Good afternoon,
I'm having several problems with my local galaxy install which may or may
not be related to one another.
The first problem I'm having is with the "Display data in browser" feature.
Some files type formats (fastqsanger, fasta) display fine. However, other
file type formats (png, svg, txt) simply do not display at all. I have
debugging turned on, but do not see any error within the browser or within
the galaxy log or web server log after clicking the "Display data in
browser" eyeball icon. It is simply a blank middle panel.
The next problem I'm having has to do with downloading files. Firefox and
Safari will download any file from a history, but will just create an empty
file on the client. Again, neither log file show an error with a clue to
the problem. Chrome will download some files, but other files give me an
error and won't download:
*This webpage is not available*
*
*
*error 100 (net::ERR_CONNECTION_CLOSED): The server unexpectedly closed the
connection.*
In this case, I don't see anything in the log files either.
Finally, I'm also having a problem logging in from the main welcome page.
It seems to authenticate fine (I get an error when I put in the wrong
password and don't when I put in the correct password), but it doesn't
actually log me in and just takes me back to the main welcome page.
For this problem, I do get an error in the galaxy log:
*Exception happened during processing of request
from---------------------------------------- *
*('myip', 50593)Exception happened during processing of request from *
*('myip', 50594)*
*Traceback (most recent call last):*
*Traceback (most recent call last):*
* File
"/raid/galaxy_user/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
line 1053, in process_request_in_thread*
* File
"/raid/galaxy_user/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py",
line 1053, in process_request_in_thread*
* self.finish_request(request, client_address)*
* self.finish_request(request, client_address)*
* File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 322, in
finish_request*
* File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 322, in
finish_request*
* self.RequestHandlerClass(request, client_address, self)*
* self.RequestHandlerClass(request, client_address, self)*
* File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 618, in
__init__*
* File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 618, in
__init__*
* self.finish()*
* File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 661, in
finish*
* self.finish()*
* self.wfile.flush()*
* File "/raid/galaxy_user/lib/python2.6/socket.py", line 297, in flush*
* self._sock.sendall(buffer(data, write_offset, buffer_size))*
* File "/raid/galaxy_user/lib/python2.6/SocketServer.py", line 661, in
finish*
*error: [Errno 32] Broken pipe*
*----------------------------------------*
* self.wfile.flush()*
* File "/raid/galaxy_user/lib/python2.6/socket.py", line 297, in flush*
* self._sock.sendall(buffer(data, write_offset, buffer_size))*
*error: [Errno 32] Broken pipe*
I am able to log in via other routes, such as going to "Options->Saved
Histories" which brings up an error "You must be logged in" to work with
multiple histories and links to /galaxy/user/login?webapp=galaxy and from
there I can log in fine. This happens with both admin and normal users. It
is not a huge problem since I have a work around, but it would be nice to
figure out the problem so I don't have to make my users do the same.
I should mention that I'm running galaxy-dist changeset 50e249442c5a on
CentOS. The problems seem to be web server independent too as they appear
with both Apache and Nginx. I've used the following instructions, but I'm
just not seeing where the problem(s) is/are:
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/nginxProxy
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScaling
Thanks,
Matt
--
Matthew Conte
Bioinformatics Scientist
Department of Biology
University of Maryland
mco...@umd.edu
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