Is this problem still related to ucsc? It looks like Galaxy thought it was serving data to IGV? Any clues why that is? -John On Fri, Mar 14, 2014 at 12:45 PM, Pete Schmitt < Peter.R.Schmitt@dartmouth.edu> wrote:
I put the galaxy server behind an apache proxy. Unfortunately the problem persists.
---------------------------------------- galaxy.webapps.galaxy.controllers.dataset DEBUG 2014-03-14 13:39:52,794 Unknown URL parameter name provided: galaxy_257f23ebf7c87bff.bam.tdf 209.222.195.118 - - [14/Mar/2014:13:39:52 -0400] "HEAD /display_application/257f23ebf7c87bff/igv_bam/web_link_main/0a34505ca0c7b470/data/galaxy_257f23ebf7c87bff.bam.tdf HTTP/1.1" 404 - "-" "IGV Version 2.3.31 (36)02/26/2014 10:24 PM" 69.173.70.148 - - [14/Mar/2014:13:40:38 -0400] "GET /display_application/257f23ebf7c87bff/igv_bam/web_link_main/0a34505ca0c7b470/data/galaxy_257f23ebf7c87bff.bam HTTP/1.1" 200 817113 "-" "Java/1.7.0_01" ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 34781)
Traceback (most recent call last): File "/nextgen3/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1068, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib64/python2.6/SocketServer.py", line 322, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib64/python2.6/SocketServer.py", line 618, in __init__ self.finish() File "/usr/lib64/python2.6/SocketServer.py", line 661, in finish self.wfile.flush() File "/usr/lib64/python2.6/socket.py", line 297, in flush self._sock.sendall(buffer(data, write_offset, buffer_size)) error: [Errno 32] Broken pipe ----------------------------------------
On 3/14/14, 11:37 AM, John Chilton wrote:
To reinforce what Peter suggestion - I don't believe that Galaxy's default web server (paste) is capable of handling partial byte ranges and so my understanding is you must set a proxy like Apache or nginx up in front of Galaxy in order to use the UCSC browser in this fashion.
-John
On Tue, Mar 11, 2014 at 8:41 AM, Pete Schmitt < Peter.R.Schmitt@dartmouth.edu> wrote:
No, the galaxy server serves up itself on port 8080.
On 3/11/14, 9:39 AM, Peter Cock wrote:
Are you using Apache? This might help: http://lists.bx.psu.edu/pipermail/galaxy-user/2012-November/005508.htmlhttps...
Peter
On Tue, Mar 11, 2014 at 1:16 PM, Pete Schmitt<Peter.R.Schmitt@dartmouth.edu> <Peter.R.Schmitt@dartmouth.edu> wrote:
Where would the configuration be in the galaxy server that would cause something like this. This worked in the previous year-old version of galaxy that was installed.
On 3/11/14, 6:21 AM, Peter Cock wrote:
This looks like Galaxy asking for part of a BAM file, using a byte range request, but the server hosting the BAM file is not handling this. It is probably a configuration error on that server, or perhaps in a proxy?
Peter
--
* Pete Schmitt Technical Director: Discovery Cluster NH INBRE Grid Computational Genetics Lab Institute for Quantitative Biomedical Sciences Dartmouth College, HB 6203 L12 Berry/Baker Library Hanover, NH 03755 Phone: 603-646-8109 <603-646-8109> http://discovery.dartmouth.edu <http://discovery.dartmouth.edu> http://columbia.dartmouth.edu/grid <http://columbia.dartmouth.edu/grid> http://www.epistasis.org <http://www.epistasis.org> http://iQBS.org <http://iQBS.org> *
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* Pete Schmitt Technical Director: Discovery Cluster NH INBRE Grid Computational Genetics Lab Institute for Quantitative Biomedical Sciences Dartmouth College, HB 6203 L12 Berry/Baker Library Hanover, NH 03755 Phone: 603-646-8109 <603-646-8109> http://discovery.dartmouth.edu <http://discovery.dartmouth.edu> http://columbia.dartmouth.edu/grid <http://columbia.dartmouth.edu/grid> http://www.epistasis.org <http://www.epistasis.org> http://iQBS.org <http://iQBS.org> *
