Re: [galaxy-dev] Display BAM with IGV
Hi Everyone, I have been tasked with getting the IGV working within our Galaxy instance. I have modified our Nginx configuration based on the more advanced configuration under "Sending files using nginx" on the nginxProxy page in the wiki. The IGV viewer component in Galaxy does not display the results from a BAM file in either the web or local instance of IGV. I have tested with IGV1.5 and with version 2.03. Neither produce a visual representation of the sequence. When attempting to use the web option we get the same error provided in the original post as noted below. Has anyone gotten this to work with Nginx-0.8.53 or any of the newer versions? Thanks, Iry Witham Applications Administrator Scientific Computing Group Computational Sciences Dept. The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6744 email: iry.witham@jax.org On Apr 27, 2011; 10:06am “Hello all, I just updated our local copy of Galaxy and just wanted to try the new IGV display application. When I try to display a BAM file with the local IGV or the web IGV I encounter following error complaining about the Null content-length. Has any of you encountered the same problem? Do I miss something? Thanks in advance Alex INFO [2011-04-27 16:00:14,440] [TrackManager.java:225] [Thread-6] Loading1 resources. ERROR [2011-04-27 16:00:14,589] [SeekableHTTPStream.java:59] [Thread-6] Null content-length for: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454... ERROR [2011-04-27 16:00:14,590] [TrackLoader.java:821] [Thread-6] Error loading sam track java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454... NULL content-length at org.broad.igv.util.SeekableHTTPStream.<init>(SeekableHTTPStream.java:60) at org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:42) at org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader.java:129) at org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader.java:70) at org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQueryReader.java:80) at org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQueryReader.java:97) at org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.java:75) at org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:69) at org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManager.java:54) at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:761) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:143) at org.broad.igv.track.TrackManager.load(TrackManager.java:271) at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241) at org.broad.igv.main.CommandExecutor.loadFiles(CommandExecutor.java:282) at org.broad.igv.main.CommandExecutor.hget(CommandExecutor.java:148) at org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java:88) at org.broad.igv.main.CommandListener.processGet(CommandListener.java:193) at org.broad.igv.main.CommandListener.run(CommandListener.java:93) at java.lang.Thread.run(Thread.java:636) ERROR [2011-04-27 16:00:14,592] [TrackLoader.java:211] [Thread-6] java.lang.RuntimeException: java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454... NULL content-length” On Apr 27, 2011; 12:33pm “Hi Alex, Displaying BAM files at external applications usually requires an http server that supports partial gets. Unfortunately, the current lightweight http server that is built into Galaxy does not support these advanced http options. However, this limitation can be overcome by using a proxy server that is able to handle http1.1 requests. Please see "Using a Proxy server" at https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer for help on setting this up. Thanks for using Galaxy, Dan” On Apr 27, 2011; 9:07pm “I’m getting this same error and I’m running nginx as a proxy server. Is there a specfic parameter we should be aware of to allow partial gets? I don’t see anything in the wiki page for setting up the ProductionServer. Thanks, Dave” On May 04, 2011; 7:47am “Could someone who has successfully gotten the IGV tool to work using NGINX as your proxy, tell me if there was anything specific they needed to do with their NGINX or galaxy config to get it working? Thanks, Dave” On May 09, 2011; 2:52pm “It's necessary to set up the more advanced configuration under "Sending files using nginx" on the nginxProxy page in the wiki. Could you let us know whether you're using that configuration or just a basic pass-through proxy? Thanks, --nate”
Iry Witham wrote:
Hi Everyone,
I have been tasked with getting the IGV working within our Galaxy instance. I have modified our Nginx configuration based on the more advanced configuration under "Sending files using nginx" on the nginxProxy page in the wiki. The IGV viewer component in Galaxy does not display the results from a BAM file in either the web or local instance of IGV. I have tested with IGV1.5 and with version 2.03. Neither produce a visual representation of the sequence. When attempting to use the web option we get the same error provided in the original post as noted below. Has anyone gotten this to work with Nginx-0.8.53 or any of the newer versions?
Hi Iry, Have you checked to make sure that your nginx server is serving the file for download, as opposed to the internal Galaxy web server? In the original email, it looked like nginx was being bypassed entirely (due to serving on port 8080 - Galaxy's intenal server's default port). But even once nginx is in use, it's necessary to set up X-Accel-Redirect to serve datasets. See the instructions here: http://usegalaxy.org/production --nate
Thanks,
Iry Witham Applications Administrator Scientific Computing Group Computational Sciences Dept. The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6744 email: iry.witham@jax.org
On Apr 27, 2011; 10:06am “Hello all, I just updated our local copy of Galaxy and just wanted to try the new IGV display application. When I try to display a BAM file with the local IGV or the web IGV I encounter following error complaining about the Null content-length. Has any of you encountered the same problem? Do I miss something? Thanks in advance
Alex
INFO [2011-04-27 16:00:14,440] [TrackManager.java:225] [Thread-6] Loading1 resources. ERROR [2011-04-27 16:00:14,589] [SeekableHTTPStream.java:59] [Thread-6] Null content-length for: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454... ERROR [2011-04-27 16:00:14,590] [TrackLoader.java:821] [Thread-6] Error loading sam track java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454... NULL content-length at org.broad.igv.util.SeekableHTTPStream.<init>(SeekableHTTPStream.java:60) at org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:42) at org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader.java:129) at org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader.java:70) at org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQueryReader.java:80) at org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQueryReader.java:97) at org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.java:75) at org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:69) at org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManager.java:54) at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:761) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:143) at org.broad.igv.track.TrackManager.load(TrackManager.java:271) at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241) at org.broad.igv.main.CommandExecutor.loadFiles(CommandExecutor.java:282) at org.broad.igv.main.CommandExecutor.hget(CommandExecutor.java:148) at org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java:88) at org.broad.igv.main.CommandListener.processGet(CommandListener.java:193) at org.broad.igv.main.CommandListener.run(CommandListener.java:93) at java.lang.Thread.run(Thread.java:636) ERROR [2011-04-27 16:00:14,592] [TrackLoader.java:211] [Thread-6] java.lang.RuntimeException: java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454... NULL content-length”
On Apr 27, 2011; 12:33pm “Hi Alex,
Displaying BAM files at external applications usually requires an http server that supports partial gets. Unfortunately, the current lightweight http server that is built into Galaxy does not support these advanced http options. However, this limitation can be overcome by using a proxy server that is able to handle http1.1 requests. Please see "Using a Proxy server" at https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer for help on setting this up.
