The Galaxy server is at http://atlas.transvar.org/galaxy

The Arabidopsis Thaliana (A_thaliana_Jun_2009.fa) is present in Galaxy.

Let me know if other sequences are needed.

atlas.transvar.org/galaxy

1. I opened a bed file in Galaxy, but it did not offer me to view it in IGB

2. I tried viewing a bam 'locally' and got this error from console:
ERROR: Error while applying symmetry properties
java.lang.NullPointerException
java.lang.NullPointerException
at java.util.prefs.AbstractPreferences.put(AbstractPreferences.java:224)
at com.affymetrix.igb.tiers.TrackStyle.setViewMode(TrackStyle.java:950)
at com.affymetrix.igb.bookmarks.BookmarkController.applyStyleProperties(BookmarkController.java:240)
at com.affymetrix.igb.bookmarks.BookmarkController.applyProperties(BookmarkController.java:223)
at com.affymetrix.igb.bookmarks.BookmarkUnibrowControlServlet$1.run(BookmarkUnibrowControlServlet.java:171)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:680)

3. Opened bam from 'Web' and it worked fine - but I still think we need to provide a popup to warn Galaxy users that they are being given the first 10K nucleotides of chr1 so that they know where they are starting in the view...

4. I don't have a bigwig or a bigbed file to check...

Checked bam and bed. Seems to be working fine.

Could you test it out?

This seems to work as expected.

Still unable to open uploaded bed file from Galaxy. Still getting the same error from 'local' of .bam

David, when you get a chance, come see what happens on my computer and let's figure out where the error is.

Next Tuesday I'll try to remember to come by and take a look.

Doesn't load data in IGB for .bam or .bed (even when .bed is specifically selected

