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 > <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 >> >> > > > > ___________________________________________________________ > 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/
