/genome_diversity_fixes 
[17.01] Fix legacy Python path for genome diversity tools from miller lab.
 2017-05-29 13:13:37 +02:00
John Chilton 55336d2c31 Fix legacy Python path for genome diversity tools from miller lab. 
Fixes #4108.
 2017-05-28 19:34:20 -04:00
Marius van den Beek 3d16319a15 Merge pull request #4114 from dannon/force_uniqueness_preserved_tags 
[17.05] Force uniqueness of preserved tags
 2017-05-27 08:38:04 +02:00
Dannon Baker 2ac04bbf09 Uniqueify hashtag display 2017-05-26 13:30:21 +01:00
Dannon Baker dd06a01746 Handle *both* paths for tag appending using the now-dict correctly. 2017-05-26 10:22:13 +01:00
Dannon Baker b6e8d3e8ac Slight refactoring to use a dict for unique'ing preserved tags. TODO: enhance object builtins to compare correctly so we can use a set, maybe. Not a big deal unless/until we have a second type of preserved tag though. 2017-05-26 10:14:48 +01:00
Dannon Baker 68433b1eff Force uniqueness of preserved tags (so, don't allow many inputs with a 'name:foo' tag to add a ton of 'name:foo' tags to a dataset; just use one) 2017-05-25 15:33:09 +01:00
Martin Cech 18ef6a6ab0 Update version to 17.05 v17.05 2017-05-24 10:47:27 -04:00
Martin Cech d8c21e1fd9 Merge pull request #4110 from nsoranzo/release_17.05 
[17.05] Improve 17.05 release notes
 2017-05-24 10:38:05 -04:00
Nicola Soranzo 4294663d53 Improve 17.05 release notes 
Also add 4 pull requests merged in the last few days.
 2017-05-24 12:10:05 +01:00
Nicola Soranzo 31015a83af Remove residual comment 
Follow-up on https://github.com/galaxyproject/galaxy/pull/4089
 2017-05-24 11:18:47 +01:00
Martin Cech 0268f5078c Merge pull request #4107 from guerler/fix_repeats_in_workflows 
[17.05] Fixes repeat handling in workflow editor, store values as passed from ui
 2017-05-23 13:50:26 -04:00
Martin Cech 3d1da8e11d Merge pull request #4089 from mvdbeek/no_global_changes 
[17.05] Do not modify self.app.config.tool_data_path
 2017-05-23 13:19:41 -04:00
Martin Cech aa8aafb109 Merge pull request #4104 from dannon/tags_continued 
[17.05] Change to only inheriting 'name' tags
 2017-05-23 13:01:19 -04:00
guerler 6f8472e525 Fixes repeat handling in workflow editor, store values as passed from ui 2017-05-23 08:08:28 -04:00
Nicola Soranzo 9ebc464ba3 Merge pull request #4100 from martenson/17.05_release_notes 
[17.05] release notes- listify new contributors
 2017-05-22 20:35:51 +01:00
Nicola Soranzo 0b3e29199f Merge pull request #4094 from bgruening/openbabel_update 
[17.05] Open Babel update for datatype converters
 2017-05-22 20:32:45 +01:00
Martin Cech 1bdd1620fe listify new contributors 2017-05-22 14:37:02 -04:00
John Chilton 15556c0a71 Merge pull request #4075 from martenson/17.05_release_notes 
[17.05] release notes
 2017-05-22 14:23:11 -04:00
Martin Cech f9f206ca45 polish release notes, add links to tutorials 2017-05-22 14:20:42 -04:00
Dannon Baker f94fa8edbe Merge pull request #4095 from martenson/contrib-email 
[17.05] add Thoba's email to contributors
 2017-05-22 15:43:42 +01:00
Martin Cech d5f298baa5 add Thoba's email 2017-05-22 10:04:31 -04:00
Bjoern Gruening 9ec6c13fa9 update openbabel to version 2.4.1 2017-05-21 14:12:58 +02:00
mvdbeek a1c14ee8fa Do not modify self.app.config.tool_data_path 
and self.app.config.tool_data_table_config_path during metadata setting.

xref https://github.com/galaxyproject/tools-iuc/issues/1315.

I suspect multiple threads installing tool simultaneously may have led
to self.app.config.tool_data_path and/or
self.app.config.tool_data_table_config_path being set to a temporary
directory. Initial testing looks like this is not necessary.
 2017-05-19 20:04:17 +02:00
Martin Cech 73bf5b4f75 Merge pull request #4086 from hrhotz/patch-1 
Update CONTRIBUTORS.md
 2017-05-19 11:17:31 -04:00
Hans-Rudolf Hotz f1d4ceeb30 Update CONTRIBUTORS.md 
completing the email address
 2017-05-19 17:14:04 +02:00
Martin Cech b1e9552e1b Merge pull request #4070 from dannon/contrib_update 
[17.05] CONTRIBUTORS update
 2017-05-19 10:37:44 -04:00
Dannon Baker 3d6dfa4f60 For people without a commit-signing email, just use the github username (for now -- they can of course change this via PR) 2017-05-19 10:34:05 -04:00
Björn Grüning 4125f79161 Merge pull request #4034 from jmchilton/k8_name_fixed 
[17.05] Sanitize container names sending to Kubernetes.
 2017-05-17 22:36:51 +02:00
Martin Cech c459cd66ba add new datatypes section to the announce 2017-05-17 15:26:10 -04:00
Martin Cech f0570a20a8 link to proper release-bound sample config 2017-05-17 15:14:19 -04:00
Martin Cech c8250ae68a add new options from galaxy.ini diff 2017-05-17 14:56:23 -04:00
Martin Cech 56874e1630 rn improvements 2017-05-17 11:55:07 -04:00
Martin Cech 5aaf95e045 fix links to wiki/hub 2017-05-17 11:13:05 -04:00
Martin Cech 4cb13b2404 add 17.05 to the release list 2017-05-17 11:06:48 -04:00
Martin Cech d1ce1a6237 initial version of RN 2017-05-17 10:59:39 -04:00
Dannon Baker 5b27ad4cb4 CONTRIBUTORS update 16.04 -> 16.07 2017-05-16 12:16:05 -04:00
Dannon Baker b88097ae39 16.07 -> 16.10 contributors update. 2017-05-16 11:13:54 -04:00
Dannon Baker 3807b5d303 16.10 -> 17.01 contributor diff. 2017-05-16 10:49:36 -04:00
Dannon Baker 8c126a8757 Update contributors, diff of 17.01->17.05. 2017-05-16 10:30:40 -04:00
Martin Cech 6614e94a49 Merge pull request #4065 from erasche/fix-4064 
[17.05] Correct webhooks to use Galaxy.root and be compatible with proxy_prefix
 2017-05-15 20:44:36 -04:00
Dannon Baker d3427a1344 Rebuild 2017-05-15 18:14:06 -04:00
guerler bd83608a2f Fix global grid action events 2017-05-15 14:21:17 -04:00
Eric Rasche 6dd145ed1a Try and document a bit 2017-05-14 16:02:09 +00:00