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