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Updates to Interactive Environment docs #2543

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merged 6 commits into from Jul 21, 2016

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commented Jun 25, 2016

Add updates to the Interactive Environment docs and split out the docs on writing IEs to developer documentation.

pvanheus added some commits Jun 25, 2016

* Update docs on Interactive Environments
* Move docs on writing IEs to developer docs

@galaxybot galaxybot added the triage label Jun 25, 2016

@galaxybot galaxybot added this to the 16.07 milestone Jun 25, 2016

@erasche erasche self-assigned this Jun 25, 2016

docker containers. Once this container is launched, we notify a proxy built
into Galaxy which helps coordinate a 1:1 mapping of users and their docker containers.
component. Galaxy vizualisation plugins are rendered using Mako templates and
Mako templates in turn can run Python code. This Python code in the Mako templates

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"code. This" -> "code. GIEs build upon visualization plugins, adding features to allow for container management and proxying. This"

Galaxy automatically launch the proxy as needed, the second is to manage it
with something like Supervisord. The command for launching the proxy manually
(or via supervisord) is
Galaxy automatically launch the proxy as needed. This is the default configuration

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launches

startsecs = 5
redirect_stderr = true

where GALAXY_ROOT is the location of your Galaxy installation and GALAXY_USER is the username of the user that

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GALAXY_ROOT -> ''GALAXY_ROOT'' (except instead of ', use `, which I can't seem to get to escape properly, sorry)

**Apache**

.. code-block:: apache

# IPython specific. Other IEs may require their own routes.
# Project Jupyter / IPython specific. Other IEs may require their own routes.

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Just jupyter now, no ipython

not on your webserver, serving Galaxy. This feature has been available since
You might want to run your IEs on a host different to the one that hosts your
Galaxy webserver, since IEs on the same host as the webserver compete for
resources with that webserver. This feature has been available since

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"with that webserver and introduce some security considerations which could be mitigated by moving containers to a separate host"

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commented Jun 25, 2016

Also you'll need to mention this in docs/dev/index.rst or something, I think

location /galaxy/gie_proxy/ipython/api/kernels {
proxy_pass http://localhost:8800/galaxy/gie_proxy/ipython/api/kernels;
location ~ ^/galaxy/gie_proxy/jupyter/(?<nbtype>[^/]+)/api/kernels(?<rest>.*?)$ {
proxy_pass http://localhost:8800/galaxy/gie_proxy/$nbtype/api/kernels$rest;

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erasche Jun 25, 2016

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@bgruening, @pvanheus says this is correct and I believe him, but just wanted a second opinion :)

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commented Jun 25, 2016

After @bgruening replies, ready to merge

@@ -3,21 +3,23 @@ Galaxy Interactive Environments (GIEs)

GIEs were a new feature back in Galaxy 15.05, leading with the release of the
IPython IE. They were presented at GCC2015, and the RStudio IE was released as
part of 15.07.
part of 15.07. The IPython IE was superceded by a Project Jupyter IE in
Galaxy XXXXX.

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bgruening Jul 5, 2016

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ping @pvanheus
Thanks for enhancing it!

@jmchilton jmchilton merged commit 8b324e8 into galaxyproject:dev Jul 21, 2016

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commented Jul 21, 2016

Awesome - thanks for the continued improvements to docs @pvanheus!

nsoranzo added a commit to nsoranzo/galaxy that referenced this pull request Oct 24, 2016

nsoranzo added a commit to nsoranzo/galaxy that referenced this pull request Oct 24, 2016

nsoranzo added a commit to nsoranzo/galaxy that referenced this pull request Oct 24, 2016

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