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Question: galaxy installation problem on CentOs
0
gravatar for paolarusso6
3.1 years ago by
paolarusso6 • 0
Italy
paolarusso6 • 0 wrote:

Good morning,

i've tried to installa galaxy on CentOs but i have this problem:

i'm logged as root

Traceback (most recent call last):
  File "./scripts/paster.py", line 32, in <module>
    serve.run()
  File "/install/shared/galaxy/lib/galaxy/util/pastescript/serve.py", line 1052, in run
    invoke(command, command_name, options, args[1:])
  File "/install/shared/galaxy/lib/galaxy/util/pastescript/serve.py", line 1058, in invoke
    exit_code = runner.run(args)
  File "/install/shared/galaxy/lib/galaxy/util/pastescript/serve.py", line 221, in run
    result = self.command()
  File "/install/shared/galaxy/lib/galaxy/util/pastescript/serve.py", line 664, in command
    serve()
  File "/install/shared/galaxy/lib/galaxy/util/pastescript/serve.py", line 648, in serve
    server(app)
  File "/install/shared/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 294, in server_wrapper
    **context.local_conf)
  File "/install/shared/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 99, in fix_call
    val = callable(*args, **kw)
  File "/install/shared/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1342, in server_runner
    serve(wsgi_app, **kwargs)
  File "/install/shared/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1291, in serve
    request_queue_size=request_queue_size)
  File "/install/shared/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1134, in __init__
    request_queue_size=request_queue_size)
  File "/install/shared/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1113, in __init__
    request_queue_size=request_queue_size)
  File "/install/shared/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 360, in __init__
    HTTPServer.__init__(self, server_address, RequestHandlerClass)
  File "/usr/lib64/python2.6/SocketServer.py", line 412, in __init__
    self.server_bind()
  File "/usr/lib64/python2.6/BaseHTTPServer.py", line 108, in server_bind
    SocketServer.TCPServer.server_bind(self)
  File "/usr/lib64/python2.6/SocketServer.py", line 423, in server_bind
    self.socket.bind(self.server_address)
  File "<string>", line 1, in bind
socket.error: [Errno 98] Address already in use
galaxy.jobs.handler INFO 2015-10-26 14:42:06,129 sending stop signal to worker thread
galaxy.jobs.handler INFO 2015-10-26 14:42:06,129 job handler queue stopped
galaxy.jobs.runners INFO 2015-10-26 14:42:06,130 LWRRunner: Sending stop signal to monitor thread
galaxy.jobs.runners INFO 2015-10-26 14:42:06,130 LWRRunner: Sending stop signal to 3 worker threads
galaxy.jobs.runners INFO 2015-10-26 14:42:06,131 LocalRunner: Sending stop signal to 5 worker threads
galaxy.jobs.handler INFO 2015-10-26 14:42:06,132 sending stop signal to worker thread
galaxy.jobs.handler INFO 2015-10-26 14:42:06,132 job handler stop queue stopped

 

Anyone can help me?

Thanks

Paola
software error galaxy • 1.3k views
ADD COMMENT • link •
modified 3.1 years ago • written 3.1 years ago by paolarusso6 • 0
0
gravatar for Hotz, Hans-Rudolf
3.1 years ago by
Hotz, Hans-Rudolf • 1.8k
Switzerland
Hotz, Hans-Rudolf • 1.8k wrote:

Hi Paola

The error message: "socket.error: [Errno 98] Address already in use"  is most likely pointing to the cause of your troubles.

Is the galaxy server already running, and you are trying to start it a second time? Or do you have another service running on that port number

 

Hope this helps

Hans-Rudolf

PS: is there any particular reason why you want to run galaxy as 'root'?

 

 
ADD COMMENT • link written 3.1 years ago by Hotz, Hans-Rudolf • 1.8k
0
gravatar for paolarusso6
3.1 years ago by
paolarusso6 • 0
Italy
paolarusso6 • 0 wrote:

Hi,

i've chaged the port number in galaxy.ini and I don't have other server's instance that is running.

