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 ___________________________________________________________ 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:

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