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Author SHA1 Message Date
John Chilton 6e71a90cdd Merge pull request #151 from natefoo/runtime_stats 
A command line script for collecting stats on job runtimes
 2015-04-28 13:11:33 -05:00
Dannon Baker 374a1826f6 Merge pull request #160 from vavrusa/drmaa-external-jobs 
Fixes for DRMAA when Galaxy instance isn't on a shared volume with compute nodes
 2015-04-27 17:57:28 -04:00
Nate Coraor 32775e9692 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev 2015-04-27 15:22:47 -04:00
Nate Coraor 7861ef5f8c Merge branch 'release_15.05' into dev 2015-04-27 15:20:42 -04:00
Martin Cech 8065fb8c25 Merge pull request #171 from dannon/release_15.05 
Merging several #stable changes forward to 15.05
 2015-04-27 15:17:08 -04:00
Dannon Baker cda6af165a Merge branch 'release_15.03' into release_15.05 2015-04-27 15:10:41 -04:00
Dannon Baker 78aa8e017d Merge pull request #174 from natefoo/fix_shed_check 
[STABLE] Make the `enable_tool_shed_check` option perform as advertised in the sample config file, disable checks at startup.
 2015-04-27 15:07:25 -04:00
Nate Coraor ffbfcc68a4 Make the enable_tool_shed_check option perform as advertised in the 
sample config file. Also disables checks at startup.
 2015-04-27 14:56:30 -04:00
Dannon Baker 4693a948e1 Merge pull request #173 from carlfeberhard/grunt.decompress 
Client build: add grunt command 'grunt decompress' to copy decompressed ...
 2015-04-27 10:48:19 -04:00
Carl Eberhard 435710f505 Client build: add grunt command 'grunt decompress' to copy decompressed scripts to static/scripts to make debugging easier 2015-04-27 10:41:50 -04:00
Dannon Baker 26451f3149 Merge stable changes forward. 2015-04-25 10:43:19 -04:00
Dannon Baker af7c97cdcd Merge pull request #146 from guerler/fix_nested_conditional_defaults 
[STABLE] Fix default values for nested conditional test parameters
 2015-04-25 10:40:50 -04:00
Dannon Baker 8586f7bcac Merge branch 'release_15.05' into dev 2015-04-24 15:19:36 -04:00
Daniel Blankenberg a91ceda3f3 Merge pull request #162 from dannon/sqlalchemy_upgrade_again 
Bump sqlalchemy again for the 1.0.1 bugfix release
 2015-04-24 14:09:12 -04:00
Dannon Baker ea6ac6d303 Bump sqlalchemy again for the 1.0.1 bugfix release 2015-04-24 11:56:02 -04:00
John Chilton e1302cb54e Merge pull request #161 from davebx/dev 
Fix base.util to get the changeset from git.
 2015-04-24 10:44:10 -05:00
Dave B 98beb9365b Fix base.util to get the changeset from git. 
Now that buildbot is using git instead of hg to clone the galaxy code, it should use git instead of hg to determine which revision was cloned.
 2015-04-24 11:41:16 -04:00
Marek Vavrusa ad97c4e83a runners/drmaa: configurable permissive mode for guest users 'allow_guests' 
If enabled, anonymous and usernames that can't be mapped to the real
users will be permitted to run as a Galaxy user.
 2015-04-24 17:34:23 +02:00
John Chilton 8d7e2d6f02 Merge pull request #156 from dannon/release_15.05 
Logging fix in toolshed install manager.
 2015-04-24 10:26:26 -05:00
Marek Vavrusa 954276340c runners/drmaa: support 'embed_metadata_in_job' parameter 
previously, the metadata was always computed in the job - which is a
good default, but it doesn't work if the compute nodes can't see the
Galaxy lib.

this patch adds an option for the 'drmaa' runner so it can compute
metadata externally, after the jobs are finished
 2015-04-24 16:18:09 +02:00
Marek Vavrusa bc7113ba5f runners/drmaa: create the job description json file if not exists 2015-04-24 16:16:10 +02:00
Marek Vavrusa 4f09010d84 runners/drmaa: revert to galaxy credentials for anonymous sessions 
there are no user credentials for anonymous sessions, and the runner
crashes on the log message

