Re: [galaxy-dev] upload error

2014-03-08 Thread ruiwang.sz
Hi John,

Thanks for the note. Please see inline.

On Fri, Mar 7, 2014 at 7:18 PM, John Chilton jmchil...@gmail.com wrote:

 Hmm... I am not certain but it sounds like the migration script ripped
 something out of your Galaxy tool panel that you did not want it to? This
 is unfortunate - but I don't think it would happen again now that the
 migration process is complete. Some future update to Galaxy may include
 additional migrations scripts but now that macs is out it won't ever be
 migrated again.  imagine you can just update your tool_conf.xml file to
 point to your existing macs wrapper you set up manually and you can either
 leave the devteam version of macs in place or uninstall it if you prefer
 your own. Is it not this easy?


Yes that's what I thought, but I was worrying that if I remove devteam
version of macs from the migrated_tool.conf, I might break something
potentially useful for galaxy. Mainly, I try not to manually change things
since that would not be maintainable over time. That's why I was asking how
to handle this properly. It's great to have your confirmation that it works
this way. :-)

Thanks,
Rui
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Re: [galaxy-dev] upload error

2014-03-08 Thread Martin Čech
Awesome. How is the upload behaving? Are you still having issues with it?

M.


On Sat, Mar 8, 2014 at 12:20 PM, ruiwang.sz ruiwang...@gmail.com wrote:

 Hi John,

 Thanks for the note. Please see inline.

 On Fri, Mar 7, 2014 at 7:18 PM, John Chilton jmchil...@gmail.com wrote:

 Hmm... I am not certain but it sounds like the migration script ripped
 something out of your Galaxy tool panel that you did not want it to? This
 is unfortunate - but I don't think it would happen again now that the
 migration process is complete. Some future update to Galaxy may include
 additional migrations scripts but now that macs is out it won't ever be
 migrated again.  imagine you can just update your tool_conf.xml file to
 point to your existing macs wrapper you set up manually and you can either
 leave the devteam version of macs in place or uninstall it if you prefer
 your own. Is it not this easy?


 Yes that's what I thought, but I was worrying that if I remove devteam
 version of macs from the migrated_tool.conf, I might break something
 potentially useful for galaxy. Mainly, I try not to manually change things
 since that would not be maintainable over time. That's why I was asking how
 to handle this properly. It's great to have your confirmation that it works
 this way. :-)

 Thanks,
 Rui

 ___
 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:
   http://lists.bx.psu.edu/

 To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/

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Re: [galaxy-dev] upload error in the local instance of galaxy

2011-10-24 Thread Nate Coraor
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

2011-10-19 Thread Brad Langhorst
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,