George Yianni Michopoulos wrote:
> To any wonderful person that can help me:
> 
>       I recently uploaded a local instance of Galaxy on a new computer at the 
> Fernald Lab at Stanford. I am not too familiar with Unix, but needed to 
> install the local instance due to the high volume of genomic data we will be 
> processing, and so that we could install/use the FastX toolkit. I managed to 
> successfully install the toolkit, but now I just realized that I can't seem 
> to upload any of my correctly formatted data files. The error I get is pasted 
> below:
> 
> "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_4; en-us) 
> AppleWebKit/533.18.1 (KHTML, like Gecko) Version/5.0.2 Safari/533.18.5"
> Debug at: http://localhost:8080/_debug/view/1303859435
> ----------------------------------------
> Exception happened during processing of request from ('127.0.0.1', 61553)
> Traceback (most recent call last):
>   File 
> "/Users/***/bin/fastx_bin/galaxy_test/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
>  line 1053, in process_request_in_thread
>     self.finish_request(request, client_address)
>   File 
> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.py",
>  line 322, in finish_request
>     self.RequestHandlerClass(request, client_address, self)
>   File 
> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.py",
>  line 617, in __init__
>     self.handle()
>   File 
> "/Users/***/bin/fastx_bin/galaxy_test/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
>  line 432, in handle
>     BaseHTTPRequestHandler.handle(self)
>   File 
> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/BaseHTTPServer.py",
>  line 329, in handle
>     self.handle_one_request()
>   File 
> "/Users/***/bin/fastx_bin/galaxy_test/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
>  line 427, in handle_one_request
>     self.wsgi_execute()
>   File 
> "/Users/***/bin/fastx_bin/galaxy_test/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
>  line 287, in wsgi_execute
>     self.wsgi_start_response)
>   File 
> "/Users/***/bin/fastx_bin/galaxy_test/eggs/Paste-1.6-py2.6.egg/paste/urlmap.py",
>  line 202, in __call__
>     return app(environ, start_response)
>   File 
> "/Users/***/bin/fastx_bin/galaxy_test/lib/galaxy/web/framework/middleware/xforwardedhost.py",
>  line 21, in __call__
>     return self.app( environ, start_response )
>   File 
> "/Users/***/bin/fastx_bin/galaxy_test/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/config.py",
>  line 164, in __call__
>     app_iter = self.application(environ, start_response)
>   File 
> "/Users/***/bin/fastx_bin/galaxy_test/lib/galaxy/web/framework/middleware/translogger.py",
>  line 68, in __call__
>     return self.application(environ, replacement_start_response)
>   File 
> "/Users/***/bin/fastx_bin/galaxy_test/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py",
>  line 226, in __call__
>     return self.respond(environ, start_response)
>   File 
> "/Users/***/bin/fastx_bin/galaxy_test/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py",
>  line 399, in respond
>     if self.xmlhttp_key in req.params:
>   File 
> "/Users/***/bin/fastx_bin/galaxy_test/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py",
>  line 900, in params
>     params = self.str_params
>   File 
> "/Users/***/bin/fastx_bin/galaxy_test/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py",
>  line 892, in str_params
>     return NestedMultiDict(self.str_GET, self.str_POST)
>   File 
> "/Users/***/bin/fastx_bin/galaxy_test/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py",
>  line 818, in str_POST
>     keep_blank_values=True)
>   File 
> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", 
> line 508, in __init__
>     self.read_multi(environ, keep_blank_values, strict_parsing)
>   File 
> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", 
> line 632, in read_multi
>     environ, keep_blank_values, strict_parsing)
>   File 
> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", 
> line 510, in __init__
>     self.read_single()
>   File 
> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", 
> line 647, in read_single
>     self.read_lines()
>   File 
> "/Users/***/bin/fastx_bin/galaxy_test/lib/galaxy/web/framework/base.py", line 
> 253, in read_lines
>     self.read_lines_to_outerboundary()
>   File 
> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", 
> line 697, in read_lines_to_outerboundary
>     line = self.fp.readline(1<<16)
>   File 
> "/Users/***/bin/fastx_bin/galaxy_test/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
>  line 467, in readline
>     data = self.file.readline(self.length - self._consumed)
>   File 
> "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/socket.py", 
> line 409, in readline
>     bline = buf.readline(size)
> OverflowError: long int too large to convert to int"
> 
> (I replaced irrelevant components of the file path with *** for 
> confidentiality purposes)
> 
> Do you have any idea what the problem is and how I can fix it? I feel like it 
> has something to do with my python, but I downloaded 2.6.6, which I thought 
> should work according to the Install Readme. Thanks so much for your help!

Hi George,

Could you set:

  debug = False

In universe_wsgi.ini, restart Galaxy, and try again?

Thanks,
--nate

> 
> Sincerely,
> 
> George Michopoulos
> Stanford University '13
> on behalf of the Fernald Lab
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