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Author SHA1 Message Date
John Chilton 620accaaad Extend workflow editor to allow output collections in tools. 
Mostly test cases - because I guess I could have sworn it was going to be harder than this.
 2015-06-04 14:38:38 -04:00
John Chilton 4872c9a895 Modify galaxy.workflow_editor.canvas.js verbage for output collections. 2015-06-04 14:38:37 -04:00
Dannon Baker 8d95a37515 Merge pull request #302 from martenson/update-admin-page 
update and clarify admin menu
 2015-06-04 12:34:06 -04:00
Daniel Blankenberg 10c3f41e68 Merge pull request #307 from martenson/fix-mako-webapp 
fix shared mako templates that would not work properly with TS
 2015-06-04 11:50:35 -04:00
Martin Cech 9c89d43875 fix shared mako templates that would not work with TS 
by also looking for 'app' within context when 'webapp' is not present
and defaulting to 'galaxy' afterwards
 2015-06-04 10:31:44 -04:00
John Chilton 0dfa1c9689 Merge pull request #191 from vavrusa/table-datatype 
[WIP] CSV datatype
 2015-06-04 10:07:04 -04:00
Marek Vavruša 14b7cd6821 Merge pull request #1 from jmchilton/table 
Updates for PR #191 (checked the 508194f)
 2015-06-04 16:02:45 +02:00
John Chilton 43166664f2 Merge pull request #297 from bgruening/patch-3 
export ENV vars from all dependend repositories
 2015-06-03 12:19:14 -04:00
John Chilton f65da5f2c7 Merge pull request #269 from martenson/future-release-notes 
include approx. dates for 15.07 release
 2015-06-03 11:04:54 -04:00
John Chilton 508194f223 Fix sample datatype definition for CSV. 
For me it seems like the viz plugins only detect the datatype if the plugin datatype (e.g. ``tabular.CSV``) is explicitly instantiated by some extension directly. In your sample config you have ``subclass="True"`` so ``tabular.CSV`` wasn't working. This is probably a bug with the datatype code - but nonetheless I think dropping subclass from the sample is an okay workaround - because it does seem to be a direct mapping.
 2015-06-03 10:52:59 -04:00
John Chilton 884e824d72 Merge remote-tracking branch 'vavrusa/table-datatype' into dev. 
Conflicts:
	lib/galaxy/datatypes/tabular.py
 2015-06-03 10:52:42 -04:00
Dannon Baker f0b4f1c81e Merge branch 'guerler-workflow_form_000' into dev 2015-06-02 18:45:16 -04:00
Dannon Baker c69945ff95 Merge new workflow editor. 2015-06-02 18:44:56 -04:00
Dannon Baker ac4740f91d Merge branch 'release_15.05' into dev 2015-06-02 11:15:51 -04:00
Dannon Baker 4eea86c8b7 Merge pull request #301 from mvdbeek/bootstrapping-fix 
Exclude curly braces from API-key to fix toolshed bootstrapping.
 2015-06-02 09:44:47 -04:00
Dannon Baker ae25e3054e Merge pull request #304 from jmchilton/1505_histories_share_fix 
[15.05] Backport Bjoern's bug in history sharing.
 2015-06-02 08:54:06 -04:00
Bjoern Gruening 4268a7ee57 fix unit test 2015-06-02 14:52:40 +02:00
Björn Grüning 7294bd0af3 Fix bug in history sharing. 2015-06-02 08:38:55 -04:00
Dannon Baker e56b2a3433 Merge pull request #274 from dpryan79/dev 
Add usage information to python cleanup scripts
 2015-06-02 07:57:02 -04:00
John Chilton 60f43733ee Merge pull request #299 from nsoranzo/dev 
Improve auth_conf.xml.sample documentation.
 2015-06-01 22:11:22 -04:00
Dannon Baker 8c3fdaa874 Merge 15.05 to dev 2015-06-01 14:14:02 -04:00
Dannon Baker ef99cca5d1 Merge branch 'release_15.03' into release_15.05 2015-06-01 14:03:09 -04:00
Martin Cech dbe91aa316 reorder; add links; show help only if option is present 2015-06-01 13:42:59 -04:00
Martin Cech 8e68ea23b6 fix minor typo 2015-06-01 10:50:31 -04:00
Martin Cech d4aa8bbd91 open links in _blank 2015-06-01 10:43:27 -04:00
Martin Cech 6d08accfa4 fix minor typos, add wiki link 2015-06-01 10:37:30 -04:00
Martin Cech a86ee81c28 update and clarify descriptions, cleanup admin menu 2015-06-01 10:30:56 -04:00
Marius van den Beek bf9f8cd283 Exclude curly braces from API-key to fix toolshed bootstrapping. 2015-06-01 16:19:14 +02:00
Nicola Soranzo 30872e72bb Improve auth_conf.xml.sample documentation. 2015-06-01 11:58:08 +01:00
John Chilton 608c827559 Merge pull request #287 from Unode/custom_ldap_options 
Allow setting connection options for LDAP authentication
 2015-05-31 21:18:23 -04:00
Martin Cech 686ac9913a Merge pull request #296 from bgruening/patch-2 
gzip is imported twice
 2015-05-31 11:35:23 -04:00
Björn Grüning 5974167407 export ENV vars from all repositories 
This will export ENV vars from all given repository dependencies and not only the last one.
Only taking the last one seems arbitrary to me and it makes the tool_dependencies.xml files a bit easier to write.
 2015-05-31 14:04:24 +02:00
Björn Grüning b4cf6dba76 gzip is imported twice 
Remove one redundant gzip import.
 2015-05-31 13:31:10 +02:00
John Chilton 0a0890a040 Merge pull request #294 from Unode/html_validation 
Remove bad HTML tags from login template
 2015-05-29 08:25:01 -05:00
Renato Alves 253493c393 Allow passing advanced options to the LDAP connection 
Useful to configure the connection if ldap.conf and/or ldaprc cannot be used

