New subject: Question Regarding Local Galaxy Installation Uploading Files Error

30 Apr 2011


      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