How to make galaxy accessible through the network?

3.6 years ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k wrote:

If you set 'host' to 0.0.0.0, Galaxy will listen on your local network instead of just the loopback device, so:

host=0.0.0.0

(note that the # is removed)

ADD COMMENT • link written 3.6 years ago by Dannon Baker ♦ 3.7k

My galaxy is running on a vm in the cloud, I've tried the setting you mentioned and it didn't work. What I'm trying to do is access the web interface host by the cloud vm in my local machine.

ADD REPLY • link written 3.6 years ago by Marc • 30

Ahh, I assumed you were running a local Galaxy. Can you give more details about how you're running this cloud vm?

ADD REPLY • link written 3.6 years ago by Dannon Baker ♦ 3.7k

Yeah, I'm running a local Galaxy. My vm is a Microsoft azure vm running a ubuntu environment.

ADD REPLY • link written 3.6 years ago by Marc • 30

Ahh! Ok, that helps a ton. What you probably need to do is expose port 8080 (or 80, and make sure to run Galaxy on port 80) in the Azure VM. I don't have hands-on experience with this, but I can dig if you're not able to find it.

ADD REPLY • link written 3.6 years ago by Dannon Baker ♦ 3.7k

what do you mean by expose port 8080? At the vm?

ADD REPLY • link written 3.6 years ago by Marc • 30

Right, you need to do something like this: http://azure.microsoft.com/en-us/documentation/articles/virtual-machines-set-up-endpoints/

Which allows the external world to communicate with the VM on port 8080 (or whatever you want to run Galaxy on)

ADD REPLY • link written 3.6 years ago by Dannon Baker ♦ 3.7k

I can't post yesterday coz I'm new to this cite. I tried your way before and i didn't get it to work. I tried with the DNS, PUBLIC VIRTUAL IP (VIP) ADDRESS, but still it didn't work. Can you help?

ADD REPLY • link written 3.6 years ago by Marc • 30

So you set up a public endpoint for "Galaxy", mapping TCP on port 8080 internal to port 8080 external, and when running Galaxy it does not respond?

ADD REPLY • link written 3.6 years ago by Dannon Baker ♦ 3.7k

This is the last part of the message when i do "sh run.sh"

##########################

galaxy.queue_worker INFO 2015-05-06 15:01:15,130 Initalizing Galaxy Queue Worker on sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE

Starting server in PID 16482.

serving on http://127.0.0.1:8080

########################

but I don't know what to use as the url to access this server

ADD REPLY • link written 3.6 years ago by Marc • 30

Ok, so that means it's actually running and listening to the loopback adapter I mentioned before, so you'll need to change the galaxy.ini (*NOT* the galaxy.ini.sample -- you need to make your own copy as galaxy.ini for edits) to have host=0.0.0.0

ADD REPLY • link written 3.6 years ago by Dannon Baker ♦ 3.7k

Just to make sure, I copied everything here:

########################################

# ---- HTTP Server ----------------------------------------------------------

# Configuration of the internal HTTP server.

[server:main]

# The internal HTTP server to use. Currently only Paste is provided. This

# option is required.

use = egg:Paste#http

# The port on which to listen.

#port = 80

# The address on which to listen. By default, only listen to localhost (Galaxy

# will not be accessible over the network). Use '0.0.0.0' to listen on all

# available network interfaces.

host = 0.0.0.0/

# Use a threadpool for the web server instead of creating a thread for each

# request.

use_threadpool = True

# Number of threads in the web server thread pool.

#threadpool_workers = 10

# Set the number of seconds a thread can work before you should kill it

# (assuming it will never finish) to 3 hours. Default is 600 (10 minutes).

threadpool_kill_thread_limit = 10800

##########################################

Once I change the host, the server couldn't start:

##########################################

galaxy.webapps.galaxy.buildapp ERROR 2015-05-06 15:26:59,704 Unable to dispose of pooled toolshed install model database connections.

Traceback (most recent call last):

File "/home/azureuser/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 113, in app_factory

galaxy.model.tool_shed_install.mapping.metadata.bind.dispose()

AttributeError: 'NoneType' object has no attribute 'dispose'

galaxy.queue_worker INFO 2015-05-06 15:26:59,705 Initalizing Galaxy Queue Worker on sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE

Starting server in PID 16545.

