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46 Commits
Author SHA1 Message Date
Eric Rasche 81f842743d Merge pull request #1131 from bgruening/IE_iobio 
Add BAM iobio visualisation as Interactive Environment
 2015-11-19 15:02:37 -06:00
Bjoern Gruening af36ca6d94 add BAM iobio visualisation as Interactive Environment 2015-11-19 18:58:43 +01:00
Nate Coraor c435141326 Built image tag differs from intended. 2015-11-13 10:55:25 -05:00
Nate Coraor d824cca31f In interactive environments, the /import volume can now be made 
conditional. Also, fix a bug when using a proxy for the node proxy and
cookie_path is /
 2015-11-12 16:56:16 -05:00
Eric Rasche 5f4502b650 Pin images for next release of Galaxy 2015-10-05 14:50:35 -05:00
John Chilton 6d3ea7ee00 Merge pull request #790 from erasche/gie-docker-launch 
Refactor GIE Launching to use -P
 2015-09-25 16:05:35 +01:00
Eric Rasche b4bbd1c2f1 Make use of proxy path in appropriate places 2015-09-23 16:12:01 -05:00
Björn Grüning b1d642a6ec Update ipython.ini.sample 2015-09-23 22:42:27 +02:00
Eric Rasche 1d78033625 Merge branch 'gie-docker-cmd' into gie-docker-launch 2015-09-23 15:09:40 -05:00
Eric Rasche 1ad3308b49 Remove small formatting issue 2015-09-23 15:09:03 -05:00
Eric Rasche a76ba39321 Update against gie-docker-cmd 2015-09-23 14:45:35 -05:00
Eric Rasche 10af450127 Move run into python from template 2015-09-23 14:22:32 -05:00
Eric Rasche a02df53f33 Correct IPython notebooks to new URL 2015-09-23 12:51:37 -05:00
Eric Rasche 04c5e6864c Merge branch 'gie-docker-cmd' into gie-docker-launch 2015-09-23 12:27:40 -05:00
Eric Rasche 175f89bdc8 Hardcode defaults, per @jmchilton's comments 2015-09-23 11:27:52 -05:00
Eric Rasche 484578936b Refactor to use -P 
This is a major refactoring to use the -P option of docker
which should simplify some of our deployment like running docker containers
on another host. In support of #372
 2015-09-23 11:24:37 -05:00
Eric Rasche 56ac2c0f13 Revert command inject and document rationale 2015-09-23 10:50:05 -05:00
Eric Rasche 52dfd589b9 Unify the docker command, command_inject, and command_wrapper 2015-09-23 10:34:36 -05:00
Jelle Scholtalbers 130b3f2d75 Add docker command wrapper. For example, to change the current group to docker, which is needed when user belongs to (too) many groups) 2015-09-23 14:28:03 +02:00
Jelle Scholtalbers fadd1990e6 moved changes to lib/galaxy/web/base/interactive_environments.py 2015-07-15 22:47:30 +02:00
Jelle Scholtalbers f8f36620ec Fix issue with docker not being able to mount tmp dir 2015-07-15 18:39:42 +02:00
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 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 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 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
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 b2b25f595b Update documentation on the get() function 2015-05-06 11:48:37 -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
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
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
John Chilton 543eb5b489 Provide convenience attribute for logging in IE mako. 2015-04-02 08:54:56 -04:00
John Chilton e8b4f8085f Remove files indicated by Bjoern. 
No need to LICENSE this differently, INSTALL.md probably should be rewritten, and .gitignore is now pointless.

https://bitbucket.org/galaxy/galaxy-central/pull-request/533.
 2014-10-19 17:38:30 -04:00
John Chilton 9ad5e12e1c Improvements to IPython configuration sample. 
Allow overiding galaxy_url directly (don't do this - use galaxy_infrastructure_url - but there will be deployments). Don't require setting older port range deployment options.
 2014-10-18 18:38:04 -04:00
John Chilton 5547bb7df5 Refactor interactive environment plugin framework out of IPython and into Galaxy. 
Rely on more Python and less on mako, setup a small shared common mako file in config/plugins/interactive_environments/common/ie.mako. Move ie.js into client/galaxy/scripts/galaxy.interactive_environments.js and extract IPython's require config out so it doesn't have to directly reference client/galaxy/scripts/galaxy.interactive_environments.js (I doubt it is where that file actually should be).
 2014-10-18 18:38:04 -04:00
John Chilton 06175f83f9 Update plugin framework to distinguish between viz and IE frameworks. 
Update IPython accordingly.
 2014-10-18 18:38:04 -04:00
John Chilton c58742e55b Use newer-style Galaxy configuration of interactive environments. 
Setup a sample file and fallback on it if a materialized .ini isn't present. Use .ini instead of .conf for consistency with the rest of the config directory.
 2014-10-18 18:38:04 -04:00
John Chilton a52f4c21ee Split interactive_environments out into their own plugin directory. 
Pragmatically this allows visualizations to be enabled by default but not IPython stuff and provides a spot to put a warning about security issues. More abstractly I think it provides a nice separation (initially though superficial) between these plugin types.
 2014-10-18 18:38:04 -04:00