Problem with Galaxy installation

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Problem with Galaxy installation

FRITSCH Emilie - L. Int
Dear all,

I installed Galaxy last week on our server following the tutorial on Admin/GetGalaxy from the wiki. I had no problem and it was running fine. However, as one of my colleague required the localhost:8080,  I had to change the port number. I followed the tutorial on the wiki « Running galaxy in a production environment ». I copied the galaxy.ini.sample, modified the port and also the additional parameters as suggested. Since then, I get an error message stating that "socket.error: [Errno 98] Address already in use ».  I checked and the port is free. 
I copy at the end of this message part of the standard and error output, hoping this could help figuring out what the problem is. Additionally I noticed that there was another warning, right at the beginning, when running the run.sh script:
/data/database/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility

I have checked on previous messages to see if someone had the same problem but usually it seemed that only changing the port in config/galaxy.ini worked.

Thanks a lot in advance, I am newbie and am a bit puzzled on that one,
Emilie

Starting server in PID 27030.
Traceback (most recent call last):
  File "./scripts/paster.py", line 33, in <module>
    serve.run()
  File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1049, in run
    invoke(command, command_name, options, args[1:])
  File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke
    exit_code = runner.run(args)
  File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 220, in run
    result = self.command()
  File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 670, in command
    serve()
  File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 654, in serve
    server(app)
  File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 292, in server_wrapper
    **context.local_conf)
  File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 97, in fix_call
    val = callable(*args, **kw)
  File "/data/database/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1342, in server_runner
    serve(wsgi_app, **kwargs)
  File "/data/database/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1291, in serve
    request_queue_size=request_queue_size)
  File "/data/database/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1134, in __init__
    request_queue_size=request_queue_size)
  File "/data/database/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1113, in __init__
    request_queue_size=request_queue_size)
  File "/data/database/galaxy-dist/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

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in your mail client.  To manage your subscriptions to this
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Re: Problem with Galaxy installation

Martin Čech
Hello Emilie,

this error often indicates that previous Galaxy process is still running and occupying the port. Try killing it.

If it is not the case could you please share your Galaxy configuration file with us (you can use e.g. https://gist.github.com/ ). Make sure you censor any login/password information e.g. DB access before sharing.

Thanks

Martin

On Tue Jan 20 2015 at 10:29:03 AM FRITSCH Emilie - L. Int <[hidden email]> wrote:
Dear all,

I installed Galaxy last week on our server following the tutorial on Admin/GetGalaxy from the wiki. I had no problem and it was running fine. However, as one of my colleague required the localhost:8080,  I had to change the port number. I followed the tutorial on the wiki « Running galaxy in a production environment ». I copied the galaxy.ini.sample, modified the port and also the additional parameters as suggested. Since then, I get an error message stating that "socket.error: [Errno 98] Address already in use ».  I checked and the port is free. 
I copy at the end of this message part of the standard and error output, hoping this could help figuring out what the problem is. Additionally I noticed that there was another warning, right at the beginning, when running the run.sh script:
/data/database/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility

I have checked on previous messages to see if someone had the same problem but usually it seemed that only changing the port in config/galaxy.ini worked.

Thanks a lot in advance, I am newbie and am a bit puzzled on that one,
Emilie

Starting server in PID 27030.
Traceback (most recent call last):
  File "./scripts/paster.py", line 33, in <module>
    serve.run()
  File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1049, in run
    invoke(command, command_name, options, args[1:])
  File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke
    exit_code = runner.run(args)
  File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 220, in run
    result = self.command()
  File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 670, in command
    serve()
  File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 654, in serve
    server(app)
  File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 292, in server_wrapper
    **context.local_conf)
  File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 97, in fix_call
    val = callable(*args, **kw)
  File "/data/database/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1342, in server_runner
    serve(wsgi_app, **kwargs)
  File "/data/database/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1291, in serve
    request_queue_size=request_queue_size)
  File "/data/database/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1134, in __init__
    request_queue_size=request_queue_size)
  File "/data/database/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1113, in __init__
    request_queue_size=request_queue_size)
  File "/data/database/galaxy-dist/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
___________________________________________________________
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/
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Re: Problem with Galaxy installation

FRITSCH Emilie - L. Int
Dear Martin,

Thanks for your answer. I found what the problem was, I had forgotten to delete the # in #port when I modified the galaxy.ini. It now works perfectly fine.

Thanks a lot again,
Emilie

De : Martin Čech <[hidden email]>
Date : mardi 20 janvier 2015 16:43
À : Emilie Fritsch <[hidden email]>, "[hidden email]" <[hidden email]>
Objet : Re: [galaxy-dev] Problem with Galaxy installation

Hello Emilie,

this error often indicates that previous Galaxy process is still running and occupying the port. Try killing it.

If it is not the case could you please share your Galaxy configuration file with us (you can use e.g. https://gist.github.com/ ). Make sure you censor any login/password information e.g. DB access before sharing.

Thanks

Martin

On Tue Jan 20 2015 at 10:29:03 AM FRITSCH Emilie - L. Int <[hidden email]> wrote:
Dear all,

I installed Galaxy last week on our server following the tutorial on Admin/GetGalaxy from the wiki. I had no problem and it was running fine. However, as one of my colleague required the localhost:8080,  I had to change the port number. I followed the tutorial on the wiki « Running galaxy in a production environment ». I copied the galaxy.ini.sample, modified the port and also the additional parameters as suggested. Since then, I get an error message stating that "socket.error: [Errno 98] Address already in use ».  I checked and the port is free. 
I copy at the end of this message part of the standard and error output, hoping this could help figuring out what the problem is. Additionally I noticed that there was another warning, right at the beginning, when running the run.sh script:
/data/database/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility

I have checked on previous messages to see if someone had the same problem but usually it seemed that only changing the port in config/galaxy.ini worked.

Thanks a lot in advance, I am newbie and am a bit puzzled on that one,
Emilie

Starting server in PID 27030.
Traceback (most recent call last):
  File "./scripts/paster.py", line 33, in <module>
    serve.run()
  File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1049, in run
    invoke(command, command_name, options, args[1:])
  File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke
    exit_code = runner.run(args)
  File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 220, in run
    result = self.command()
  File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 670, in command
    serve()
  File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 654, in serve
    server(app)
  File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 292, in server_wrapper
    **context.local_conf)
  File "/data/database/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 97, in fix_call
    val = callable(*args, **kw)
  File "/data/database/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1342, in server_runner
    serve(wsgi_app, **kwargs)
  File "/data/database/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1291, in serve
    request_queue_size=request_queue_size)
  File "/data/database/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1134, in __init__
    request_queue_size=request_queue_size)
  File "/data/database/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1113, in __init__
    request_queue_size=request_queue_size)
  File "/data/database/galaxy-dist/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
___________________________________________________________
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/