Thanks for using Galaxy,
Dan”
On Apr 27, 2011; 9:07pm “I’m getting this same error and I’m running nginx as a proxy server. Is there a specfic parameter we should be aware of to allow partial gets? I don’t see anything in the wiki page for setting up the ProductionServer.
Thanks,
Dave”
On May 04, 2011; 7:47am “Could someone who has successfully gotten the IGV tool to work using NGINX as your proxy, tell me if there was anything specific they needed to do with their NGINX or galaxy config to get it working?
Thanks,
Dave”
On May 09, 2011; 2:52pm “It's necessary to set up the more advanced configuration under "Sending files using nginx" on the nginxProxy page in the wiki. Could you let us know whether you're using that configuration or just a basic pass-through proxy?
Thanks, --nate”
___________________________________________________________ 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:
Hi Nate, I have checked the nginx.conf file and they comply to the documentation: # added to allow nginx to handle file downloads location /_x_accel_redirect/ { internal; alias /; I have also confirmed that the universe_wsgi.ini file contains the following: And the following to the [app:main] section of universe_wsgi.ini: nginx_x_accel_redirect_base = /_x_accel_redirect Iry On 8/15/11 10:46 AM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Iry Witham wrote:
Hi Everyone,
I have been tasked with getting the IGV working within our Galaxy instance. I have modified our Nginx configuration based on the more advanced configuration under "Sending files using nginx" on the nginxProxy page in the wiki. The IGV viewer component in Galaxy does not display the results from a BAM file in either the web or local instance of IGV. I have tested with IGV1.5 and with version 2.03. Neither produce a visual representation of the sequence. When attempting to use the web option we get the same error provided in the original post as noted below. Has anyone gotten this to work with Nginx-0.8.53 or any of the newer versions?
Hi Iry,
Have you checked to make sure that your nginx server is serving the file for download, as opposed to the internal Galaxy web server? In the original email, it looked like nginx was being bypassed entirely (due to serving on port 8080 - Galaxy's intenal server's default port). But even once nginx is in use, it's necessary to set up X-Accel-Redirect to serve datasets. See the instructions here:
http://usegalaxy.org/production
--nate
Thanks,
Iry Witham Applications Administrator Scientific Computing Group Computational Sciences Dept. The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6744 email: iry.witham@jax.org
On Apr 27, 2011; 10:06am ³Hello all, I just updated our local copy of Galaxy and just wanted to try the new IGV display application. When I try to display a BAM file with the local IGV or the web IGV I encounter following error complaining about the Null content-length. Has any of you encountered the same problem? Do I miss something? Thanks in advance
Alex
INFO [2011-04-27 16:00:14,440] [TrackManager.java:225] [Thread-6] Loading1 resources. ERROR [2011-04-27 16:00:14,589] [SeekableHTTPStream.java:59] [Thread-6] Null content-length for: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454... df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam ERROR [2011-04-27 16:00:14,590] [TrackLoader.java:821] [Thread-6] Error loading sam track java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454... df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length at org.broad.igv.util.SeekableHTTPStream.<init>(SeekableHTTPStream.java:60) at org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFactory.j ava:42) at org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader.jav a:129) at org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader.java :70) at org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQueryRead er.java:80) at org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQueryRead er.java:97) at org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.java:7 5) at org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:69) at org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManager.ja va:54) at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:761) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:143) at org.broad.igv.track.TrackManager.load(TrackManager.java:271) at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241) at org.broad.igv.main.CommandExecutor.loadFiles(CommandExecutor.java:282) at org.broad.igv.main.CommandExecutor.hget(CommandExecutor.java:148) at org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java:88) at org.broad.igv.main.CommandListener.processGet(CommandListener.java:193) at org.broad.igv.main.CommandListener.run(CommandListener.java:93) at java.lang.Thread.run(Thread.java:636) ERROR [2011-04-27 16:00:14,592] [TrackLoader.java:211] [Thread-6] java.lang.RuntimeException: java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454... df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length²
On Apr 27, 2011; 12:33pm ³Hi Alex,
Displaying BAM files at external applications usually requires an http server that supports partial gets. Unfortunately, the current lightweight http server that is built into Galaxy does not support these advanced http options. However, this limitation can be overcome by using a proxy server that is able to handle http1.1 requests. Please see "Using a Proxy server" at https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer for help on setting this up.
Thanks for using Galaxy,
Dan²
On Apr 27, 2011; 9:07pm ³I¹m getting this same error and I¹m running nginx as a proxy server. Is there a specfic parameter we should be aware of to allow partial gets? I don¹t see anything in the wiki page for setting up the ProductionServer.
Thanks,
Dave²
On May 04, 2011; 7:47am ³Could someone who has successfully gotten the IGV tool to work using NGINX as your proxy, tell me if there was anything specific they needed to do with their NGINX or galaxy config to get it working?
Thanks,
Dave²
On May 09, 2011; 2:52pm ³It's necessary to set up the more advanced configuration under "Sending files using nginx" on the nginxProxy page in the wiki. Could you let us know whether you're using that configuration or just a basic pass-through proxy?
Thanks, --nate²
___________________________________________________________ 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:
Iry Witham wrote:
Hi Nate,
I have checked the nginx.conf file and they comply to the documentation:
# added to allow nginx to handle file downloads location /_x_accel_redirect/ { internal; alias /;
I have also confirmed that the universe_wsgi.ini file contains the following:
And the following to the [app:main] section of universe_wsgi.ini: nginx_x_accel_redirect_base = /_x_accel_redirect
Iry
This will need some in-depth debugging, then. If you access Galaxy directly via the port of its built-in web server (by default, 8080), and request to display a dataset, does it set the X-Accel-Redirect header in the response? If you access the same dataset via the nginx address but rename the underlying disk file, do you get an error message from nginx or from Galaxy? --nate
On 8/15/11 10:46 AM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Iry Witham wrote:
Hi Everyone,
I have been tasked with getting the IGV working within our Galaxy instance. I have modified our Nginx configuration based on the more advanced configuration under "Sending files using nginx" on the nginxProxy page in the wiki. The IGV viewer component in Galaxy does not display the results from a BAM file in either the web or local instance of IGV. I have tested with IGV1.5 and with version 2.03. Neither produce a visual representation of the sequence. When attempting to use the web option we get the same error provided in the original post as noted below. Has anyone gotten this to work with Nginx-0.8.53 or any of the newer versions?
