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2546030c66fb453f98035ddf176ffb2b103d8d8d
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11832 Commits
Author SHA1 Message Date
John Chilton 2546030c66 Do not require use_remote_user to be explicitly set if single_user is set. 
Based on comments from @erasche - https://github.com/galaxyproject/galaxy/pull/2165#issuecomment-210048830.
 2016-04-14 12:41:18 -04:00
John Chilton e67506802d Implement config.single_user = <email> option. 
Let Planemo and other such applications serve a full-fledged Galaxy instance without having to worry about logins, etc....
 2016-04-14 12:41:18 -04:00
Nate Coraor a919e98be3 Merge branch 'release_16.04' into dev 2016-04-14 11:15:43 -04:00
Nicola Soranzo 148d4ee88d Merge pull request #2145 from mvdbeek/pbs_ncpu 
Use "$NCPUS" if defined to set GALAXY_SLOTS
 2016-04-14 15:50:06 +01:00
Nate Coraor 84ef4fd99f Update pulsar-galaxy-lib in pinned-requirements.txt (it was already 
updated in requirements.txt).
 2016-04-14 10:09:26 -04:00
Nate Coraor 9bb5978d53 Merge pull request #2156 from guerler/fix_data_001 
[16.04] Add tool parameters back to parameters and expose for certain tools
 2016-04-14 09:56:29 -04:00
guerler a889e19af7 Fix parameter wrapping 2016-04-14 07:23:06 -04:00
Eric Rasche 3d5663e97f Remove double escaping 2016-04-13 21:35:50 +00:00
guerler ac14139714 Add blank line 2016-04-13 15:50:44 -04:00
guerler 82e9ce827c Add tool parameters back to parameters 2016-04-13 15:34:11 -04:00
Eric Rasche dd05f0ab24 Escape everything 2016-04-13 18:36:36 +00:00
Eric Rasche 6ce9bd8220 Minor touch up for consistency 2016-04-13 18:21:19 +00:00
Eric Rasche 4d729ff890 Typo 2016-04-13 17:27:14 +00:00
Eric Rasche a3e925cc1b Fix second nitpick 2016-04-13 17:24:26 +00:00
Eric Rasche cba10c812b Fix nitpick 2016-04-13 17:23:32 +00:00
Eric Rasche df481dabe0 Remove unused import 2016-04-13 16:34:26 +00:00
Eric Rasche a6d95d0909 Fix flake8 by reverting a previous commit 2016-04-13 16:32:37 +00:00
Marius van den Beek 3c97d30cd6 Use "$NCPUS" if defined to set GALAXY_SLOTS 
On our PBS cluster we do not have $PBS_NCPUS, and $PBS_NODEFILE contains the
hostname of the nodes the task runs on. But we do have "$NCPUS" with the
correct number of CPUS.
 2016-04-13 10:39:43 +02:00
Eric Rasche 5923a67301 Fix sanitization completely 2016-04-13 00:48:09 +00:00
Eric Rasche c2cff25826 Use CGI for escaping 2016-04-13 00:38:25 +00:00
Eric Rasche e9823573e3 Add HTML Template 2016-04-13 00:25:31 +00:00
Eric Rasche 024ae7a286 bail earlier if no SMTP server is configured 2016-04-12 23:40:39 +00:00
Nicola Soranzo 408827e251 Merge branch 'release_16.04' into dev 2016-04-12 14:35:37 +01:00
Nate Coraor f03c037556 Merge pull request #2122 from jmchilton/pulsar_metadata 
[16.04] Rev Pulsar to 0.7.0.dev3.
 2016-04-12 09:01:27 -04:00
Nicola Soranzo baf1bd639f Merge branch 'release_16.04' into dev 2016-04-11 20:26:42 +01:00
Nicola Soranzo 6317297cad Merge branch 'release_16.01' into release_16.04 2016-04-11 20:24:46 +01:00
Martin Cech f759961a29 mention planemo in the error message for disabled TS pushing 
rephrase to Norwegian
 2016-04-11 12:56:42 -04:00
carlfeberhard 99c2a6b623 API: add server_starttime to api/configuration 
Adds key server_starttime to the JSON returned from api/configuration.