Mar 29, 2012 3:30:10 PM com.affymetrix.igb.bookmarks.BookmarkUnibrowControlServlet parseValues
WARNING: No start value found in the bookmark URL. Setting start=0
Mar 29, 2012 3:30:10 PM com.affymetrix.igb.bookmarks.BookmarkUnibrowControlServlet parseValues
WARNING: No end value found in the bookmark URL. Setting end=10,000
Mar 29, 2012 3:30:10 PM com.affymetrix.igb.util.UnibrowControlServlet loadServer
SEVERE: Couldn't find server galaxy. Creating a local server.
net.sf.samtools.util.RuntimeEOFException: Premature EOF; BinaryCodec in readmode; streamed file (filename not available)
at net.sf.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:373)
at net.sf.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:357)
at net.sf.samtools.BAMFileReader.readHeader(BAMFileReader.java:355)
at net.sf.samtools.BAMFileReader.<init>(BAMFileReader.java:118)
at net.sf.samtools.BAMFileReader.<init>(BAMFileReader.java:106)
at net.sf.samtools.SAMFileReader.init(SAMFileReader.java:477)
at net.sf.samtools.SAMFileReader.<init>(SAMFileReader.java:177)
at com.affymetrix.genometryImpl.symloader.BAM.init(BAM.java:79)
at com.affymetrix.genometryImpl.symloader.XAM.getChromosomeList(XAM.java:98)
at com.affymetrix.igb.featureloader.QuickLoad.loadAndAddSymmetries(QuickLoad.java:235)
at com.affymetrix.igb.featureloader.QuickLoad.loadSymmetriesThread(QuickLoad.java:177)
at com.affymetrix.igb.featureloader.QuickLoad.loadFeatures(QuickLoad.java:155)
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:930)
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:858)
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:853)
at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:38)
at javax.swing.SwingWorker$1.call(SwingWorker.java:277)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at javax.swing.SwingWorker.run(SwingWorker.java:316)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:680)
net.sf.samtools.util.RuntimeEOFException: Premature EOF; BinaryCodec in readmode; streamed file (filename not available)
at net.sf.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:373)
at net.sf.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:357)
at net.sf.samtools.BAMFileReader.readHeader(BAMFileReader.java:355)
at net.sf.samtools.BAMFileReader.<init>(BAMFileReader.java:118)
at net.sf.samtools.BAMFileReader.<init>(BAMFileReader.java:106)
at net.sf.samtools.SAMFileReader.init(SAMFileReader.java:477)
at net.sf.samtools.SAMFileReader.<init>(SAMFileReader.java:177)
at com.affymetrix.genometryImpl.symloader.BAM.init(BAM.java:79)
at com.affymetrix.genometryImpl.symloader.XAM.getChromosomeList(XAM.java:98)
at com.affymetrix.igb.featureloader.QuickLoad.loadAndAddSymmetries(QuickLoad.java:235)
at com.affymetrix.igb.featureloader.QuickLoad.loadSymmetriesThread(QuickLoad.java:177)
at com.affymetrix.igb.featureloader.QuickLoad.loadFeatures(QuickLoad.java:155)
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:930)
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:858)
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:853)
at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:38)
at javax.swing.SwingWorker$1.call(SwingWorker.java:277)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at javax.swing.SwingWorker.run(SwingWorker.java:316)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:680)
net.sf.samtools.util.RuntimeEOFException: Premature EOF; BinaryCodec in readmode; streamed file (filename not available)
at net.sf.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:373)
at net.sf.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:357)
at net.sf.samtools.BAMFileReader.readHeader(BAMFileReader.java:355)
at net.sf.samtools.BAMFileReader.<init>(BAMFileReader.java:118)
at net.sf.samtools.BAMFileReader.<init>(BAMFileReader.java:106)
at net.sf.samtools.SAMFileReader.init(SAMFileReader.java:477)
at net.sf.samtools.SAMFileReader.<init>(SAMFileReader.java:177)
at com.affymetrix.genometryImpl.symloader.BAM.init(BAM.java:79)
at com.affymetrix.genometryImpl.symloader.XAM.getChromosomeList(XAM.java:98)
at com.affymetrix.igb.featureloader.QuickLoad.loadAndAddSymmetries(QuickLoad.java:235)
at com.affymetrix.igb.featureloader.QuickLoad.loadSymmetriesThread(QuickLoad.java:177)
at com.affymetrix.igb.featureloader.QuickLoad.loadFeatures(QuickLoad.java:155)
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:930)
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:858)
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:853)
at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:38)
at javax.swing.SwingWorker$1.call(SwingWorker.java:277)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at javax.swing.SwingWorker.run(SwingWorker.java:316)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:680)
WARNING: BAM index file /Users/auser/Desktop/IGB testing and designing/Files for Testing/our data downloaded/CoolL1T1.sm.bam.bai is older than BAM /Users/auser/Desktop/IGB testing and designing/Files for Testing/our data downloaded/CoolL1T1.sm.bam
Mar 29, 2012 3:33:34 PM com.affymetrix.igb.view.load.GeneralLoadUtils loadFeaturesForSym
INFO: All of new query covered by previous queries for feature CoolL1T1_sm_bam_b847e822bdc195d0.bam
Mar 29, 2012 3:35:26 PM com.affymetrix.igb.util.UnibrowControlServlet loadServer
SEVERE: Couldn't find server galaxy. Creating a local server.
net.sf.samtools.util.RuntimeEOFException: Premature EOF; BinaryCodec in readmode; streamed file (filename not available)
at net.sf.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:373)
at net.sf.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:357)
at net.sf.samtools.BAMFileReader.readHeader(BAMFileReader.java:355)
at net.sf.samtools.BAMFileReader.<init>(BAMFileReader.java:118)
at net.sf.samtools.BAMFileReader.<init>(BAMFileReader.java:106)
at net.sf.samtools.SAMFileReader.init(SAMFileReader.java:477)
at net.sf.samtools.SAMFileReader.<init>(SAMFileReader.java:177)
at com.affymetrix.genometryImpl.symloader.BAM.init(BAM.java:79)
at com.affymetrix.genometryImpl.symloader.XAM.getChromosomeList(XAM.java:98)
at com.affymetrix.igb.featureloader.QuickLoad.loadAndAddSymmetries(QuickLoad.java:235)
at com.affymetrix.igb.featureloader.QuickLoad.loadSymmetriesThread(QuickLoad.java:177)
at com.affymetrix.igb.featureloader.QuickLoad.loadFeatures(QuickLoad.java:155)
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:930)
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:858)
at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:853)
at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:38)
at javax.swing.SwingWorker$1.call(SwingWorker.java:277)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at javax.swing.SwingWorker.run(SwingWorker.java:316)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:680)

Always use http://atlas.transvar.org/galaxy and not http://atlas.transvar.org:8080

Recently someone complained that IGB from galaxy is not working. (http://sourceforge.net/p/genoviz/discussion/439787/thread/a6e9045d/?limit=25#28d8/3fb4)

Please go ahead and test this again for main galaxy site.

