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 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> 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