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 <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> wrote:
> >
> > 19. des. 2015 1.17 a.m. skrev "Mic" <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> wrote:
> >>>
> >>> Hi Mic,
> >>>
> >>> Since you asked for the supervisord config... it would look something
> >>> like this:]
> >>>
> >>> [program:galaxy_proxy]
> >>> command=/usr/local/bin/node
> >>> /path/to/galaxy/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 --port
> 8800
> >>> --sessions /path/to/galaxy/database/session_map.sqlite --cookie
> >>> galaxysession --verbose
> >>> numprocs=1
> >>> autostart=true
> >>> autorestart=true
> >>> startsecs=10
> >>> user=galaxy-user
> >>> directory=/galaxy/home/directory
> >>> umask=022
> >>>
> >>>
> >>> Galaxy can also automatically manage the proxy for you, if you set
> >>> "dynamic_proxy_manage_proxy=True" in your galaxy.ini
> >>>
> >>> On 12/18/2015 01:23 AM, Björn Grüning wrote:
> >>> > Hi,
> >>> >
> >>> > you need to have node installed.
> >>> >
> >>> > And then simply run: ./lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \
> >>> >  --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \
> >>> >  --cookie galaxysession --verbose
> >>> >
> >>> > from your Galaxy root dir.
> >>> >
> >>> > Cheers,
> >>> > Bjoern
> >>> >
> >>> > Am 18.12.2015 um 06:58 schrieb Mic:
> >>> >> Hello,
> >>> >> I am using the latest stable Galaxy with PostgreSQL and Apache
> Proxy.
> >>> >> I am
> >>> >> trying to follow this instruction
> >>> >>
> >>> >>
> http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html
> >>> >> in order  to be able to setup IE (Rstudio and Ipython). However, I
> do
> >>> >> not
> >>> >> know how to setup automatically Supervisord for this command:
> >>> >>
> >>> >> node $GALAXY_ROOT/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \
> >>> >> --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \
> >>> >> --cookie galaxysession --verbose
> >>> >>
> >>> >> Thank you in advance
> >>> >>
> >>> >> Mic
> >>> >>
> >>> >>
> >>> >>
> >>> >> ___________________________________________________________
> >>> >> Please keep all replies on the list by using "reply all"
> >>> >> in your mail client.  To manage your subscriptions to this
> >>> >> and other Galaxy lists, please use the interface at:
> >>> >>   https://lists.galaxyproject.org/
> >>> >>
> >>> >> To search Galaxy mailing lists use the unified search at:
> >>> >>   http://galaxyproject.org/search/mailinglists/
> >>> >>
> >>> > ___________________________________________________________
> >>> > Please keep all replies on the list by using "reply all"
> >>> > in your mail client.  To manage your subscriptions to this
> >>> > and other Galaxy lists, please use the interface at:
> >>> >   https://lists.galaxyproject.org/
> >>> >
> >>> > To search Galaxy mailing lists use the unified search at:
> >>> >   http://galaxyproject.org/search/mailinglists/
> >>>
> >>> --
> >>> Eric Rasche
> >>> Programmer II
> >>>
> >>> Center for Phage Technology
> >>> Rm 312A, BioBio
> >>> Texas A&M University
> >>> College Station, TX 77843
> >>> 404-692-2048
> >>> e...@tamu.edu
> >>>
> >>
> >
> >
> > ___________________________________________________________
> > Please keep all replies on the list by using "reply all"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >   https://lists.galaxyproject.org/
> >
> > To search Galaxy mailing lists use the unified search at:
> >   http://galaxyproject.org/search/mailinglists/
>

Attachment: galaxy.ini
Description: Binary data

Attachment: 000-default.conf
Description: Binary data

Attachment: Galaxy6-[ANNOVAR_Annotate_VCF_on_data_1].tabular
Description: Binary data

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