 

Thanks
ADD COMMENT • link written 3.1 years ago by paolarusso6 • 0

and you get the same error?

ADD REPLY • link written 3.1 years ago by Hotz, Hans-Rudolf • 1.8k 
Unfortunately yes :( i don't have any idea!
ADD REPLY • link written 3.1 years ago by paolarusso6 • 0
1

what port number do you use, how does the line in the galaxy.ini file look like?

ADD REPLY • link written 3.1 years ago by Hotz, Hans-Rudolf • 1.8k

I attach a part of galaxy.ini, tell me if you want to see the entire file!

 ---- 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 = 7870

ADD REPLY • link written 3.1 years ago by paolarusso6 • 0
1

just double checking: the file is called "galaxy.ini" and not "galaxy.ini.sample"?

also, what is the output of 

netstat -anp | grep 7870

 

 

ADD REPLY • link written 3.1 years ago by Hotz, Hans-Rudolf • 1.8k

yes the name is "galaxy.ini".

The output is:

 

Last login: Mon Oct 26 13:30:45 2015 from 10.193.148.100
IBM Platform HPC 4.2 (build 243748) Management Node
[root@hpcc ~]# netstat -anp | grep 7870
tcp        0      0 0.0.0.0:7870                0.0.0.0:*                   LISTEN      1                               2537/vemkd
tcp        0      0 172.16.193.5:46848          172.16.193.5:7870           TIME_WAIT   -                               
tcp        0      0 172.16.193.5:50060          172.16.193.5:7870           TIME_WAIT   -                               
tcp        0      0 172.16.193.5:51470          172.16.193.5:7870           ESTABLISHED 7                               608/wsm
tcp        0      0 172.16.193.5:49168          172.16.193.5:7870           ESTABLISHED 1                               2677/egosc
tcp        0      0 172.16.193.5:41404          172.16.193.5:7870           ESTABLISHED 9                               421/java
tcp        0      0 172.16.193.5:7870           172.16.193.5:49168          ESTABLISHED 1                               2537/vemkd
tcp        0      0 172.16.193.5:7870           172.16.193.5:51470          ESTABLISHED 1                               2537/vemkd
tcp        0      0 172.16.193.5:37569          172.16.193.5:7870           TIME_WAIT   -                               
tcp        0      0 172.16.193.5:54310          172.16.193.5:7870           CLOSE_WAIT  9                               421/java
tcp        0      0 172.16.193.5:59768          172.16.193.5:7870           ESTABLISHED 1                               2536/pem
tcp        0      0 172.16.193.5:60656          172.16.193.5:7870           TIME_WAIT   -                               
tcp        0      0 172.16.193.5:37944          172.16.193.5:7870           TIME_WAIT   -                               
tcp        0      0 172.16.193.5:7870           172.16.193.5:41404          ESTABLISHED 1                               2537/vemkd
tcp        0      0 172.16.193.5:53781          172.16.193.5:7870           CLOSE_WAIT  9                               421/java
tcp        0      0 172.16.193.5:7870           172.16.193.5:59768          ESTABLISHED 1                               2537/vemkd
tcp        0      0 172.16.193.5:56230          172.16.193.5:7870           TIME_WAIT   -                               
tcp        0      0 172.16.193.5:56026          172.16.193.5:7870           TIME_WAIT   - 

 

ADD REPLY • link written 3.1 years ago by paolarusso6 • 0

I am not a sysadmin, but to me this looks like something else is using that port number already, isn't-it?

ADD REPLY • link written 3.1 years ago by Hotz, Hans-Rudolf • 1.8k

Yes, thanks for everything, the problem was the port, i've changed with 8082!

 

Thank you so much!

ADD REPLY • link written 3.1 years ago by paolarusso6 • 0
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