Re: [galaxy-dev] upload error in the local instance of galaxy
Brad Langhorst wrote:
On 10/19/11 3:09 AM, Amit Anand a...@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
You probably also need to set:
debug = False
use_interactive = False
In universe_wsgi.ini
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(116)
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
Re: [galaxy-dev] upload error in the local instance of galaxy
On 10/19/11 3:09 AM, Amit Anand a...@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(116)
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,