auth_conf.xml.sample includes an example to connect to LDAPS using
self-signed certificates.
 2015-05-29 13:56:48 +01:00
Aysam Guerler 4445092410 Merge pull request #293 from jmchilton/history_tag_fix_15.03 
[15.03] Fix tag creation via /tags API endpoints.
 2015-05-28 11:44:53 -04:00
Renato Alves aa857fcdbd Remove bad HTML tags from login template 2015-05-28 16:16:14 +01:00
John Chilton 5949abb2ce Merge pull request #289 from dpryan79/condor_fixes 
Condor fixes
 2015-05-28 09:16:03 -05:00
John Chilton 2ca8f7665b Fix tag creation via /tags API endpoints. 
Add test case to at least check for exceptions such as those reported.

Closes galaxyproject/bioblend#145.
 2015-05-27 12:51:53 -04:00
John Chilton 0b825676e7 Merge pull request #291 from guerler/trackster_000 
Trackster: Fix load order of require and d3
 2015-05-27 10:45:14 -05:00
guerler e76e8229ee Trackster: Fix load order of require and d3 2015-05-27 11:31:55 -04:00
carlfeberhard 3c12d90730 Merge pull request #290 from guerler/charts_000 
Fix load order of require and d3
 2015-05-27 11:27:02 -04:00
guerler cc1f56a118 Fix load order of require and d3 2015-05-27 11:18:04 -04:00
dpryan79 6cc83bf0b9 Ensure that asbool is imported 2015-05-27 13:16:29 +02:00
dpryan79 3536ff923c Allow the condor job runner to respect the embed_metadata_in_job parameter 2015-05-27 13:02:23 +02:00
Dannon Baker 9f754357d9 Merge pull request #288 from jmchilton/history_tag_fix_15.05 
[15.05] Fix tag creation via /tags API endpoints.
 2015-05-26 11:42:19 -04:00
John Chilton 44c8e74c29 Fix tag creation via /tags API endpoints. 
Add test case to at least check for exceptions such as those reported.

Closes galaxyproject/bioblend#145.
 2015-05-25 22:31:09 -04:00
guerler 229577b5c2 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into workflow_form_000 2015-05-24 15:38:50 -04:00
guerler d01c108375 Reduce form mako to json generation, load form just once 2015-05-24 15:37:00 -04:00
John Chilton 3946ff50bb Merge pull request #80 from erasche/jbrowse-ie 
Add EDAM IDs to datatypes
 2015-05-22 09:42:59 -05:00