Hi Iry,
Have you checked to make sure that your nginx server is serving the file for download, as opposed to the internal Galaxy web server? In the original email, it looked like nginx was being bypassed entirely (due to serving on port 8080 - Galaxy's intenal server's default port). But even once nginx is in use, it's necessary to set up X-Accel-Redirect to serve datasets. See the instructions here:
http://usegalaxy.org/production
--nate
Thanks,
Iry Witham Applications Administrator Scientific Computing Group Computational Sciences Dept. The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6744 email: iry.witham@jax.org
On Apr 27, 2011; 10:06am ³Hello all, I just updated our local copy of Galaxy and just wanted to try the new IGV display application. When I try to display a BAM file with the local IGV or the web IGV I encounter following error complaining about the Null content-length. Has any of you encountered the same problem? Do I miss something? Thanks in advance
Alex
INFO [2011-04-27 16:00:14,440] [TrackManager.java:225] [Thread-6] Loading1 resources. ERROR [2011-04-27 16:00:14,589] [SeekableHTTPStream.java:59] [Thread-6] Null content-length for: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454... df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam ERROR [2011-04-27 16:00:14,590] [TrackLoader.java:821] [Thread-6] Error loading sam track java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454... df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length at org.broad.igv.util.SeekableHTTPStream.<init>(SeekableHTTPStream.java:60) at org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFactory.j ava:42) at org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader.jav a:129) at org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader.java :70) at org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQueryRead er.java:80) at org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQueryRead er.java:97) at org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.java:7 5) at org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:69) at org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManager.ja va:54) at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:761) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:143) at org.broad.igv.track.TrackManager.load(TrackManager.java:271) at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241) at org.broad.igv.main.CommandExecutor.loadFiles(CommandExecutor.java:282) at org.broad.igv.main.CommandExecutor.hget(CommandExecutor.java:148) at org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java:88) at org.broad.igv.main.CommandListener.processGet(CommandListener.java:193) at org.broad.igv.main.CommandListener.run(CommandListener.java:93) at java.lang.Thread.run(Thread.java:636) ERROR [2011-04-27 16:00:14,592] [TrackLoader.java:211] [Thread-6] java.lang.RuntimeException: java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454... df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length²
On Apr 27, 2011; 12:33pm ³Hi Alex,
Displaying BAM files at external applications usually requires an http server that supports partial gets. Unfortunately, the current lightweight http server that is built into Galaxy does not support these advanced http options. However, this limitation can be overcome by using a proxy server that is able to handle http1.1 requests. Please see "Using a Proxy server" at https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer for help on setting this up.
Thanks for using Galaxy,
Dan²
On Apr 27, 2011; 9:07pm ³I¹m getting this same error and I¹m running nginx as a proxy server. Is there a specfic parameter we should be aware of to allow partial gets? I don¹t see anything in the wiki page for setting up the ProductionServer.
Thanks,
Dave²
On May 04, 2011; 7:47am ³Could someone who has successfully gotten the IGV tool to work using NGINX as your proxy, tell me if there was anything specific they needed to do with their NGINX or galaxy config to get it working?
Thanks,
Dave²
On May 09, 2011; 2:52pm ³It's necessary to set up the more advanced configuration under "Sending files using nginx" on the nginxProxy page in the wiki. Could you let us know whether you're using that configuration or just a basic pass-through proxy?
Thanks, --nate²
___________________________________________________________ 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:
On 8/15/11 2:46 PM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Iry Witham wrote:
Hi Nate,
I have checked the nginx.conf file and they comply to the documentation:
# added to allow nginx to handle file downloads location /_x_accel_redirect/ { internal; alias /;
I have also confirmed that the universe_wsgi.ini file contains the following:
And the following to the [app:main] section of universe_wsgi.ini: nginx_x_accel_redirect_base = /_x_accel_redirect
Iry
This will need some in-depth debugging, then.
If you access Galaxy directly via the port of its built-in web server (by default, 8080), and request to display a dataset, does it set the X-Accel-Redirect header in the response?
If you access the same dataset via the nginx address but rename the underlying disk file, do you get an error message from nginx or from Galaxy?
--nate
When I add the port (8080, 8081 or 8082) I don't get the error and the IGV opens. That a great thing. However, it is now minus any alignments. But that is a different issue. Iry
On 8/15/11 10:46 AM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Iry Witham wrote:
Hi Everyone,
I have been tasked with getting the IGV working within our Galaxy instance. I have modified our Nginx configuration based on the more advanced configuration under "Sending files using nginx" on the nginxProxy page in the wiki. The IGV viewer component in Galaxy does not display the results from a BAM file in either the web or local instance of IGV. I have tested with IGV1.5 and with version 2.03. Neither produce a visual representation of the sequence. When attempting to use the web option we get the same error provided in the original post as noted below. Has anyone gotten this to work with Nginx-0.8.53 or any of the newer versions?
