subject:"\[galaxy\-dev\] IE setup problem"

Re: [galaxy-dev] IE setup problem

2015-12-28 Thread Mic

Hello,
Is there any docker container which include working IE with Apache Proxy?

Thank you in advance.

Best wishes,

Mic

On Wed, Dec 23, 2015 at 10:49 AM, Mic  wrote:

> Hello,
> The images have been downloaded and stated, but now I get the following
> error:
>
>
>
> *127.0.0.1 - - [23/Dec/2015:10:57:25 +1000] "GET
> /gie_proxy/ipython/login?next=%2F%2Fgie_proxy%2Fipython%2Ftree HTTP/1.1"
> 404 -
> "http://localhost/visualization/show/ipython?dataset_id=ba7576120c38e626
> "
> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:43.0) Gecko/20100101
> Firefox/43.0"*
> I think the Apache config file is still wrong. Galaxy is located on the
> proxy *localhost* and *not* *localhost/galaxy. *This is my config file:
>
> 
> 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]
> RewriteRule ^/ipython/(.*) http://localhost:8800/ipython/$1 [P]
>
> # IPython specific. Other IEs may require their own routes.
> ProxyPass/gie_proxy/ipython/api/kernels
> ws://localhost:8800/gie_proxy/ipython/api/kernels
>
> # Global GIE configuration
> ProxyPass/gie_proxy http://localhost:8800/gie_proxy
> ProxyPassReverse /gie_proxy http://localhost:8800/gie_proxy
>
> # Normal Galaxy configuration
> ProxyPass/ http://localhost:8080
> ProxyPassReverse / http://localhost:8080
>
> 
>
> 
> # Compress all uncompressed content.
> SetOutputFilter DEFLATE
> SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary
> SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary
> SetEnvIfNoCase Request_URI /history/export_archive no-gzip dont-vary
> # Sending files using Apache
> XSendFile on
> XSendFilePath /
> Require all granted
> 
> 
> # Allow browsers to cache everything from /static for 6 hours
> ExpiresActive On
> ExpiresDefault "access plus 6 hours"
> Require all granted
> 
> 
>ProxyPassReverse http://localhost:8800/ipython/
>Require all granted
> 
>
>
> What did I do wrong?
>
> Thank you in advance.
>
> Mic
>
>
>
>
> On Wed, Dec 23, 2015 at 10:19 AM, Mic  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  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
>>>

Re: [galaxy-dev] IE setup problem

2015-12-22 Thread Mic

Hello,
The images have been downloaded and stated, but now I get the following
error:



*127.0.0.1 - - [23/Dec/2015:10:57:25 +1000] "GET
/gie_proxy/ipython/login?next=%2F%2Fgie_proxy%2Fipython%2Ftree HTTP/1.1"
404 -
"http://localhost/visualization/show/ipython?dataset_id=ba7576120c38e626
"
"Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:43.0) Gecko/20100101
Firefox/43.0"*
I think the Apache config file is still wrong. Galaxy is located on the
proxy *localhost* and *not* *localhost/galaxy. *This is my config file:


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]
RewriteRule ^/ipython/(.*) http://localhost:8800/ipython/$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




# Compress all uncompressed content.
SetOutputFilter DEFLATE
SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary
SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary
SetEnvIfNoCase Request_URI /history/export_archive no-gzip dont-vary
# Sending files using Apache
XSendFile on
XSendFilePath /
Require all granted


# Allow browsers to cache everything from /static for 6 hours
ExpiresActive On
ExpiresDefault "access plus 6 hours"
Require all granted


   ProxyPassReverse http://localhost:8800/ipython/
   Require all granted



What did I do wrong?

Thank you in advance.

Mic




On Wed, Dec 23, 2015 at 10:19 AM, Mic  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  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
>>

Re: [galaxy-dev] IE setup problem

2015-12-22 Thread Mic

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  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
>

Re: [galaxy-dev] IE setup problem

2015-12-22 Thread Björn Grüning

Hi Mic,

do you see in your logs that the image is fetched?
For the first time this can happen if the IPython or RStudio image is
not fetched and stored locally. Try again and check with `docker ps` if
an image is started.

Cheers,
Bjoern

Am 23.12.2015 um 01:03 schrieb Mic:
> 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
>

Re: [galaxy-dev] IE setup problem

2015-12-22 Thread Mic

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

Re: [galaxy-dev] IE setup problem

2015-12-22 Thread Eric Rasche

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  > 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  > 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  >:
>
> 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
> mailto: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.

Re: [galaxy-dev] IE setup problem

2015-12-21 Thread Mic

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  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 onRewriteRule ^/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
> configurationProxyPass/gie_proxy http://localhost:8800/gie_proxy
> ProxyPassReverse /gie_proxy
> http://localhost:8800/gie_proxy # Normal
> Galaxy configurationProxyPass/ 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  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 :
>>
>>> 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 
>>> 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  wrote:
 >
 > 19. des. 2015 1.17 a.m. skrev "Mic" :
 >>
 >> 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  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

Re: [galaxy-dev] IE setup problem

2015-12-21 Thread Mic

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 onRewriteRule ^/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
configurationProxyPass/gie_proxy http://localhost:8800/gie_proxy
ProxyPassReverse /gie_proxy
http://localhost:8800/gie_proxy # Normal
Galaxy configurationProxyPass/ 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  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 :
>
>> 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 
>> 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  wrote:
>>> >
>>> > 19. des. 2015 1.17 a.m. skrev "Mic" :
>>> >>
>>> >> 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  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
>>> >>> "dyna

Re: [galaxy-dev] IE setup problem

2015-12-20 Thread Mic

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  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  wrote:
> >
> > 19. des. 2015 1.17 a.m. skrev "Mic" :
> >>
> >> 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  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

Re: [galaxy-dev] IE setup problem

2015-12-18 Thread John Chilton

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  wrote:
>
> 19. des. 2015 1.17 a.m. skrev "Mic" :
>>
>> 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  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
>>> 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/
>
> 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/

Re: [galaxy-dev] IE setup problem

2015-12-18 Thread Eric Rasche

19. des. 2015 1.17 a.m. skrev "Mic" :
>
> 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  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
>> 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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] IE setup problem

2015-12-18 Thread Mic

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?

Thank you in advance.

Mic



On Sat, Dec 19, 2015 at 12:26 AM, Eric Rasche  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
> 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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] IE setup problem

2015-12-18 Thread Eric Rasche

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
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/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] IE setup problem

2015-12-17 Thread Björn Grüning

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/

Re: [galaxy-dev] IE setup problem

2015-12-17 Thread Mic

...
or is there is another way to start automatically nodejs  without  to use
Supervisord?

On Fri, Dec 18, 2015 at 3:58 PM, Mic  wrote:

> 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/

[galaxy-dev] IE setup problem

2015-12-17 Thread 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/

Re: [galaxy-dev] IE setup problem

Re: [galaxy-dev] IE setup problem

Re: [galaxy-dev] IE setup problem

Re: [galaxy-dev] IE setup problem

Re: [galaxy-dev] IE setup problem

Re: [galaxy-dev] IE setup problem

Re: [galaxy-dev] IE setup problem

Re: [galaxy-dev] IE setup problem

Re: [galaxy-dev] IE setup problem

Re: [galaxy-dev] IE setup problem

Re: [galaxy-dev] IE setup problem

Re: [galaxy-dev] IE setup problem

Re: [galaxy-dev] IE setup problem

Re: [galaxy-dev] IE setup problem

Re: [galaxy-dev] IE setup problem

[galaxy-dev] IE setup problem

16 matches

Site Navigation

Mail list logo

Footer information