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
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.
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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.
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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
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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
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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
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
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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
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.
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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.
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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.
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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.
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Update IPython accordingly.
2014-10-18 18:38:04 -04:00
John Chilton
c58742e55b
Use newer-style Galaxy configuration of interactive environments.
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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.
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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
Eric Rasche