Traceback (most recent call last):

File "./scripts/paster.py", line 37, in <module>

serve.run()

File "/home/azureuser/galaxy/lib/galaxy/util/pastescript/serve.py", line 1049, in run

invoke(command, command_name, options, args[1:])

File "/home/azureuser/galaxy/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke

exit_code = runner.run(args)

File "/home/azureuser/galaxy/lib/galaxy/util/pastescript/serve.py", line 220, in run

result = self.command()

File "/home/azureuser/galaxy/lib/galaxy/util/pastescript/serve.py", line 670, in command

serve()

File "/home/azureuser/galaxy/lib/galaxy/util/pastescript/serve.py", line 654, in serve

server(app)

File "/home/azureuser/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 292, in server_wrapper

**context.local_conf)

File "/home/azureuser/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 97, in fix_call

val = callable(*args, **kw)

File "/home/azureuser/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1342, in server_runner

serve(wsgi_app, **kwargs)

File "/home/azureuser/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1291, in serve

request_queue_size=request_queue_size)

File "/home/azureuser/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1134, in __init__

request_queue_size=request_queue_size)

File "/home/azureuser/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1113, in __init__

request_queue_size=request_queue_size)

File "/home/azureuser/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 360, in __init__

HTTPServer.__init__(self, server_address, RequestHandlerClass)

File "/usr/lib/python2.7/SocketServer.py", line 419, in __init__

self.server_bind()

File "/usr/lib/python2.7/BaseHTTPServer.py", line 108, in server_bind

SocketServer.TCPServer.server_bind(self)

File "/usr/lib/python2.7/SocketServer.py", line 430, in server_bind

self.socket.bind(self.server_address)

File "/usr/lib/python2.7/socket.py", line 224, in meth

return getattr(self._sock,name)(*args)

socket.gaierror: [Errno -2] Name or service not known

galaxy.jobs.handler INFO 2015-05-06 15:26:59,751 sending stop signal to worker thread

galaxy.jobs.handler INFO 2015-05-06 15:26:59,751 job handler queue stopped

galaxy.jobs.runners INFO 2015-05-06 15:26:59,759 LWRRunner: Sending stop signal to monitor thread

galaxy.jobs.runners INFO 2015-05-06 15:26:59,759 LWRRunner: Sending stop signal to 3 worker threads

galaxy.jobs.runners INFO 2015-05-06 15:26:59,759 LocalRunner: Sending stop signal to 5 worker threads

galaxy.jobs.handler INFO 2015-05-06 15:26:59,760 sending stop signal to worker thread

galaxy.jobs.handler INFO 2015-05-06 15:26:59,761 job handler stop queue stopped

ADD REPLY • link written 3.6 years ago by Marc • 30

Take the trailing slash off of host, so it's exactly:

host = 0.0.0.0

ADD REPLY • link written 3.6 years ago by Dannon Baker ♦ 3.7k

the server is working now, but how can I access it on my local web browser?

######################

Traceback (most recent call last):

File "/home/azureuser/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 113, in app_factory

galaxy.model.tool_shed_install.mapping.metadata.bind.dispose()

AttributeError: 'NoneType' object has no attribute 'dispose'

galaxy.queue_worker INFO 2015-05-06 15:40:18,944 Initalizing Galaxy Queue Worker on sqlalchemy+sqlite:///./database/control.sqlite?isolation_level=IMMEDIATE

Starting server in PID 16683.

serving on 0.0.0.0:8080 view at http://127.0.0.1:8080

ADD REPLY • link written 3.6 years ago by Marc • 30

That looks correct, now you just have to go to the URL of the azure VM (or the IP you ssh'd to to get in) at port 8080, if you have the endpoint configured as we previously discussed.

ADD REPLY • link written 3.6 years ago by Dannon Baker ♦ 3.7k

I've tried with my DNS name: *.cloudapp.net:8080, and it didn't work; and my PUBLIC VIRTUAL IP (VIP) ADDRESS: ***.***.***.***:8080, and it didn't work. I don't know what url I should use. And this is probably the last post in the next 6 hours.....

ADD REPLY • link written 3.6 years ago by Marc • 30

It may be easier to email galaxy-dev with questions like this -- others with azure experience on the developer list will be able to hopefully chime in. See http://dev.list.galaxyproject.org/

ADD REPLY • link written 3.6 years ago by Dannon Baker ♦ 3.7k

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