Hello Eric,
I added *interactive_environment_plugins_directory =
/home/galaxy/galaxy/config/plugins/interactive_environments* to
*galaxy.ini*. Now I got the below error while clicking Rstudio and Ipython.
Please find attached my config files and I was not sure how to change
apache proxy config file:


Error Traceback:
View as:   Interactive
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
 |  Text
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
 |  XML
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
(full)
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
⇝ AttributeError: 'Bunch' object has no attribute 'proxy_url'
URL: http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626
Module weberror.evalexception.middleware:*364* in respond
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
view
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
>>
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
app_iter *=* self*.*application*(*environ*,* detect_start_response*)*
Module paste.recursive:*84* in __call__
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
view
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
>>
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
*return* self*.*application*(*environ*,* start_response*)*
Module paste.httpexceptions:*633* in __call__
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
view
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
>>
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
*return* self*.*application*(*environ*,* start_response*)*
Module galaxy.web.framework.base:*133* in __call__
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
view
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
>>
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
*return* self*.*handle_request*(* environ*,* start_response *)*
Module galaxy.web.framework.base:*191* in handle_request
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
view
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
>>
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
body *=* method*(* trans*,* ****kwargs *)*
Module galaxy.web.framework.decorators:*68* in decorator
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
view
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
>>
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
*return* func*(* self*,* trans*,* ***args*,* ****kwargs *)*
Module galaxy.webapps.galaxy.controllers.visualization:*751* in render
  <http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
view
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
>>
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
self*.*_handle_plugin_error*(* trans*,* visualization_name*,* exception *)*
Module galaxy.webapps.galaxy.controllers.visualization:*749* in render
  <http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
view
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
>>
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
*return* plugin*.*render*(* trans*=*trans*,* embedded*=*embedded*,* ****
kwargs *)*
Module galaxy.visualization.plugins.plugin:*138* in render
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
view
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
>>
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
*return* self*.*_render*(* render_vars*,* trans*=*trans*,* embedded*=*
embedded *)*
Module galaxy.visualization.plugins.plugin:*284* in _render
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
view
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
>>
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
*return* trans*.*fill_template*(* template_filename*,* template_lookup*=*
self*.*template_lookup*,* ****render_vars *)*
Module galaxy.web.framework.webapp:*811* in fill_template
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
view
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
>>
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
*return* self*.*fill_template_mako*(* filename*,* ****kwargs *)*
Module galaxy.web.framework.webapp:*825* in fill_template_mako
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
view
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
>>
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
*return* template*.*render*(* ****data *)*
Module mako.template:*296* in render
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
view
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
>>
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
*return* runtime*.*_render*(*self*,* self*.*callable_*,* args*,* data*)*
Module mako.runtime:*660* in _render
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
view
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
>>
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
****_kwargs_for_callable*(*callable_*,* data*)**)*
Module mako.runtime:*692* in _render_context
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
view
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
>>
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
_exec_template*(*inherit*,* lclcontext*,* args*=*args*,* kwargs*=*kwargs*)*
Module mako.runtime:*718* in _exec_template
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
view
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
>>
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
callable_*(*context*,* ***args*,* ****kwargs*)*
Module rstudio_mako:*63* in render_body
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
view
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
>>
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
notebook_pubkey_url *=* ie_request*.*url_template*(*
'${PROXY_URL}/rstudio/auth-public-key'*)*
Module galaxy.web.base.interactive_environments:*171* in url_template
  <http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
view
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
>>
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#>
url *=* url_template*.*replace*(*'${PROXY_URL}'*,* str*(*self*.*attr*.*
proxy_url*)**)*
*AttributeError: 'Bunch' object has no attribute 'proxy_url'*

Thank you in advance.

