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 <http://localhost:8800/gie_proxy>ProxyPassReverse /gie_proxy http://localhost:8800/gie_proxy <http://localhost:8800/gie_proxy># Normal Galaxy configurationProxyPass / 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 <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 <http://0.0.0.0:8080>* view at *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 <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
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 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 <http://localhost:8800/gie_proxy>ProxyPassReverse /gie_proxy http://localhost:8800/gie_proxy <http://localhost:8800/gie_proxy># Normal Galaxy configurationProxyPass / 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 <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 <http://0.0.0.0:8080>* view at *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 <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
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 <mailto: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 <mailto: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 <mailto: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 <http://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 <http://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/. 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 <mailto: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 <mailto:esr@tamu.edu>> wrote: > > 19. des. 2015 1.17 a.m. skrev "Mic" <mictadlo@gmail.com <mailto: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 <mailto: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 <tel:404-692-2048> >>> esr@tamu.edu <mailto: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 <tel:404-692-2048> esr@tamu.edu <mailto: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
<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#>
<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*.*
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#> 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#> 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>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 < <esr@tamu.edu>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>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 <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 < <jmchilton@gmail.com> 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> esr@tamu.edu> wrote:
19. des. 2015 1.17 a.m. skrev "Mic" < <mictadlo@gmail.com>
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> 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> 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 >> <esr@tamu.edu>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/> 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 esr@tamu.edu
-- Eric Rasche Programmer II
Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843404-692-2048esr@tamu.edu
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:
<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#>
<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*.*
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#> 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#> 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>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 < <esr@tamu.edu>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>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 <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 < <jmchilton@gmail.com> 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> esr@tamu.edu> wrote: > > 19. des. 2015 1.17 a.m. skrev "Mic" < <mictadlo@gmail.com> 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> 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> 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 >>> <esr@tamu.edu>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/> 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 esr@tamu.edu
-- Eric Rasche Programmer II
Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843404-692-2048esr@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/
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:
<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#>
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#> 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#> url *=* url_template*.*replace*(*'${PROXY_URL}'*,* str*(*self*.*attr*.*
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#> view <http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#> 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>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 < <esr@tamu.edu> 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>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 <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 < <jmchilton@gmail.com> 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> esr@tamu.edu> wrote: > > 19. des. 2015 1.17 a.m. skrev "Mic" < <mictadlo@gmail.com> 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> 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> 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 >>> <esr@tamu.edu>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/> 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 esr@tamu.edu
-- Eric Rasche Programmer II
Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843404-692-2048esr@tamu.edu
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 <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: <VirtualHost> 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/$1 [P] # IPython specific. Other IEs may require their own routes. ProxyPass /gie_proxy/ipython/api/kernels ws://localhost:8800/gie_proxy/ipython/api/kernels # Global GIE configuration ProxyPass /gie_proxy http://localhost:8800/gie_proxy ProxyPassReverse /gie_proxy http://localhost:8800/gie_proxy # Normal Galaxy configuration ProxyPass / http://localhost:8080 ProxyPassReverse / http://localhost:8080 </VirtualHost> <Location "/"> # Compress all uncompressed content. SetOutputFilter DEFLATE SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ 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 </Location> <Location "/home/galaxy/"> # Allow browsers to cache everything from /static for 6 hours ExpiresActive On ExpiresDefault "access plus 6 hours" Require all granted </Location> <Location "/ipython/"> ProxyPassReverse http://localhost:8800/ipython/ Require all granted </Location> What did I do wrong? Thank you in advance. Mic 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:
<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#>
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#> 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*(* '${PROXY_URL}/rstudio/auth-public-key'*)* Module galaxy.web.base.interactive_environments:*171* in url_template
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#> url *=* url_template*.*replace*(*'${PROXY_URL}'*,* str*(*self*.*attr*.*
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#> view <http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#> 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>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 < <esr@tamu.edu> 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> 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 <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 < <jmchilton@gmail.com> 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> > esr@tamu.edu> wrote: > > > > 19. des. 2015 1.17 a.m. skrev "Mic" < <mictadlo@gmail.com> > 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> > 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> > 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 > >>> <esr@tamu.edu>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/> > 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 esr@tamu.edu
-- Eric Rasche Programmer II
Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843404-692-2048esr@tamu.edu
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 <mictadlo@gmail.com> 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 <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:
<VirtualHost> 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/$1 [P]
# IPython specific. Other IEs may require their own routes. ProxyPass /gie_proxy/ipython/api/kernels ws://localhost:8800/gie_proxy/ipython/api/kernels
# Global GIE configuration ProxyPass /gie_proxy http://localhost:8800/gie_proxy ProxyPassReverse /gie_proxy http://localhost:8800/gie_proxy
# Normal Galaxy configuration ProxyPass / http://localhost:8080 ProxyPassReverse / http://localhost:8080
</VirtualHost>
<Location "/"> # Compress all uncompressed content. SetOutputFilter DEFLATE SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ 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 </Location> <Location "/home/galaxy/"> # Allow browsers to cache everything from /static for 6 hours ExpiresActive On ExpiresDefault "access plus 6 hours" Require all granted </Location> <Location "/ipython/"> ProxyPassReverse http://localhost:8800/ipython/ Require all granted </Location>
What did I do wrong?
Thank you in advance.
Mic
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:
<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#>
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#> 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*(* '${PROXY_URL}/rstudio/auth-public-key'*)* Module galaxy.web.base.interactive_environments:*171* in url_template
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#> url *=* url_template*.*replace*(*'${PROXY_URL}'*,* str*(*self*.*attr*.*
<http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#> view <http://localhost/visualization/show/rstudio?dataset_id=ba7576120c38e626#> 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>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 < <esr@tamu.edu> 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> 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 <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 < > <jmchilton@gmail.com>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> >> esr@tamu.edu> wrote: >> > >> > 19. des. 2015 1.17 a.m. skrev "Mic" < <mictadlo@gmail.com> >> 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> >> 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> >> 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 >> >>> <esr@tamu.edu>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/> >> 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 esr@tamu.edu
-- Eric Rasche Programmer II
Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843404-692-2048esr@tamu.edu
participants (3)
-
Björn Grüning -
Eric Rasche -
Mic