Hi Iry,
Have you checked to make sure that your nginx server is serving the file for download, as opposed to the internal Galaxy web server? In the original email, it looked like nginx was being bypassed entirely (due to serving on port 8080 - Galaxy's intenal server's default port). But even once nginx is in use, it's necessary to set up X-Accel-Redirect to serve datasets. See the instructions here:
http://usegalaxy.org/production
--nate
Thanks,
Iry Witham Applications Administrator Scientific Computing Group Computational Sciences Dept. The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6744 email: iry.witham@jax.org
On Apr 27, 2011; 10:06am ³Hello all, I just updated our local copy of Galaxy and just wanted to try the new IGV display application. When I try to display a BAM file with the local IGV or the web IGV I encounter following error complaining about the Null content-length. Has any of you encountered the same problem? Do I miss something? Thanks in advance
Alex
INFO [2011-04-27 16:00:14,440] [TrackManager.java:225] [Thread-6] Loading1 resources. ERROR [2011-04-27 16:00:14,589] [SeekableHTTPStream.java:59] [Thread-6] Null content-length for: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/45 4e df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam ERROR [2011-04-27 16:00:14,590] [TrackLoader.java:821] [Thread-6] Error loading sam track java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/45 4e df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length at org.broad.igv.util.SeekableHTTPStream.<init>(SeekableHTTPStream.java:60) at org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFactory .j ava:42) at org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader.j av a:129) at org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader.ja va :70) at org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQueryRe ad er.java:80) at org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQueryRe ad er.java:97) at org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.java :7 5) at org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:69) at org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManager. ja va:54) at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:761) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:143) at org.broad.igv.track.TrackManager.load(TrackManager.java:271) at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241) at org.broad.igv.main.CommandExecutor.loadFiles(CommandExecutor.java:282) at org.broad.igv.main.CommandExecutor.hget(CommandExecutor.java:148) at org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java:88) at org.broad.igv.main.CommandListener.processGet(CommandListener.java:193) at org.broad.igv.main.CommandListener.run(CommandListener.java:93) at java.lang.Thread.run(Thread.java:636) ERROR [2011-04-27 16:00:14,592] [TrackLoader.java:211] [Thread-6] java.lang.RuntimeException: java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/45 4e df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length²
On Apr 27, 2011; 12:33pm ³Hi Alex,
Displaying BAM files at external applications usually requires an http server that supports partial gets. Unfortunately, the current lightweight http server that is built into Galaxy does not support these advanced http options. However, this limitation can be overcome by using a proxy server that is able to handle http1.1 requests. Please see "Using a Proxy server" at https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer for help on setting this up.
Thanks for using Galaxy,
Dan²
On Apr 27, 2011; 9:07pm ³I¹m getting this same error and I¹m running nginx as a proxy server. Is there a specfic parameter we should be aware of to allow partial gets? I don¹t see anything in the wiki page for setting up the ProductionServer.
Thanks,
Dave²
On May 04, 2011; 7:47am ³Could someone who has successfully gotten the IGV tool to work using NGINX as your proxy, tell me if there was anything specific they needed to do with their NGINX or galaxy config to get it working?
Thanks,
Dave²
On May 09, 2011; 2:52pm ³It's necessary to set up the more advanced configuration under "Sending files using nginx" on the nginxProxy page in the wiki. Could you let us know whether you're using that configuration or just a basic pass-through proxy?
Thanks, --nate²
___________________________________________________________ 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:
Hi Nate, I have been able to get this to work on a Mac and Windows XP within limited guide lines. The following are what I had to do to make it work: My Mac is now running Java 1.6.0_26, Firefox 3.6.20, Google Crome ver.13.0.782.215 and Safari 5.1 (6534.50). In addition I have installed Max OS 10.6.8 Supplemental Update 1.0. My PC is running Windows XP SP3 with Java 1.6.0_26, Firefox 3.6.20 and IE8. Windows updates are at current levels. I have not tested this on Windows 7. I am currently able to run the IGV-web tool from Galaxy via Firefox, Crome and Safari on the Mac and IE8 only on Windows. When I use either Firefox or Crome on Windows I get the following error. ERROR [2011-08-24 09:22:40,169] [TrackLoader.java:211] [SwingWorker-pool-20352093-thread-1] java.lang.RuntimeException: java.lang.RuntimeException: Error loading file: http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908 0aa/data/galaxy_afa21414c9c9e7eb.bam NULL content-length ERROR [2011-08-24 09:22:40,169] [TrackManager.java:245] [SwingWorker-pool-20352093-thread-1] Error loading tracks org.broad.igv.exceptions.DataLoadException: <html>An error occurred while loading: http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908 0aa/data/galaxy_afa21414c9c9e7eb.bam<br>java.lang.RuntimeException: Error loading file: http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908 0aa/data/galaxy_afa21414c9c9e7eb.bam NULL content-length at org.broad.igv.track.TrackLoader.load(TrackLoader.java:212) at org.broad.igv.track.TrackManager.load(TrackManager.java:271) at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241) at org.broad.igv.ui.IGVMainFrame$StartupWorker.doInBackground(IGVMainFrame.java :2775) at com.jidesoft.utils.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at com.jidesoft.utils.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) This error appears to be different from the original, at least in details though the results are the same. I am also going to post this with IGV support. Thanks, Iry On 8/15/11 2:46 PM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Iry Witham wrote:
Hi Nate,
I have checked the nginx.conf file and they comply to the documentation:
# added to allow nginx to handle file downloads location /_x_accel_redirect/ { internal; alias /;
I have also confirmed that the universe_wsgi.ini file contains the following:
And the following to the [app:main] section of universe_wsgi.ini: nginx_x_accel_redirect_base = /_x_accel_redirect
Iry
This will need some in-depth debugging, then.
If you access Galaxy directly via the port of its built-in web server (by default, 8080), and request to display a dataset, does it set the X-Accel-Redirect header in the response?
If you access the same dataset via the nginx address but rename the underlying disk file, do you get an error message from nginx or from Galaxy?
--nate
On 8/15/11 10:46 AM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Iry Witham wrote:
Hi Everyone,
I have been tasked with getting the IGV working within our Galaxy instance. I have modified our Nginx configuration based on the more advanced configuration under "Sending files using nginx" on the nginxProxy page in the wiki. The IGV viewer component in Galaxy does not display the results from a BAM file in either the web or local instance of IGV. I have tested with IGV1.5 and with version 2.03. Neither produce a visual representation of the sequence. When attempting to use the web option we get the same error provided in the original post as noted below. Has anyone gotten this to work with Nginx-0.8.53 or any of the newer versions?