Best wishes,

Mic




On Wed, Dec 23, 2015 at 4:14 AM, Eric Rasche <e...@tamu.edu> wrote:

> Hi Mic,
>
> Some comments/questions after looking over your conf:
>
>    - you've set "prefix" to /home/galaxy/galaxy, that prefix is used in
>    web proxying (not in finding paths to on-disk galaxy stuff), so unless
>    you're running under a url prefix like http://fqdn/galaxy/ you may not
>    want to set that (though I don't know if it will negatively affect you
>    there. My gut says it won't cause an issue, but you never know)
>    - You'll need to set
>    
> interactive_environment_plugins_directory=/path/to/galaxy_root/config/plugins/interactive_environments
>
> Let me know if that helps.
>
> Cheers,
> Eric
>
>
> On 12/22/2015 12:29 AM, Mic wrote:
>
> Hello,
> I was trying more, but still no luck. Please find attached the new config
> files.
>
> Thank you in advance.
>
> Best wishes,
>
> Mic
>
> On Tue, Dec 22, 2015 at 11:26 AM, Mic <micta...@gmail.com> wrote:
>
>> Hi Eric,
>> Thank you for your email. I have Galaxy installed in
>> */home/galaxy/galaxy* and Apache Proxy is setup for *localhost:8080*. I
>> modified the Apache config file further for GIE:
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *RewriteEngine on RewriteRule ^/static/style/(.*)
>> /home/galaxy/galaxy/static/june_2007_style/blue/$1 [L] RewriteRule
>> ^/static/scripts/(.*) /home/galaxy/galaxy/static/scripts/packed/$1 [L]
>> RewriteRule ^/static/(.*) /home/galaxy/galaxy/static/$1 [L] RewriteRule
>> ^/favicon.ico /home/galaxy/galaxy/static/favicon.ico [L] RewriteRule
>> ^/robots.txt /home/galaxy/galaxy/static/robots.txt [L] RewriteRule ^(.*)
>> http://localhost:8080$1 [P] # IPython specific. Other IEs may require their
>> own routes. ProxyPass        /gie_proxy/ipython/api/kernels
>> ws://localhost:8800/gie_proxy/ipython/api/kernels # Global GIE
>> configuration ProxyPass        /gie_proxy
>> <http://localhost:8800/gie_proxy>http://localhost:8800/gie_proxy
>> <http://localhost:8800/gie_proxy> ProxyPassReverse /gie_proxy
>> <http://localhost:8800/gie_proxy>http://localhost:8800/gie_proxy
>> <http://localhost:8800/gie_proxy> # Normal Galaxy configuration
>> ProxyPass        / http://localhost:8080 <http://localhost:8080>
>> ProxyPassReverse / http://localhost:8080 <http://localhost:8080> *
>> Did I modify the above files correctly?
>>
>>
>>
>> *Thank you in advance, *
>>
>> *Mic *
>>
>>
>>
>> On Tue, Dec 22, 2015 at 4:15 AM, Eric Rasche < <e...@tamu.edu>e...@tamu.edu
>> > wrote:
>>
>>> I'll look at this tonight, if no one else replies earlier today. Sorry
>>> to hear you're having these troubles Mic. GIEs can be tough to deploy.
>>> Thanks for bearing with us.
>>>
>>> Cheers,
>>> Eric
>>>
>>> 2015-12-20 20:57 GMT-06:00 Mic < <micta...@gmail.com>micta...@gmail.com>
>>> :
>>>
>>>> Hi all,
>>>> I tried with *dynamic_proxy_manage=True* and
>>>> *dynamic_proxy_manage=False*, but IE does not start inside Galaxy on a
>>>> Annovar tab separated file (see attached).
>>>>
>>>> I also tried the following commands, but without any luck:
>>>>
>>>> $ node /home/galaxy/galaxy/lib/galaxy/web/proxy/js/lib/main.js --ip
>>>> 0.0.0.0 --port 8800 --sessions
>>>> /home/galaxy/galaxy/database/session_map.sqlite --cookie galaxysession
>>>> --verbose
>>>> Watching path /home/galaxy/galaxy/database/session_map.sqlite
>>>> Listening on 0.0.0.0:8800
>>>>
>>>> $ node /home/galaxy/galaxy/lib/galaxy/web/proxy/js/lib/main.js --ip
>>>> 127.0.0.1 --port 8800 --sessions
>>>> /home/galaxy/galaxy/database/session_map.sqlite --cookie galaxysession
>>>> --verbose