Currently Galaxy is throwing the following error when IGB attempts to connect via the link http://localhost:7085/UnibrowControl?version=?&feature_url_0=http://localhost:8888/display_application/ebfb8f50c6abde6d/igb_bam/Local/None/data/GES1_bam_ebfb8f50c6abde6d.bam&sym_name_0=GES1_bam&sym_method_0=http://localhost:8888/display_application/ebfb8f50c6abde6d/igb_bam/Local/None/data/GES1_bam_ebfb8f50c6abde6d.bam&query_url=http://localhost:8888/display_application/ebfb8f50c6abde6d/igb_bam/Local/None/data/GES1_bam_ebfb8f50c6abde6d.bam&server_url=galaxy

Starting server in PID 22545.
serving on http://127.0.0.1:8888
/home/lorainelab/Apps/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/types.py:215: SAWarning: Dialect sqlite+pysqlite does not support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage.
127.0.0.1 - - [15/Jan/2014:16:49:16 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:26.0) Gecko/20100101 Firefox/26.0"
127.0.0.1 - - [15/Jan/2014:16:49:18 -0400] "GET /root/welcome HTTP/1.1" 302 - "http://localhost:8888/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:26.0) Gecko/20100101 Firefox/26.0"
127.0.0.1 - - [15/Jan/2014:16:49:18 -0400] "GET /history HTTP/1.1" 200 - "http://localhost:8888/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:26.0) Gecko/20100101 Firefox/26.0"
127.0.0.1 - - [15/Jan/2014:16:49:19 -0400] "GET /history/get_display_application_links HTTP/1.1" 200 - "http://localhost:8888/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:26.0) Gecko/20100101 Firefox/26.0"
127.0.0.1 - - [15/Jan/2014:16:49:26 -0400] "GET /display_application/ebfb8f50c6abde6d/igb_bam/Local HTTP/1.1" 302 - "http://localhost:8888/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:26.0) Gecko/20100101 Firefox/26.0"
127.0.0.1 - - [15/Jan/2014:16:49:26 -0400] "GET /display_application/ebfb8f50c6abde6d/igb_bam/Local/None/data/GES1_bam_ebfb8f50c6abde6d.bam HTTP/1.1" 200 1532838900 "-" "Java/1.6.0_27"
----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 52970)
Traceback (most recent call last):
File "/home/lorainelab/Apps/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 323, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 640, in _init_
self.finish()
File "/usr/lib/python2.7/SocketServer.py", line 693, in finish
self.wfile.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
----------------------------------------

To debug:

1) Check that the file IGB is attempting to access actually exists on the server.

2) This part of the URL looks wrong: &server_url=galaxy because "galaxy" is not a URL

3) This part of the URL also looks wrong: version=? Why is there a "?" character?

4) The problem may be due to a change w/ IGB because it can't access either the public or the local Galaxy site. Try older versions of IGB. Check out and build IGB 7.0 and see if that works.

Answer for (1) they exist since galaxy can access them and they are persistent over restarts and sessions. I can download all 3 files and they are of equal size. Running md5checks on them vs the original end up being the same hash so the files are not becoming corrupt.

Partial Answer for (2) IGB still hangs in downloading when using usegalaxy.org and the url looks like this

http://localhost:7085/UnibrowControl?version=Arabidopsis_thaliana_TAIR10&feature_url_0=http://usegalaxy.org/display_application/bbd44e69cb8906b592d8a8b480c348c2/igb_bam/Local/68a04b13966e1364/data/GES1_bam_bbd44e69cb8906b592d8a8b480c348c2.bam&sym_name_0=GES1_bam&sym_method_0=http://usegalaxy.org/display_application/bbd44e69cb8906b592d8a8b480c348c2/igb_bam/Local/68a04b13966e1364/data/GES1_bam_bbd44e69cb8906b592d8a8b480c348c2.bam&query_url=http://usegalaxy.org/display_application/bbd44e69cb8906b592d8a8b480c348c2/igb_bam/Local/68a04b13966e1364/data/GES1_bam_bbd44e69cb8906b592d8a8b480c348c2.bam&server_url=galaxy

server_url=galaxy is still the same on both usegalaxy.org and the local version.

Answer for (3) version=? is that way because the local hosted version of galaxy does not have A. thal as a choice for reference genome. I can test around this by version=? from the link then manually opening A. Thal in IGB before clicking the IGB links above.

The issue may be with suggestion (4) or (2) which I am working on currently

link labeled "local" in UseGalaxy.org for BA1 reads file (a BAM file)

What wget printed when we tried to access the link (see attached) when IGB r16004 branch was running and showing A_thaliana_Jun_2009.

David Norris is changing how Galaxy and IGB interact.

Please review this old testing ticket and migrate information to our newer testing system for Galaxy. When that is done, please close.

Note: The workflow attached to this from an older board.