Question: Error in loading data to IGB from Galaxy
0
gravatar for jchen015
3.1 years ago by
jchen01580
Singapore
jchen01580 wrote:

Dear All

I have installed Integrated Genome Browser in my local workstation.

I uploading the same data file (BAM format) to both public galaxy server and my local server.

After which i click on "display in IGB view" to visualize it. The data were properly visualized in through public Galaxy server but when I view in through my local server, it appears the following error:

 

Exception happened during processing of request from ('172.20.0.85', 52434)
Traceback (most recent call last):
  File "/addhdd/project/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
    self.finish_request(request, client_address)
  File "/usr/lib/python2.7/SocketServer.py", line 334, in finish_request
    self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib/python2.7/SocketServer.py", line 651, in __init__
    self.finish()
  File "/usr/lib/python2.7/SocketServer.py", line 710, in finish
    self.wfile.close()
  File "/usr/lib/python2.7/socket.py", line 279, in close
    self.flush()
  File "/usr/lib/python2.7/socket.py", line 303, in flush
    self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
----------------------------------------

Anyone know whats the issue?

 

Best,

Julius

igb galaxy • 921 views
ADD COMMENTlink modified 3.1 years ago by Daniel Blankenberg ♦♦ 1.7k • written 3.1 years ago by jchen01580
0
gravatar for jchen015
3.1 years ago by
jchen01580
Singapore
jchen01580 wrote:

Dear all, 

the attached is the image that show a displaying of no data (that is linked from Galaxy).

URL: https://www.dropbox.com/s/h4q55w7qzoxzh08/image.PNG?dl=0

ADD COMMENTlink written 3.1 years ago by jchen01580
0
gravatar for Daniel Blankenberg
3.1 years ago by
Daniel Blankenberg ♦♦ 1.7k
United States
Daniel Blankenberg ♦♦ 1.7k wrote:

You'll want to have a byte-range accepting proxy, such as nginx or apache, infront of your Galaxy instance. Many of these external displays require using byte-ranges to get only the relevant chunks of data at a time, instead of having to download e.g. the whole BAM file.

See also the proxy options in https://wiki.galaxyproject.org/Admin/Config/

ADD COMMENTlink written 3.1 years ago by Daniel Blankenberg ♦♦ 1.7k
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