>>>> Watching path /home/galaxy/galaxy/database/session_map.sqlite
>>>> Listening on 127.0.0.1:8800
>>>>
>>>> $ node /home/galaxy/galaxy/lib/galaxy/web/proxy/js/lib/main.js --ip
>>>> localhost  --port 8800 --sessions
>>>> /home/galaxy/galaxy/database/session_map.sqlite --cookie galaxysession
>>>> --verbose
>>>> Watching path /home/galaxy/galaxy/database/session_map.sqlite
>>>> Listening on localhost:8800
>>>>
>>>> My Galaxy is running on *0.0.0.0:8080 <http://0.0.0.0:8080>* view at *
>>>> <http://127.0.0.1:8080>http://127.0.0.1:8080 <http://127.0.0.1:8080>*.
>>>> I use Docker version 1.9.1, build a34a1d5.
>>>>
>>>> Please find attached my *galaxy.ini* and apache proxy config file (
>>>> *000-default.conf*).
>>>>
>>>> The following Apache modules I have enabled (*sudo a2enmod rewrite
>>>> deflate expires proxy proxy_html xsendfile xml2enc proxy_wstunnel*)
>>>>
>>>> What did I do wrong so I can not start Rstudio and IPython inside
>>>> Galaxy?
>>>>
>>>> Thank you in advance.
>>>>
>>>> Mic
>>>>
>>>>
>>>>
>>>>
>>>> On Sat, Dec 19, 2015 at 1:12 PM, John Chilton < <jmchil...@gmail.com>
>>>> jmchil...@gmail.com> wrote:
>>>>
>>>>> dynamic_proxy_manage_proxy=True is a terrible hack, I would set it to
>>>>> False and use supervisord if you have any inclination to at all. Like
>>>>> sqlite or the local job runner, it is just an attempt to make sure
>>>>> things work out of the box but it isn't that robust.
>>>>>
>>>>> -John
>>>>>
>>>>> On Sat, Dec 19, 2015 at 1:20 AM, Eric Rasche < <e...@tamu.edu>
>>>>> e...@tamu.edu> wrote:
>>>>> >
>>>>> > 19. des. 2015 1.17 a.m. skrev "Mic" < <micta...@gmail.com>
>>>>> micta...@gmail.com>:
>>>>> >>
>>>>> >> Hi all,
>>>>> >> Thank you for the responses. If I would use
>>>>> >> "dynamic_proxy_manage_proxy=True" than Galaxy would execute
>>>>> automatically:
>>>>> >>
>>>>> >> /lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \
>>>>> >>  --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \
>>>>> >>  --cookie galaxysession --verbose
>>>>> >>
>>>>> >> without the need to use supervisors config?
>>>>> >
>>>>> > Yes. That's the idea. I'm not sure I trust it quite as much as
>>>>> supervisord,
>>>>> > but it has worked quite well for us so far :-)
>>>>> >
>>>>> >>
>>>>> >> Thank you in advance.
>>>>> >>
>>>>> >> Mic
>>>>> >>
>>>>> >>
>>>>> >>
>>>>> >> On Sat, Dec 19, 2015 at 12:26 AM, Eric Rasche < <e...@tamu.edu>
>>>>> e...@tamu.edu> wrote:
>>>>> >>>
>>>>> >>> Hi Mic,
>>>>> >>>
>>>>> >>> Since you asked for the supervisord config... it would look
>>>>> something
>>>>> >>> like this:]
>>>>> >>>
>>>>> >>> [program:galaxy_proxy]
>>>>> >>> command=/usr/local/bin/node
>>>>> >>> /path/to/galaxy/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0
>>>>> --port 8800
>>>>> >>> --sessions /path/to/galaxy/database/session_map.sqlite --cookie
>>>>> >>> galaxysession --verbose
>>>>> >>> numprocs=1
>>>>> >>> autostart=true
>>>>> >>> autorestart=true
>>>>> >>> startsecs=10
>>>>> >>> user=galaxy-user
>>>>> >>> directory=/galaxy/home/directory
>>>>> >>> umask=022
>>>>> >>>
>>>>> >>>
>>>>> >>> Galaxy can also automatically manage the proxy for you, if you set
>>>>> >>> "dynamic_proxy_manage_proxy=True" in your galaxy.ini
>>>>> >>>
>>>>> >>> On 12/18/2015 01:23 AM, Björn Grüning wrote:
>>>>> >>> > Hi,
>>>>> >>> >
>>>>> >>> > you need to have node installed.
>>>>> >>> >
>>>>> >>> > And then simply run: ./lib/galaxy/web/proxy/js/main.js --ip
>>>>> 0.0.0.0 \
>>>>> >>> >  --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite
>>>>> \
>>>>> >>> >  --cookie galaxysession --verbose
>>>>> >>> >
