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18,557 Commits 69 Branches 243 Tags
1f62be4e1aec00a82b4c66209d486ebda695554a
Commit Graph
421 Commits
Author SHA1 Message Date
Dannon Baker 79562cf8d2 Merge branch 'master' into dev 2015-07-01 14:29:13 -04:00
guerler 8b7a455b01 Disable custome tooltips for histograms 2015-06-30 13:46:12 -04:00
Eric Rasche fcc706e8d0 Whitespace/other small fixes 2015-06-30 11:50:27 -05:00
Bjoern Gruening 43b2b7929b change docker_host to docker_hostname to be more explicit 2015-06-17 15:54:18 +02:00
Bjoern Gruening 77169a2078 add docker_host as configurable option 2015-06-16 17:23:58 +02:00
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
guerler cc1f56a118 Fix load order of require and d3 2015-05-27 11:18:04 -04:00
Nicola Soranzo 48023ed374 Remove outdated sentence. 2015-05-15 12:45:16 +01:00
Björn Grüning 8965dd2cbf Pin the IPython Docker Image to the 15.05. 
From now on we pin every Galaxy release to a special ipython-notebook image.
 2015-05-14 21:23:27 +02:00
John Chilton ed8112b422 Fix problems introduced in IE refactorings. 2015-05-14 14:32:49 -04:00
John Chilton 998d0e8a8c IE: Move IPython-specific password hashing out of framework into plugin. 
See dicussion here - https://github.com/erasche/galaxy/commit/23459f318507255a2bb1d1fb647e1581bd2090e1.
 2015-05-14 10:15:49 -04:00
John Chilton 624d540c04 IEs: Move temp dir handling into ie_request to simplify interface. 2015-05-13 23:08:21 -04:00
John Chilton 55e523ea63 Introduce new IE launch abstraction. 
In addition to reducing duplication between IPython and RStudio - it also shields them from low-level details and creates an interface we could more reasonably generalize to something like qsubing the docker commands or using Docker Swarm.
 2015-05-13 23:08:20 -04:00
John Chilton 23459f3185 Expose and cache raw IE password to simplify RStudio plugin. 2015-05-13 23:08:20 -04:00
John Chilton 0a5ec3e8d3 Merge remote-tracking branch 'jmchilton/dev' into rstudio 2015-05-13 21:06:21 -04:00
Eric Rasche a9fb12a146 Update RStudio to new IE infrastructure 2015-05-11 17:11:04 -05:00
Eric Rasche 285eece97a Update RStudio to new IE infrastructure 2015-05-11 17:07:33 -05:00
John Chilton f3e81f148f Eliminate potential boilerplate code in new IE env stuff. 2015-05-11 09:07:45 -04:00
John Chilton eb2034ac6e Merge remote-tracking branch 'erasche/ie-updates2' into pr229 
Conflicts:
	config/plugins/interactive_environments/ipython/config/ipython.ini.sample
 2015-05-10 23:17:17 -04:00
Eric Rasche 213f21f890 Updates to take advantage of #229 infrastructure 2015-05-10 21:52:04 -05:00
Eric Rasche 201f2db184 Pin to :dev 2015-05-08 17:07:04 -05:00
Nate Coraor a85eadfb74 Merge pull request #243 from carlfeberhard/vis.remove-template 
Visualizations registry: switch to entry_point config definition for …
 2015-05-08 10:26:29 -04:00
Carl Eberhard 11b2fbcb3b Visualizations registry: switch to entry_point config definition for built-in visualizations 2015-05-07 16:04:25 -04:00
Martin Cech d28ea45556 Merge branch 'release_15.05' into dev 
Conflicts:
	config/plugins/visualizations/common/templates/script_entry_point.mako
 2015-05-07 13:09:24 -04:00
Eric Rasche 2c04d1a768 Pin to :dev 2015-05-07 11:12:02 -05:00
Nate Coraor 049e9e8024 Merge remote-tracking branch 'upstream/release_15.03' into release_15.05 
Conflicts:
	config/plugins/interactive_environments/ipython/config/ipython.ini.sample
 2015-05-07 11:57:59 -04:00
Eric Rasche 7e9df4714a Migrated to correct location 2015-05-06 16:31:28 -05:00