Hi Iry,
Have you checked to make sure that your nginx server is serving the file for download, as opposed to the internal Galaxy web server? In the original email, it looked like nginx was being bypassed entirely (due to serving on port 8080 - Galaxy's intenal server's default port). But even once nginx is in use, it's necessary to set up X-Accel-Redirect to serve datasets. See the instructions here:
http://usegalaxy.org/production
--nate
Thanks,
Iry Witham Applications Administrator Scientific Computing Group Computational Sciences Dept. The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6744 email: iry.witham@jax.org
On Apr 27, 2011; 10:06am ³Hello all, I just updated our local copy of Galaxy and just wanted to try the new IGV display application. When I try to display a BAM file with the local IGV or the web IGV I encounter following error complaining about the Null content-length. Has any of you encountered the same problem? Do I miss something? Thanks in advance
Alex
INFO [2011-04-27 16:00:14,440] [TrackManager.java:225] [Thread-6] Loading1 resources. ERROR [2011-04-27 16:00:14,589] [SeekableHTTPStream.java:59] [Thread-6] Null content-length for: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/45 4e df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam ERROR [2011-04-27 16:00:14,590] [TrackLoader.java:821] [Thread-6] Error loading sam track java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/45 4e df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length at org.broad.igv.util.SeekableHTTPStream.<init>(SeekableHTTPStream.java:60) at org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFactory .j ava:42) at org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader.j av a:129) at org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader.ja va :70) at org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQueryRe ad er.java:80) at org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQueryRe ad er.java:97) at org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.java :7 5) at org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:69) at org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManager. ja va:54) at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:761) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:143) at org.broad.igv.track.TrackManager.load(TrackManager.java:271) at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241) at org.broad.igv.main.CommandExecutor.loadFiles(CommandExecutor.java:282) at org.broad.igv.main.CommandExecutor.hget(CommandExecutor.java:148) at org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java:88) at org.broad.igv.main.CommandListener.processGet(CommandListener.java:193) at org.broad.igv.main.CommandListener.run(CommandListener.java:93) at java.lang.Thread.run(Thread.java:636) ERROR [2011-04-27 16:00:14,592] [TrackLoader.java:211] [Thread-6] java.lang.RuntimeException: java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/45 4e df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length²
On Apr 27, 2011; 12:33pm ³Hi Alex,
Displaying BAM files at external applications usually requires an http server that supports partial gets. Unfortunately, the current lightweight http server that is built into Galaxy does not support these advanced http options. However, this limitation can be overcome by using a proxy server that is able to handle http1.1 requests. Please see "Using a Proxy server" at https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer for help on setting this up.
Thanks for using Galaxy,
Dan²
On Apr 27, 2011; 9:07pm ³I¹m getting this same error and I¹m running nginx as a proxy server. Is there a specfic parameter we should be aware of to allow partial gets? I don¹t see anything in the wiki page for setting up the ProductionServer.
Thanks,
Dave²
On May 04, 2011; 7:47am ³Could someone who has successfully gotten the IGV tool to work using NGINX as your proxy, tell me if there was anything specific they needed to do with their NGINX or galaxy config to get it working?
Thanks,
Dave²
On May 09, 2011; 2:52pm ³It's necessary to set up the more advanced configuration under "Sending files using nginx" on the nginxProxy page in the wiki. Could you let us know whether you're using that configuration or just a basic pass-through proxy?
Thanks, --nate²
___________________________________________________________ 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:
Iry Witham wrote:
Hi Nate,
I have been able to get this to work on a Mac and Windows XP within limited guide lines. The following are what I had to do to make it work:
My Mac is now running Java 1.6.0_26, Firefox 3.6.20, Google Crome ver.13.0.782.215 and Safari 5.1 (6534.50). In addition I have installed Max OS 10.6.8 Supplemental Update 1.0. My PC is running Windows XP SP3 with Java 1.6.0_26, Firefox 3.6.20 and IE8. Windows updates are at current levels. I have not tested this on Windows 7.
I am currently able to run the IGV-web tool from Galaxy via Firefox, Crome and Safari on the Mac and IE8 only on Windows. When I use either Firefox or Crome on Windows I get the following error.
ERROR [2011-08-24 09:22:40,169] [TrackLoader.java:211] [SwingWorker-pool-20352093-thread-1] java.lang.RuntimeException: java.lang.RuntimeException: Error loading file: http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908 0aa/data/galaxy_afa21414c9c9e7eb.bam NULL content-length
ERROR [2011-08-24 09:22:40,169] [TrackManager.java:245] [SwingWorker-pool-20352093-thread-1] Error loading tracks
org.broad.igv.exceptions.DataLoadException: <html>An error occurred while loading: http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908 0aa/data/galaxy_afa21414c9c9e7eb.bam<br>java.lang.RuntimeException: Error loading file: http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908 0aa/data/galaxy_afa21414c9c9e7eb.bam NULL content-length
at org.broad.igv.track.TrackLoader.load(TrackLoader.java:212)
at org.broad.igv.track.TrackManager.load(TrackManager.java:271)
at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241)
at org.broad.igv.ui.IGVMainFrame$StartupWorker.doInBackground(IGVMainFrame.java :2775)
at com.jidesoft.utils.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at com.jidesoft.utils.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
This error appears to be different from the original, at least in details though the results are the same. I am also going to post this with IGV support.
Hi Iry, If you get anything back from the IGV folks please post a followup. Since IGV runs in the local JVM, that it works with one browser and not another on the same system doesn't make a lot of sense. --nate
Thanks, Iry
On 8/15/11 2:46 PM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Iry Witham wrote:
Hi Nate,
I have checked the nginx.conf file and they comply to the documentation:
# added to allow nginx to handle file downloads location /_x_accel_redirect/ { internal; alias /;
I have also confirmed that the universe_wsgi.ini file contains the following:
And the following to the [app:main] section of universe_wsgi.ini: nginx_x_accel_redirect_base = /_x_accel_redirect
Iry
This will need some in-depth debugging, then.
If you access Galaxy directly via the port of its built-in web server (by default, 8080), and request to display a dataset, does it set the X-Accel-Redirect header in the response?
If you access the same dataset via the nginx address but rename the underlying disk file, do you get an error message from nginx or from Galaxy?
--nate
On 8/15/11 10:46 AM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Iry Witham wrote:
Hi Everyone,
I have been tasked with getting the IGV working within our Galaxy instance. I have modified our Nginx configuration based on the more advanced configuration under "Sending files using nginx" on the nginxProxy page in the wiki. The IGV viewer component in Galaxy does not display the results from a BAM file in either the web or local instance of IGV. I have tested with IGV1.5 and with version 2.03. Neither produce a visual representation of the sequence. When attempting to use the web option we get the same error provided in the original post as noted below. Has anyone gotten this to work with Nginx-0.8.53 or any of the newer versions?
