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