This is the epoch time since the last server restart and may be
convenient for use in client-side caching.

This moves server_starttime from web/framework/helpers/__init__.py
(for use in script cache-busting) to web/framework/base.py.

On the client, this should be available to all pages as:
Galaxy.config.server_starttime.
 2016-04-11 10:38:20 -04:00
John Chilton 84ad9c2ee2 Rev Pulsar to 0.7.0.dev3. 
- Fixes numerous problems mostly notably fixes external metadata generation and job metrics collection for recent Pulsar. This was broken when tools were given clean working directory.
 - Produce a new message if an older Pulsar version is targetted via REST of library (should help with upgrading to Galaxy 16.04).
 - Newer pulsar lib allows more flexible configuration of managers - update documntation to reflect this.
 2016-04-10 23:54:02 -04:00
John Chilton 5739f25003 Update version to 16.07.dev 2016-04-08 14:00:47 -04:00
John Chilton 579846fdfb Update version to 16.04.rc1 2016-04-08 13:59:37 -04:00
John Chilton 0945809099 Merge remote-tracking branch 'upstream/release_16.01' into dev 2016-04-08 13:22:03 -04:00
John Chilton ce27863086 Merge pull request #2099 from davebx/shed_model_trim 
Consolidate duplicated method in tool_shed/model.
 2016-04-08 13:21:59 -04:00
John Chilton 0d616af28a Merge pull request #2106 from davebx/hg_middleware 
Workaround for the toolshed's hgweb.
 2016-04-08 13:20:22 -04:00
John Chilton 6f6554ea8c Merge pull request #2104 from Christian-B/unlinked_depenency_resolver_update_to_new_dependency 
Updated to Dependency change in b167a741a4
 2016-04-08 13:18:26 -04:00
Dave Bouvier 5ead1c089f Remove refactoring that belongs in a different PR. 2016-04-08 12:38:56 -04:00
John Chilton be10253b69 Remove stray print statements. 
Not Python 3 compat.
 2016-04-08 10:28:09 -04:00
John Chilton 2744d5541f Merge pull request #2093 from davebx/move_scripts 
Move scripts out of lib/tool_shed.
 2016-04-08 09:54:44 -04:00
John Chilton ef604a75e5 Merge pull request #2102 from natefoo/global-drmaa-session 
Convert the DRMAA runner to use Pulsar's DRMAA session wrapper
 2016-04-08 09:47:24 -04:00
John Chilton 40953369e6 Merge pull request #2107 from ThomasWollmann/master 
Fix cli runner: use embed_metadata_in_job parameter
 2016-04-08 09:44:53 -04:00
Thomas Wollmann fb26d27b97 fixed lint error 2016-04-08 13:48:13 +02:00
Thomas Wollmann bf8292ecc1 fixed lint error 2016-04-08 12:30:56 +02:00
Thomas Wollmann 0548e8ed30 added missing import 2016-04-08 12:20:50 +02:00
Thomas Wollmann 4e15dc4e74 typo 2016-04-08 12:17:36 +02:00
Thomas Wollmann 91c4ccfc90 added default DEFAULT_EMBED_METADATA_IN_JOB value 2016-04-08 12:09:58 +02:00
Thomas Wollmann 987aac34bb removed comment 2016-04-08 11:00:34 +02:00
Thomas Wollmann ab242a84b1 fixed bug with cli runner analogous to https://github.com/dpryan79/galaxy/commit/3536ff923cf736b2dbefab3e04b7fcd79b909d22 2016-04-08 11:00:13 +02:00
Dave Bouvier 2a76eb19c1 Remove unused import, restore used import. 2016-04-07 20:38:11 -04:00
Martin Cech 50268cb8ca fix missing call; add docs and refactor a bit 2016-04-07 18:22:42 -04:00
Dave Bouvier b4e768b828 Workaround for the toolshed's hgweb. 2016-04-07 16:54:43 -04:00