problems when install galaxy locally with python2.7.3 interpreter and platform ubuntu12.04
Hello, galaxy developers and maintainers: I'm a user from the Chinese mainland. I have ubuntu 12.04 OS and python2.7.3 interpreter. After confirming that I've installed openssl-dev and bzip-dev and python version >2.5, I use virtualenv to create galaxy_env and just run "hg clone https:xxxxxxxx/galaxy-dist; cd galaxy-dist; sh run.sh" in the directory of galaxy. It seems that it's not the problem of linux w/r/x permission. After downloading some egg of python, the shell display as follows: ############################################################################################ /home/don/galaxy-dist/lib/galaxy/__init__.py:79: UserWarning: Module markupsafe was already imported from /usr/lib/python2.7/dist-packages/markupsafe/__init__.pyc, but /home/don/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg is being added to sys.path self.check_version_conflict() .................. .................. Starting server in PID 12288. Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/home/don/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/home/don/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/home/don/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 218, in run result = self.command() File "/home/don/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 303, in command serve() File "/home/don/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 287, in serve server(app) File "/home/don/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 151, in server_wrapper **context.local_conf) File "/home/don/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/home/don/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1314, in server_runner serve(wsgi_app, **kwargs) File "/home/don/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1264, in serve threadpool_options=threadpool_options) File "/home/don/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1114, in __init__ RequestHandlerClass, ssl_context) File "/home/don/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1094, in __init__ RequestHandlerClass, ssl_context) File "/home/don/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 358, in __init__ HTTPServer.__init__(self, server_address, RequestHandlerClass) File "/usr/lib/python2.7/SocketServer.py", line 408, 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 419, 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.error: [Errno 98] Address already in use ############################################################################################ And I really have no idea what's wrong with galaxy and python. Thanks for your help and advice. Wangdan 2012.10.17
Hello,
socket.error: [Errno 98] Address already! in use
This error message indicates that Galaxy is trying to bind to a port that is in use by another application. Changing the port option in your universe_wsgi.ini to a different value should resolve this issue. --Dave B. On 10/17/12 08:26:39.000, 王聃 wrote:
Hello, galaxy developers and maintainers: I'm a user from the Chinese mainland. I have ubuntu 12.04 OS and python2.7.3 interpreter. After confirming that I've installed openssl-dev and bzip-dev and python version >2.5, I use virtualenv to create galaxy_env and just run "hg clone https:xxxxxxxx/galaxy-dist; cd galaxy-dist; sh run.sh" in the directory of galaxy. It seems that it's not the problem of linux w/r/x permission. After downloading some egg of python, the shell display as follows: ############################################################################################ /home/don/galaxy-dist/lib/galaxy/__init__.py:79: UserWarning: Module markupsafe was already imported from /usr/lib/python2.7/dist-packages/markupsafe/__init__.pyc, but /home/don/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg is being added to sys.path self.check_version_conflict() .................. ..................
Starting server in PID 12288. Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/home/don/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/home/don/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/home/don/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 218, in run result = self.command() File "/home/don/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 303, in command serve() File "/home/don/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 287, in serve server(app) File "/home/don/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 151, in server_wrapper **context.local_conf) File "/home/don/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/home/don/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1314, in server_runner serve(wsgi_app, **kwargs) File "/home/don/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1264, in serve threadpool_options=threadpool_options) File "/home/don/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line ! 1114, in __init__ RequestHandlerClass, ssl_cont! ext) File "/home/don/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 1094, in __init__ RequestHandlerClass, ssl_context) File "/home/don/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 358, in __init__ HTTPServer.__init__(self, server_address, RequestHandlerClass) File "/usr/lib/python2.7/SocketServer.py", line 408, 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 419, 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.error: [Errno 98] Address already! in use ############################################################################################ And I really have no idea what's wrong with galaxy and python. Thanks for your help and advice.
Wangdan 2012.10.17
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Dave Bouvier -
王聃