>>>>> >>> > from your Galaxy root dir.
>>>>> >>> >
>>>>> >>> > Cheers,
>>>>> >>> > Bjoern
>>>>> >>> >
>>>>> >>> > Am 18.12.2015 um 06:58 schrieb Mic:
>>>>> >>> >> Hello,
>>>>> >>> >> I am using the latest stable Galaxy with PostgreSQL and Apache
>>>>> Proxy.
>>>>> >>> >> I am
>>>>> >>> >> trying to follow this instruction
>>>>> >>> >>
>>>>> >>> >>
>>>>> <http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html>
>>>>> http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html
>>>>> >>> >> in order  to be able to setup IE (Rstudio and Ipython).
>>>>> However, I do
>>>>> >>> >> not
>>>>> >>> >> know how to setup automatically Supervisord for this command:
>>>>> >>> >>
>>>>> >>> >> node $GALAXY_ROOT/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \
>>>>> >>> >> --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite
>>>>> \
>>>>> >>> >> --cookie galaxysession --verbose
>>>>> >>> >>
>>>>> >>> >> Thank you in advance
>>>>> >>> >>
>>>>> >>> >> Mic
>>>>> >>> >>
>>>>> >>> >>
>>>>> >>> >>
>>>>> >>> >> ___________________________________________________________
>>>>> >>> >> Please keep all replies on the list by using "reply all"
>>>>> >>> >> in your mail client.  To manage your subscriptions to this
>>>>> >>> >> and other Galaxy lists, please use the interface at:
>>>>> >>> >>    <https://lists.galaxyproject.org/>
>>>>> https://lists.galaxyproject.org/
>>>>> >>> >>
>>>>> >>> >> To search Galaxy mailing lists use the unified search at:
>>>>> >>> >>    <http://galaxyproject.org/search/mailinglists/>
>>>>> http://galaxyproject.org/search/mailinglists/
>>>>> >>> >>
>>>>> >>> > ___________________________________________________________
>>>>> >>> > Please keep all replies on the list by using "reply all"
>>>>> >>> > in your mail client.  To manage your subscriptions to this
>>>>> >>> > and other Galaxy lists, please use the interface at:
>>>>> >>> >    <https://lists.galaxyproject.org/>
>>>>> https://lists.galaxyproject.org/
>>>>> >>> >
>>>>> >>> > To search Galaxy mailing lists use the unified search at:
>>>>> >>> >    <http://galaxyproject.org/search/mailinglists/>
>>>>> http://galaxyproject.org/search/mailinglists/
>>>>> >>>
>>>>> >>> --
>>>>> >>> Eric Rasche
>>>>> >>> Programmer II
>>>>> >>>
>>>>> >>> Center for Phage Technology
>>>>> >>> Rm 312A, BioBio
>>>>> >>> Texas A&M University
>>>>> >>> College Station, TX 77843
>>>>> >>> 404-692-2048
>>>>> >>> <e...@tamu.edu>e...@tamu.edu
>>>>> >>>
>>>>> >>
>>>>> >
>>>>> >
>>>>> > ___________________________________________________________
>>>>> > Please keep all replies on the list by using "reply all"
>>>>> > in your mail client.  To manage your subscriptions to this
>>>>> > and other Galaxy lists, please use the interface at:
>>>>> >    <https://lists.galaxyproject.org/>
>>>>> https://lists.galaxyproject.org/
>>>>> >
>>>>> > To search Galaxy mailing lists use the unified search at:
>>>>> >    <http://galaxyproject.org/search/mailinglists/>
>>>>> http://galaxyproject.org/search/mailinglists/
>>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Eric Rasche
>>> Programmer II
>>>
>>> Center for Phage Technology
>>> Rm 312A, BioBio
>>> Texas A&M University
>>> College Station, TX 77843
>>> 404-692-2048
>>> e...@tamu.edu
>>>
>>
>>
>
> --
> Eric Rasche
> Programmer II
>
> Center for Phage Technology
> Rm 312A, BioBio
> Texas A&M University
> College Station, TX 77843404-692-2048...@tamu.edu
>
>

Attachment: galaxy.ini
Description: Binary data

Attachment: 000-default.conf
Description: Binary data

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