John Chilton a15a2bd2b2 Fix Python 2.6 incompat in script_entry_point.mako. 2015-05-06 14:06:16 -04:00
Eric Rasche b2b25f595b Update documentation on the get() function 2015-05-06 11:48:37 -05:00
Eric Rasche 7d85ae2229 Merge remote-tracking branch 'bgruening/ie-updates' into ie-updates2 2015-05-06 11:42:31 -05:00
Bjoern Gruening 9cdd688595 Bind the IPython IE to a fixed Docker Image 2015-05-01 20:54:53 +02:00
Bjoern Gruening 71c51e9a83 Remove write_conf_file() 2015-04-30 18:09:43 +02:00
Marek Vavrusa bc8bdadca8 datatypes: extracted TabularData superclass from Tabular, CSV subclass 2015-04-30 17:20:32 +02:00
Bjoern Gruening 04b8a884bd Pass all configuration variables to Docker using ENV, rather than a config file. 2015-04-30 14:26:12 +02:00
Bjoern Gruening 72bbace9c4 add debug option to the example inject command 2015-04-30 14:17:49 +02:00
Carl Eberhard ed36e625bb Visualizations registry: refactor the relationship between plugins, the visualization controller, rendering, and rendering saved visualizations, minor fixes; Extend testing; Scatterplot: fix baseUrl resolution when used in own window 2015-04-28 15:41:01 -04:00
Carl Eberhard d14aba2408 Visualizations registry: test script entry point; minor cleanup 2015-04-24 16:53:30 -04:00
Carl Eberhard c4053f1427 Visualizations registry: add script_entry_point.mako and late_javascripts to visualization_base.mako 2015-04-24 13:07:55 -04:00
Carl Eberhard 2fe38db10b Visualizations registry: *actually* correct the default title in visualization_base.mako 2015-04-24 12:57:27 -04:00
Carl Eberhard 385b4e71d6 Visualizations registry: split plugin classes: interactive environments, script entry, static file entry; correct default title in visualization_base.mako 2015-04-24 12:51:47 -04:00
Bjoern Gruening cef67fb4f1 Add command_inject to IE config files. This makes it possible to modify the executed "docker run" command from the config file. 2015-04-18 16:54:34 +02:00
yhoogstrate b29ea767d9 Update scatterplot-display.js 2015-04-07 15:51:55 +02:00
yhoogstrate fc51b85d2c Update scatterplot-edit.js 
automatically generated by grunt
 2015-04-07 15:50:30 +02:00
yhoogstrate af8ddb14a3 ScatterPlot No API connection for nested www_root 
ScatterPlot makes use of a hardcoded API url which is incorrect for certain server configuratoins. Currently these servers need to be manually configured to link to the correct API URL. This patch creates the correct URL from the parental variable parent.galaxy_config.root and returns "/" if this variable can not be found. More visualisations suffer from this bug and have to be patched as well.
 2015-04-07 14:59:29 +02:00
John Chilton 543eb5b489 Provide convenience attribute for logging in IE mako. 2015-04-02 08:54:56 -04:00
Carl Eberhard 4e5218f4dc Charts: fix script tag order to prevent new version of Backbone loading as AMD; UI, Histories: remove debug statement 2015-03-16 10:48:52 -04:00
guerler 5bee11df4c Charts: Add data point labels to all nvd3 charts (without this gene expression analysis using scatter plots is not very useful) 2015-02-28 12:12:10 -05:00
guerler e6399874e8 Charts: Fix missing data message 2015-02-24 19:41:30 -05:00
guerler e2f5e9e326 Charts: Rebuild and update charts 2015-02-24 19:08:36 -05:00
Carl Eberhard 8a79dfe99e UI, multi-history: minor fixes, tabindeces, cleanup; Scatterplot: refactor mako and fix missing figure tag; Client build, styles: add jstree to cleaned files 2015-02-16 11:43:22 -05:00