Hi Iry,
Have you checked to make sure that your nginx server is serving the file for download, as opposed to the internal Galaxy web server? In the original email, it looked like nginx was being bypassed entirely (due to serving on port 8080 - Galaxy's intenal server's default port). But even once nginx is in use, it's necessary to set up X-Accel-Redirect to serve datasets. See the instructions here:
http://usegalaxy.org/production
--nate
Thanks,
Iry Witham Applications Administrator Scientific Computing Group Computational Sciences Dept. The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6744 email: iry.witham@jax.org
On Apr 27, 2011; 10:06am ³Hello all, I just updated our local copy of Galaxy and just wanted to try the new IGV display application. When I try to display a BAM file with the local IGV or the web IGV I encounter following error complaining about the Null content-length. Has any of you encountered the same problem? Do I miss something? Thanks in advance
Alex
INFO [2011-04-27 16:00:14,440] [TrackManager.java:225] [Thread-6] Loading1 resources. ERROR [2011-04-27 16:00:14,589] [SeekableHTTPStream.java:59] [Thread-6] Null content-length for: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/45 4e df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam ERROR [2011-04-27 16:00:14,590] [TrackLoader.java:821] [Thread-6] Error loading sam track java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/45 4e df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length at org.broad.igv.util.SeekableHTTPStream.<init>(SeekableHTTPStream.java:60) at org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFactory .j ava:42) at org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader.j av a:129) at org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader.ja va :70) at org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQueryRe ad er.java:80) at org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQueryRe ad er.java:97) at org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.java :7 5) at org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:69) at org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManager. ja va:54) at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:761) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:143) at org.broad.igv.track.TrackManager.load(TrackManager.java:271) at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241) at org.broad.igv.main.CommandExecutor.loadFiles(CommandExecutor.java:282) at org.broad.igv.main.CommandExecutor.hget(CommandExecutor.java:148) at org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java:88) at org.broad.igv.main.CommandListener.processGet(CommandListener.java:193) at org.broad.igv.main.CommandListener.run(CommandListener.java:93) at java.lang.Thread.run(Thread.java:636) ERROR [2011-04-27 16:00:14,592] [TrackLoader.java:211] [Thread-6] java.lang.RuntimeException: java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/45 4e df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length²
On Apr 27, 2011; 12:33pm ³Hi Alex,
Displaying BAM files at external applications usually requires an http server that supports partial gets. Unfortunately, the current lightweight http server that is built into Galaxy does not support these advanced http options. However, this limitation can be overcome by using a proxy server that is able to handle http1.1 requests. Please see "Using a Proxy server" at https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer for help on setting this up.
Thanks for using Galaxy,
Dan²
On Apr 27, 2011; 9:07pm ³I¹m getting this same error and I¹m running nginx as a proxy server. Is there a specfic parameter we should be aware of to allow partial gets? I don¹t see anything in the wiki page for setting up the ProductionServer.
Thanks,
Dave²
On May 04, 2011; 7:47am ³Could someone who has successfully gotten the IGV tool to work using NGINX as your proxy, tell me if there was anything specific they needed to do with their NGINX or galaxy config to get it working?
Thanks,
Dave²
On May 09, 2011; 2:52pm ³It's necessary to set up the more advanced configuration under "Sending files using nginx" on the nginxProxy page in the wiki. Could you let us know whether you're using that configuration or just a basic pass-through proxy?
Thanks, --nate²
___________________________________________________________ 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:
Hi Nate, We have found the solution to our/this issue. The way we have our Galaxy instance configured is to have users required to log on. So in the universe.wsgi.webapp.ini file we had set the User and Security settings to: # Force everyone to log in (disable anonymous access). #require_login = True This was where we found the issue. We have changed the settings as follows and we can now view BAM files through IGV: # Force everyone to log in (disable anonymous access). require_login = False #require_login = True Thanks for all of you assistance. Iry On 8/29/11 2:50 PM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Iry Witham wrote:
Hi Nate,
I have been able to get this to work on a Mac and Windows XP within limited guide lines. The following are what I had to do to make it work:
My Mac is now running Java 1.6.0_26, Firefox 3.6.20, Google Crome ver.13.0.782.215 and Safari 5.1 (6534.50). In addition I have installed Max OS 10.6.8 Supplemental Update 1.0. My PC is running Windows XP SP3 with Java 1.6.0_26, Firefox 3.6.20 and IE8. Windows updates are at current levels. I have not tested this on Windows 7.
I am currently able to run the IGV-web tool from Galaxy via Firefox, Crome and Safari on the Mac and IE8 only on Windows. When I use either Firefox or Crome on Windows I get the following error.
ERROR [2011-08-24 09:22:40,169] [TrackLoader.java:211] [SwingWorker-pool-20352093-thread-1] java.lang.RuntimeException: java.lang.RuntimeException: Error loading file: http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908 0aa/data/galaxy_afa21414c9c9e7eb.bam NULL content-length
ERROR [2011-08-24 09:22:40,169] [TrackManager.java:245] [SwingWorker-pool-20352093-thread-1] Error loading tracks
org.broad.igv.exceptions.DataLoadException: <html>An error occurred while loading: http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908 0aa/data/galaxy_afa21414c9c9e7eb.bam<br>java.lang.RuntimeException: Error loading file: http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908 0aa/data/galaxy_afa21414c9c9e7eb.bam NULL content-length
at org.broad.igv.track.TrackLoader.load(TrackLoader.java:212)
at org.broad.igv.track.TrackManager.load(TrackManager.java:271)
at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241)
at org.broad.igv.ui.IGVMainFrame$StartupWorker.doInBackground(IGVMainFrame.java :2775)
at com.jidesoft.utils.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at com.jidesoft.utils.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
This error appears to be different from the original, at least in details though the results are the same. I am also going to post this with IGV support.
Hi Iry,
If you get anything back from the IGV folks please post a followup. Since IGV runs in the local JVM, that it works with one browser and not another on the same system doesn't make a lot of sense.
--nate
Thanks, Iry
On 8/15/11 2:46 PM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Iry Witham wrote:
Hi Nate,
I have checked the nginx.conf file and they comply to the documentation:
# added to allow nginx to handle file downloads location /_x_accel_redirect/ { internal; alias /;
I have also confirmed that the universe_wsgi.ini file contains the following:
And the following to the [app:main] section of universe_wsgi.ini: nginx_x_accel_redirect_base = /_x_accel_redirect
Iry
This will need some in-depth debugging, then.
If you access Galaxy directly via the port of its built-in web server (by default, 8080), and request to display a dataset, does it set the X-Accel-Redirect header in the response?
If you access the same dataset via the nginx address but rename the underlying disk file, do you get an error message from nginx or from Galaxy?