this patch reverts to galaxy instance credentials for anonymous sessions
 2015-04-24 16:13:55 +02:00
Marek Vavrusa 43cd2083f6 runners/drmaa: set 'workingDirectory' correctly 
this fixes an issue with when the Galaxy lib (and therefore working
directory) is not shared with the compute nodes
 2015-04-24 16:12:33 +02:00
Dannon Baker 54feee9071 Fix old typo. 2015-04-24 08:39:50 -04:00
Dannon Baker c91ab81ac9 Merge pull request #158 from jmchilton/wf_fix 
Workflow fix for SA 1.0.0.
 2015-04-24 08:38:12 -04:00
John Chilton 034f0f12df Workflow fix for SQ 1.0.0. 
All backgrounded workflows were failing.
 2015-04-24 08:26:30 -04:00
Dannon Baker 96091a5300 Add logging for the case where there's no response (but no exception) in install manager's check versions. 2015-04-24 08:21:00 -04:00
Dannon Baker 48cfa2b8aa Logging fix in toolshed install manager. 2015-04-24 08:02:25 -04:00
Dannon Baker 78ceeae309 Merge pull request #153 from guerler/release_15.03 
[STABLE] Fix base url tool parameter
 2015-04-23 17:02:42 -04:00
Nate Coraor 2ab61d787d Merge pull request #139 from jmchilton/metadata_fixes 
[STABLE] Metadata Fixes
 2015-04-23 16:48:58 -04:00
Nate Coraor 73dd0b1a6f Add some additional documentation/usage in the doc string 2015-04-23 16:03:58 -04:00
Dannon Baker acf9e1bbe9 Merge branch 'release_15.05' into dev 2015-04-23 15:56:59 -04:00
Dannon Baker b55393b85a consistent spacing 2015-04-23 15:56:29 -04:00
Dannon Baker 9a8249f883 Fix external set_meta under sqlalchemy 1.0.0. I have *no* idea how this actually worked before -- we shouldn't have been directly assigning ids when a mapping exists. 2015-04-23 15:56:18 -04:00
Dannon Baker 261bf02dc2 Merge branch 'release_15.05' into dev 2015-04-23 15:47:39 -04:00
Nate Coraor bdbc98c47c Fix the connection string when a database username is provided (reported 
by @afgane in #151).
 2015-04-23 15:46:46 -04:00
Dannon Baker 1e756f84c7 Merge pull request #152 from afgane/node_fix 
Explicitly set eventemitter3 package version (it's a dependency of http-...
 2015-04-23 15:45:00 -04:00
Nate Coraor fd5c41e902 Pull runtime stats from metrics by default (job state history remains an 
option), a couple other minor improvements to the script.
 2015-04-23 15:42:46 -04:00
Dannon Baker 8b0b4ae645 Merge pull request #155 from jmchilton/rollback_async 
[next-stable] Revert "Reduce default step count for beta workflow scheduling to 40."
 2015-04-23 15:32:03 -04:00
John Chilton a9e0297e2e Revert "Reduce default step count for beta workflow scheduling to 40." 
This reverts commit ce90b2da27.

From IRC:

19:01 < g2roboto> [jgoecks] so, about the asynch workflow submission...
19:02 < g2roboto> [jgoecks] ...what happens when there's an error?
19:02 < jmchilton> jgoecks: yes indeed - one of the reasons it is not on by default
19:03 < g2roboto> [jgoecks] hmm, I just updated my dev branch, made no other changes, and it was "on"
19:03 < jmchilton> Big workflow?
19:03 < g2roboto> [jgoecks] yes
19:03 < jmchilton> how many steps?
19:03 < g2roboto> [jgoecks] 43
19:03 < jmchilton> Ah - just over the 40 cutoff
19:03 < jmchilton> I can turn the default back up if you would like
19:04 < g2roboto> [jgoecks] where the threshold? I need to figure out why the workflow is failing, which is my
                  biggest issue right now
19:04 < jmchilton> we just dropped it from 250 to 40
19:05 < jmchilton> if you want to just change it - I can give you the option , one second
19:05 < jmchilton> force_beta_workflow_scheduled_min_steps=40
19:06 < g2roboto> [jgoecks] If there's no way to show or recover from error, 40 may be too low.
19:06 < jmchilton> yeah - I think you are right
19:06 < jmchilton> clearly - the fact that someone has already hit the problem
19:07 < jmchilton> the long term solution was I think to a invocations into the history panel - but maybe a medium
                   term solution is just to montior the workflow invocations like tool shed installs... hmm... at
                   any rate I'll put the default back up
 2015-04-23 15:11:30 -04:00
guerler d3ba1a748a Fix base url tool parameter 2015-04-23 15:05:00 -04:00
John Chilton be9796f2eb Merge pull request #150 from dannon/fix_external_meta 
Fix external set_meta under sqlalchemy 1.0.0.
 2015-04-23 13:57:20 -05:00
Enis Afgan 5abb8ad3ca Explicitly set eventemitter3 package version (it's a dependency of http-proy but the just released v1.0.0+ broke compatibility) 2015-04-23 14:14:54 -04:00
Nate Coraor ef69881e56 Added a command line script for collecting stats on job runtimes to help 
admins make decisions about how/where to run jobs.
 2015-04-23 12:56:06 -04:00
Dannon Baker b946e3a38f consistent spacing 2015-04-23 12:34:06 -04:00
Dannon Baker cbba7f4927 Fix external set_meta under sqlalchemy 1.0.0. I have *no* idea how this actually worked before -- we shouldn't have been directly assigning ids when a mapping exists. 2015-04-23 12:22:10 -04:00
Nate Coraor e44c8db9de Bump version to 15.07.dev 2015-04-22 15:11:53 -04:00
Nate Coraor 52a2a8d649 Bump version to 15.05rc1 2015-04-22 15:11:09 -04:00
Nate Coraor 86880990a8 Bump version to 15.03.2 v15.03.2 2015-04-22 15:05:21 -04:00
Nate Coraor b7e252c2af Merge branch 'release_15.03' into dev 2015-04-22 14:31:45 -04:00