On 10/19/11 3:09 AM, "Amit Anand" amit@tll.org.sg wrote:
Hi,
I have just installed a local instance of galaxy. Though I am not too familiar with unix, I preferred a local instance because of large amount of data I have to process. However, I am unable to upload a file more that 2 GB in size, the error log is pased below
Hi anand: It¹s not possible to upoad such big files. You need to use FTP or local file import methods to do that.
See: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files ?highlight=%28import%29
Brad
127.0.0.1 - - [19/Oct/2011:15:06:08 +0800] "POST /tool_runner/index HTTP/1.1" 500 - "http://127.0.0.1:8080/tool_runner?tool_id=upload1" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:6.0.2) Gecko/20100101 Firefox/6.0.2" Debug at: http://127.0.0.1:8080/_debug/view/1319007854
Exception happened during processing of request from ('127.0.0.1', 61099) Traceback (most recent call last): File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv er.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/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv er.py", line 432, in handle BaseHTTPRequestHandler.handle(self) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/BaseHTTPServe r.py", line 329, in handle self.handle_one_request() File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv er.py", line 427, in handle_one_request self.wsgi_execute() File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv er.py", line 287, in wsgi_execute self.wsgi_start_response) File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/urlmap.p y", line 202, in __call__ return app(environ, start_response) File "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/middleware/xfo rwardedhost.py", line 21, in __call__ return self.app( environ, start_response ) File "/Users/amit/galaxy-python/galaxy-dist/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/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/middleware/tra nslogger.py", line 68, in __call__ return self.application(environ, replacement_start_response) File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/e valexception/middleware.py", line 226, in __call__ return self.respond(environ, start_response) File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/e valexception/middleware.py", line 399, in respond if self.xmlhttp_key in req.params: File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init __.py", line 900, in params params = self.str_params File "/Users/amit/galaxy-python/galaxy-dist/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/amit/galaxy-python/galaxy-dist/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/amit/galaxy-python/galaxy-dist/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/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv er.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
Please help me to fix this, the python version is 2.6.6. Thank you.
Sincerely,
Amit,
Germline biology group Temasek Life Sciences Laboratory Singapore