--nate
On 8/15/11 10:46 AM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Iry Witham wrote:
Hi Everyone,
I have been tasked with getting the IGV working within our Galaxy instance. I have modified our Nginx configuration based on the more advanced configuration under "Sending files using nginx" on the nginxProxy page in the wiki. The IGV viewer component in Galaxy does not display the results from a BAM file in either the web or local instance of IGV. I have tested with IGV1.5 and with version 2.03. Neither produce a visual representation of the sequence. When attempting to use the web option we get the same error provided in the original post as noted below. Has anyone gotten this to work with Nginx-0.8.53 or any of the newer versions?
Hi Iry,
Have you checked to make sure that your nginx server is serving the file for download, as opposed to the internal Galaxy web server? In the original email, it looked like nginx was being bypassed entirely (due to serving on port 8080 - Galaxy's intenal server's default port). But even once nginx is in use, it's necessary to set up X-Accel-Redirect to serve datasets. See the instructions here:
http://usegalaxy.org/production
--nate
Thanks,
Iry Witham Applications Administrator Scientific Computing Group Computational Sciences Dept. The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6744 email: iry.witham@jax.org
On Apr 27, 2011; 10:06am ³Hello all, I just updated our local copy of Galaxy and just wanted to try the new IGV display application. When I try to display a BAM file with the local IGV or the web IGV I encounter following error complaining about the Null content-length. Has any of you encountered the same problem? Do I miss something? Thanks in advance
Alex
INFO [2011-04-27 16:00:14,440] [TrackManager.java:225] [Thread-6] Loading1 resources. ERROR [2011-04-27 16:00:14,589] [SeekableHTTPStream.java:59] [Thread-6] Null content-length for: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/ 45 4e df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam ERROR [2011-04-27 16:00:14,590] [TrackLoader.java:821] [Thread-6] Error loading sam track java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/ 45 4e df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length at org.broad.igv.util.SeekableHTTPStream.<init>(SeekableHTTPStream.java:60) at org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFacto ry .j ava:42) at org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader .j av a:129) at org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader. ja va :70) at org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQuery Re ad er.java:80) at org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQuery Re ad er.java:97) at org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.ja va :7 5) at org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:6 9) at org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManage r. ja va:54) at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:761) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:143) at org.broad.igv.track.TrackManager.load(TrackManager.java:271) at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241) at org.broad.igv.main.CommandExecutor.loadFiles(CommandExecutor.java:282) at org.broad.igv.main.CommandExecutor.hget(CommandExecutor.java:148) at org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java:88) at org.broad.igv.main.CommandListener.processGet(CommandListener.java:193) at org.broad.igv.main.CommandListener.run(CommandListener.java:93) at java.lang.Thread.run(Thread.java:636) ERROR [2011-04-27 16:00:14,592] [TrackLoader.java:211] [Thread-6] java.lang.RuntimeException: java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/ 45 4e df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length²
On Apr 27, 2011; 12:33pm ³Hi Alex,
Displaying BAM files at external applications usually requires an http server that supports partial gets. Unfortunately, the current lightweight http server that is built into Galaxy does not support these advanced http options. However, this limitation can be overcome by using a proxy server that is able to handle http1.1 requests. Please see "Using a Proxy server" at https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer for help on setting this up.
Thanks for using Galaxy,
Dan²
On Apr 27, 2011; 9:07pm ³I¹m getting this same error and I¹m running nginx as a proxy server. Is there a specfic parameter we should be aware of to allow partial gets? I don¹t see anything in the wiki page for setting up the ProductionServer.
Thanks,
Dave²
On May 04, 2011; 7:47am ³Could someone who has successfully gotten the IGV tool to work using NGINX as your proxy, tell me if there was anything specific they needed to do with their NGINX or galaxy config to get it working?
Thanks,
Dave²
On May 09, 2011; 2:52pm ³It's necessary to set up the more advanced configuration under "Sending files using nginx" on the nginxProxy page in the wiki. Could you let us know whether you're using that configuration or just a basic pass-through proxy?
Thanks, --nate²
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Minor correction. It wasn't commented out... # Force everyone to log in (disable anonymous access). require_login = True But yes, changing to Require_login = False Fixed the problem. Thanks Iry. Dave On 9/1/11 8:42 AM, "Iry Witham" <iry.witham@jax.org> wrote:
Hi Nate,
We have found the solution to our/this issue. The way we have our Galaxy instance configured is to have users required to log on. So in the universe.wsgi.webapp.ini file we had set the User and Security settings to:
# Force everyone to log in (disable anonymous access). #require_login = True
This was where we found the issue. We have changed the settings as follows and we can now view BAM files through IGV:
# Force everyone to log in (disable anonymous access). require_login = False #require_login = True
Thanks for all of you assistance.
Iry
On 8/29/11 2:50 PM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Iry Witham wrote:
Hi Nate,
I have been able to get this to work on a Mac and Windows XP within limited guide lines. The following are what I had to do to make it work:
My Mac is now running Java 1.6.0_26, Firefox 3.6.20, Google Crome ver.13.0.782.215 and Safari 5.1 (6534.50). In addition I have installed Max OS 10.6.8 Supplemental Update 1.0. My PC is running Windows XP SP3 with Java 1.6.0_26, Firefox 3.6.20 and IE8. Windows updates are at current levels. I have not tested this on Windows 7.
I am currently able to run the IGV-web tool from Galaxy via Firefox, Crome and Safari on the Mac and IE8 only on Windows. When I use either Firefox or Crome on Windows I get the following error.
ERROR [2011-08-24 09:22:40,169] [TrackLoader.java:211] [SwingWorker-pool-20352093-thread-1] java.lang.RuntimeException: java.lang.RuntimeException: Error loading file: http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908 0aa/data/galaxy_afa21414c9c9e7eb.bam NULL content-length
ERROR [2011-08-24 09:22:40,169] [TrackManager.java:245] [SwingWorker-pool-20352093-thread-1] Error loading tracks
org.broad.igv.exceptions.DataLoadException: <html>An error occurred while loading: http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908 0aa/data/galaxy_afa21414c9c9e7eb.bam<br>java.lang.RuntimeException: Error loading file: http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908 0aa/data/galaxy_afa21414c9c9e7eb.bam NULL content-length
at org.broad.igv.track.TrackLoader.load(TrackLoader.java:212)
at org.broad.igv.track.TrackManager.load(TrackManager.java:271)
at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241)
at org.broad.igv.ui.IGVMainFrame$StartupWorker.doInBackground(IGVMainFrame.java :2775)
at com.jidesoft.utils.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at com.jidesoft.utils.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
This error appears to be different from the original, at least in details though the results are the same. I am also going to post this with IGV support.
