Hey Pete, I have exactly the same problem haven’t find a solution yet but previous versions was working without any problem.
Let me know if you solve it.
Alper Kucukural, PhD Bioinformatics Core, University of Massachusetts Medical School 368 Plantation St.Room AS4.2067 Worcester, MA 01605-2324 Phone: 774-312-4493 E-mail: alper@kucukural.com
On Mar 10, 2014, at 7:09 PM, Pete Schmitt Peter.R.Schmitt@dartmouth.edu wrote:
Latest version of galaxy running on CentOS 5.10 with python 2.6.8
When attempting to use display at UCSC main test
There is an error at UCSC: unable to get the display-data <Screen Shot 2014-03-10 at 7.08.12 PM.png>
Error from paster.log:
128.114.119.136 - - [10/Mar/2014:18:52:56 -0400] "GET /display_application/257f23ebf7c87bff/ucsc_bam/main/0a34505ca0c7b470/data/galaxy_257f23ebf7c87bff.bam HTTP/1.0" 200 817113 "-" "genome.ucsc.edu/net.c"
Exception happened during processing of request from ('128.114.119.136', 29811) 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
I'm not sure what the error above means.
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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
On Mon, Mar 10, 2014 at 11:09 PM, Pete Schmitt < Peter.R.Schmitt@dartmouth.edu> wrote:
Latest version of galaxy running on CentOS 5.10 with python 2.6.8
When attempting to use display at UCSC mainhttp://dirigo.mdibl.org:8080/display_application/257f23ebf7c87bff/ucsc_bam/main testhttp://dirigo.mdibl.org:8080/display_application/257f23ebf7c87bff/ucsc_bam/test
There is an error at UCSC: unable to get the display-data
Error from paster.log:
128.114.119.136 - - [10/Mar/2014:18:52:56 -0400] "GET /display_application/257f23ebf7c87bff/ucsc_bam/main/0a34505ca0c7b470/data/galaxy_257f23ebf7c87bff.bam HTTP/1.0" 200 817113 "-" "genome.ucsc.edu/net.c"
Exception happened during processing of request from ('128.114.119.136', 29811) 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
I'm not sure what the error above means.
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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
On Mon, Mar 10, 2014 at 11:09 PM, Pete Schmitt <Peter.R.Schmitt@dartmouth.edu mailto:Peter.R.Schmitt@dartmouth.edu> wrote:
Latest version of galaxy running on CentOS 5.10 with python 2.6.8 When attempting to use display at UCSC main <http://dirigo.mdibl.org:8080/display_application/257f23ebf7c87bff/ucsc_bam/main> test <http://dirigo.mdibl.org:8080/display_application/257f23ebf7c87bff/ucsc_bam/test> There is an error at UCSC: unable to get the display-data Error from paster.log: 128.114.119.136 - - [10/Mar/2014:18:52:56 -0400] "GET /display_application/257f23ebf7c87bff/ucsc_bam/main/0a34505ca0c7b470/data/galaxy_257f23ebf7c87bff.bam HTTP/1.0" 200 817113 "-" "genome.ucsc.edu/net.c <http://genome.ucsc.edu/net.c>" ---------------------------------------- Exception happened during processing of request from ('128.114.119.136', 29811) 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 I'm not sure what the error above means. ___________________________________________________________ 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/
Are you using Apache? This might help:
http://lists.bx.psu.edu/pipermail/galaxy-user/2012-November/005508.html https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
Peter
On Tue, Mar 11, 2014 at 1:16 PM, Pete Schmitt 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
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.html https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
Peter
On Tue, Mar 11, 2014 at 1:16 PM, Pete Schmitt 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
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 SchmittPeter.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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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 SchmittPeter.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 *
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/
--
- 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 *
galaxy-dev@lists.galaxyproject.org
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Alper Kucukural -
John Chilton -
Pete Schmitt -
Peter Cock