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IE Updates#229

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jmchilton merged 25 commits intogalaxyproject:devfrom
hexylena:ie-updates2
May 14, 2015
Merged

IE Updates#229
jmchilton merged 25 commits intogalaxyproject:devfrom
hexylena:ie-updates2

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@hexylena
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@hexylena hexylena commented May 6, 2015

  • These updates switch IEs over to using the environment to configure them, rather than a yaml file.
  • Updates to the proxy to provide for our special snowflake RStudio IE.

To resolve before merging:

  • @bgruening, with this we'll need to push a new branch/tag for the next release of IPython, and then pin Galaxy to it here. What release number should that be/what branch? :)

Labelled WIP due to above, single commit that has to happen before OK to merge.

CC @bgruening @jmchilton

bgruening and others added 12 commits April 23, 2015 15:45
@bgruening
add emboss datatypes
660b920
@bgruening
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev
e31e8d3
@bgruening
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev
21e10e7
@bgruening
Merge branch 'dev' of https://github.com/galaxyproject/galaxy into dev
8ce2c86
@bgruening
add debug option to the example inject command
72bbace
@bgruening
Refactore the configuration handling and add a new get_conf_dict() fu…
618078c 
…nction.
@bgruening
Pass all configuration variables to Docker using ENV, rather than a c…
04b8a88 
…onfig file.
@bgruening
Remove write_conf_file()
71c51e9
Merge remote-tracking branch 'bgruening/ie-updates' into ie-updates2
7d85ae2
Unstage @bgruening's datatype conf changes
b202c45
Update documentation on the get() function
b2b25f5
RStudio non-standards-compliant hacks
8bf094e 
RStudio doesn't like lower case HTTP headers. It also doesn't like
a charset specified in content type. Thus, those get modified appropriately
and everything plays nicely
@hexylena hexylena mentioned this pull request May 6, 2015
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@bgruening
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bgruening commented May 7, 2015

Obviously +1 from me :)
We need the get_conf_file() function also for other IE's.

@erasche if we now label every release and make Galaxy releases tracking them, we could track master (aka :latest) and not use :dev in IPython, otherwise Galaxy:dev should track IPython:dev. In the latter case master is not really used, we could sync master with the latest-stable branch.

[Edit: s/write_/get_/]

@hexylena
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hexylena commented May 7, 2015

write_conf_file() you renamed to get_conf_dict()...is there any way you could modify your other IEs to use the environment instead? Or maybe add something into your startup scripts for them that would write out a yaml file? Sorry...just want to avoid bringing that back since I like the environment so much more than special yaml files.

@bgruening hmm, ok. So I should set the image to bgruening/galaxy-ipython-notebook:dev then? I'll do the same for RStudio.

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bgruening commented May 7, 2015

@erasche everything fine, was a s/write_/get_/ typo.
bgruening/galaxy-ipython-notebook:dev sounds good.
I need also to change the next-stable branch of Galaxy to bgruening/galaxy-ipython-notebook:15.05

@hexylena hexylena mentioned this pull request May 7, 2015
Merged
@hexylena hexylena force-pushed the ie-updates2 branch 2 times, most recently from b434140 to 8bf094e Compare May 7, 2015 19:13
Eric Rasche and others added 6 commits May 7, 2015 14:15
Remove unused import
9ab9297
@carlfeberhard
Visualizations registry: switch to entry_point config definition for …
11b2fbc 
…built-in visualizations
@natefoo
Merge pull request galaxyproject#243 from carlfeberhard/vis.remove-te…
a85eadf 
…mplate

Visualizations registry: switch to entry_point config definition for …
@dannon
Merge pull request galaxyproject#248 from Unode/patch-1
f20c961 
Ignore sample files from toolshed installed tools
@jmchilton
Merge pull request galaxyproject#239 from erasche/rdata2
f7af19b 
Add RData and RData.gz formats
Pin to :dev
201f2db
@hexylena
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hexylena commented May 8, 2015

This should be ready to go as-is, @jmchilton

@jmchilton jmchilton removed the wip label May 8, 2015
hexylena pushed a commit to hexylena/galaxy that referenced this pull request May 11, 2015
Updates to take advantage of galaxyproject#229 infrastructure
213f21f
hexylena added a commit to hexylena/galaxy that referenced this pull request May 11, 2015
@hexylena
Merge pull request #2 from erasche/rstudio2
67e7dcf 
Updates to take advantage of galaxyproject#229 infrastructure
@jmchilton
Merge remote-tracking branch 'erasche/ie-updates2' into pr229
eb2034a 
Conflicts:
	config/plugins/interactive_environments/ipython/config/ipython.ini.sample
@hexylena hexylena changed the title [WIP] IE Updates IE Updates May 11, 2015
@jmchilton
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jmchilton commented May 11, 2015

Have you tried this with the latest IPython dev image - I'm having trouble getting this to work but I don't know if it is user error, this change, an IPython change, or Docker issues inside the VM?

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hexylena commented May 11, 2015

@jmchilton will play with it shortly...

@hexylena
Merge pull request #3 from jmchilton/pr229
7851c7e 
Merge dev and add tighter env abstraction.
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hexylena commented May 11, 2015

@jmchilton okay, I can confirm that the ipython:dev (1d542ae65161) is working fine for me. This is on a test branch with ie-updates2 and rstudio merged in. You have any debugging information regarding it?

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hexylena commented May 11, 2015

Notes to self/@bgruening: this is the latest change to IE framework. jmchilton@f3e81f1

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bgruening commented May 11, 2015

@jmchilton also works for me. Is the container starting at all?

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jmchilton commented May 11, 2015

Container is starting but my proxy is stating "Proxy target undefined". I'll keep working on this - thanks for the confirmation.

Eric Rasche added 2 commits May 11, 2015 17:15
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jmchilton commented May 14, 2015

Finally got it - found a bug in bgruening/docker-ipython-notebook I think and will follow up there. On this end - everything looks really good! Thanks a ton @bgruening and @erasche - the awesomeness never stops with you guys.

jmchilton added a commit that referenced this pull request May 14, 2015
@jmchilton
Merge pull request #229 from erasche/ie-updates2
687a894 
IE Updates
@jmchilton jmchilton merged commit 687a894 into galaxyproject:dev May 14, 2015
jmchilton added a commit to jmchilton/galaxy-rstudio-machine that referenced this pull request May 14, 2015
@jmchilton
Update for galaxyproject/galaxy#229 being merged.
df8484e
@jmchilton jmchilton mentioned this pull request May 14, 2015
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bgruening commented May 14, 2015

Great! Thanks for merging!

hexylena pushed a commit to hexylena/galaxy that referenced this pull request May 14, 2015
Pin to :dev
38bfe86 
CC @jmchilton @bgruening, pending the next Galaxy release, I've pinned both
images to their :dev tags.

This commit is really backing out a previous commit pinning to :15.05
which was the wrong thing to do as of galaxyproject#229
@hexylena hexylena deleted the ie-updates2 branch June 17, 2015 16:55
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6 participants

@hexylena @bgruening @jmchilton @carlfeberhard @natefoo @dannon