Hi Iry,
If you get anything back from the IGV folks please post a followup. Since IGV runs in the local JVM, that it works with one browser and not another on the same system doesn't make a lot of sense.
--nate
Thanks, Iry
On 8/15/11 2:46 PM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Iry Witham wrote:
Hi Nate,
I have checked the nginx.conf file and they comply to the documentation:
# added to allow nginx to handle file downloads location /_x_accel_redirect/ { internal; alias /;
I have also confirmed that the universe_wsgi.ini file contains the following:
And the following to the [app:main] section of universe_wsgi.ini: nginx_x_accel_redirect_base = /_x_accel_redirect
Iry
This will need some in-depth debugging, then.
If you access Galaxy directly via the port of its built-in web server (by default, 8080), and request to display a dataset, does it set the X-Accel-Redirect header in the response?
If you access the same dataset via the nginx address but rename the underlying disk file, do you get an error message from nginx or from Galaxy?
--nate
On 8/15/11 10:46 AM, "Nate Coraor" <nate@bx.psu.edu> wrote:
Iry Witham wrote: > Hi Everyone, > > I have been tasked with getting the IGV working within our Galaxy > instance. I have modified our Nginx configuration based on the more > advanced > configuration under "Sending files using nginx" on the nginxProxy page > in > the > wiki. The IGV viewer component in Galaxy does not display the results > from > a > BAM file in either the web or local instance of IGV. I have tested with > IGV1.5 and with version 2.03. Neither produce a visual representation > of > the > sequence. When attempting to use the web option we get the same error > provided in the original post as noted below. Has anyone gotten this to > work > with Nginx-0.8.53 or any of the newer versions?
Hi Iry,
Have you checked to make sure that your nginx server is serving the file for download, as opposed to the internal Galaxy web server? In the original email, it looked like nginx was being bypassed entirely (due to serving on port 8080 - Galaxy's intenal server's default port). But even once nginx is in use, it's necessary to set up X-Accel-Redirect to serve datasets. See the instructions here:
http://usegalaxy.org/production
--nate
> > Thanks, > > Iry Witham > Applications Administrator > Scientific Computing Group > Computational Sciences Dept. > The Jackson Laboratory > 600 Main Street > Bar Harbor, ME 04609 > Phone: 207-288-6744 > email: iry.witham@jax.org > > > > > > On Apr 27, 2011; 10:06am > ³Hello all, > I just updated our local copy of Galaxy and just wanted to try the new > IGV > display application. > When I try to display a BAM file with the local IGV or the web IGV I > encounter following error complaining about the Null content-length. > Has any of you encountered the same problem? Do I miss something? > Thanks in advance > > Alex > > > INFO [2011-04-27 16:00:14,440] [TrackManager.java:225] [Thread-6] > Loading1 > resources. > ERROR [2011-04-27 16:00:14,589] [SeekableHTTPStream.java:59] [Thread-6] > Null content-length for: >
http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local>>>>>>> /
> 45 > 4e > df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam > ERROR [2011-04-27 16:00:14,590] [TrackLoader.java:821] [Thread-6] > Error > loading sam track > java.lang.RuntimeException: Error loading file: > http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local>>>>>>> / > 45 > 4e > df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length > at > org.broad.igv.util.SeekableHTTPStream.<init>(SeekableHTTPStream.java:60) > at > org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFact>>>>>>> o > ry > .j > ava:42) > at > org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReade>>>>>>> r > .j > av > a:129) > at > org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader>>>>>>> . > ja > va > :70) > at > org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQuer>>>>>>> y > Re > ad > er.java:80) > at > org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQuer>>>>>>> y > Re > ad > er.java:97) > at > org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.j>>>>>>> a > va > :7 > 5) > at > org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:>>>>>>> 6 > 9) > at > org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManag>>>>>>> e > r. > ja > va:54) > at > org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:761>>>>>>> ) > at org.broad.igv.track.TrackLoader.load(TrackLoader.java:143) > at org.broad.igv.track.TrackManager.load(TrackManager.java:271) > at > org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241) > at > org.broad.igv.main.CommandExecutor.loadFiles(CommandExecutor.java:282) > at org.broad.igv.main.CommandExecutor.hget(CommandExecutor.java:148) > at > org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java:88) > at > org.broad.igv.main.CommandListener.processGet(CommandListener.java:193) > at org.broad.igv.main.CommandListener.run(CommandListener.java:93) > at java.lang.Thread.run(Thread.java:636) > ERROR [2011-04-27 16:00:14,592] [TrackLoader.java:211] [Thread-6] > java.lang.RuntimeException: java.lang.RuntimeException: Error loading > file: > http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local>>>>>>> / > 45 > 4e > df2520b73a7e/data/galaxy_a1f8a55a946ee078.bam NULL content-length² > > > On Apr 27, 2011; 12:33pm > ³Hi Alex, > > Displaying BAM files at external applications usually requires an http > server > that supports partial gets. Unfortunately, the current lightweight http > server that is built into Galaxy does not support these advanced http > options. However, this limitation can be overcome by using a proxy > server > that is able to handle http1.1 requests. Please see "Using a Proxy > server" > at > https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer > for > help on setting this up. > > Thanks for using Galaxy, > > Dan² > > On Apr 27, 2011; 9:07pm > ³I¹m getting this same error and I¹m running nginx as a proxy server. > Is > there a specfic parameter we should be aware of to allow partial gets? > I > don¹t see anything in the wiki page for setting up the ProductionServer. > > Thanks, > > Dave² > > On May 04, 2011; 7:47am > ³Could someone who has successfully gotten the IGV tool to work using > NGINX > as your proxy, tell me if there was anything specific they needed to do > with > their NGINX or galaxy config to get it working? > > Thanks, > > Dave² > > On May 09, 2011; 2:52pm > ³It's necessary to set up the more advanced configuration under "Sending > files using nginx" on the nginxProxy page in the wiki. Could you let us > know whether you're using that configuration or just a basic > pass-through proxy? > > Thanks, > --nate²
> ___________________________________________________________ > 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/
___________________________________________________________ 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:
participants (3)
-
Dave Walton -
Iry Witham -
Nate Coraor