On Wed, Dec 23, 2015 at 10:19 AM, Mic <mictadlo@gmail.com> wrote:

Hi Bjoern,
I tried sudo docker ps, but it shows nothing is running and I tried it multiple times to refresh Galaxy. Maybe I have to change docker to use without sudo?

Thank you in advance.

Mic
On Wed, Dec 23, 2015 at 10:03 AM, Mic <mictadlo@gmail.com> wrote:
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 | Text | XML (full)

⇝ AttributeError: 'Bunch' object has no attribute 'proxy_url'

URL: http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626

Module weberror.evalexception.middleware:364 in respond view
>> app_iter = self.application(environ, detect_start_response)

Module paste.recursive:84 in __call__ view
>> return self.application(environ, start_response)

Module paste.httpexceptions:633 in __call__ view
>> return self.application(environ, start_response)

Module galaxy.web.framework.base:133 in __call__ view
>> return self.handle_request( environ, start_response )

Module galaxy.web.framework.base:191 in handle_request view
>> body = method( trans, **kwargs )

Module galaxy.web.framework.decorators:68 in decorator view
>> return func( self, trans, *args, **kwargs )

Module galaxy.webapps.galaxy.controllers.visualization:751 in render view
>> self._handle_plugin_error( trans, visualization_name, exception )

Module galaxy.webapps.galaxy.controllers.visualization:749 in render view
>> return plugin.render( trans=trans, embedded=embedded, **kwargs )

Module galaxy.visualization.plugins.plugin:138 in render view
>> return self._render( render_vars, trans=trans, embedded=embedded )

Module galaxy.visualization.plugins.plugin:284 in _render view
>> return trans.fill_template( template_filename, template_lookup=self.template_lookup, **render_vars )

Module galaxy.web.framework.webapp:811 in fill_template view
>> return self.fill_template_mako( filename, **kwargs )

Module galaxy.web.framework.webapp:825 in fill_template_mako view
>> return template.render( **data )

Module mako.template:296 in render view
>> return runtime._render(self, self.callable_, args, data)

Module mako.runtime:660 in _render view
>> **_kwargs_for_callable(callable_, data))

Module mako.runtime:692 in _render_context view
>> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs)

Module mako.runtime:718 in _exec_template view
>> callable_(context, *args, **kwargs)

Module rstudio_mako:63 in render_body view
>> notebook_pubkey_url = ie_request.url_template('${PROXY_URL}/rstudio/auth-public-key')

Module galaxy.web.base.interactive_environments:171 in url_template view
>> 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 <esr@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 <mictadlo@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
ProxyPassReverse /gie_proxy http://localhost:8800/gie_proxy

# Normal Galaxy configuration
ProxyPass        / http://localhost:8080
ProxyPassReverse / 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 <esr@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 <mictadlo@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 view at 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 <jmchilton@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 <esr@tamu.edu> wrote:
>
> 19. des. 2015 1.17 a.m. skrev "Mic" <mictadlo@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 <esr@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
>>> >> 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/
>>> >>
>>> >> To search Galaxy mailing lists use the unified search at:
>>> >> 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/
>>> >
>>> > To search Galaxy mailing lists use the unified search at:
>>> > 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
>>> esr@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/
>
> To search Galaxy mailing lists use the unified search at:
> 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

esr@tamu.edu
-- 
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A&M University
College Station, TX 77843
404-692-2048
esr@tamu.edu