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  1. IGB 8.1
  2. IGBE-91

Test galaxy data access

          Details

          • Type: Bug
          • Status: Reopened (View Workflow)
          • Priority: Major
          • Resolution: Unresolved
          • Labels:
            None
          • Environment:

            6.7

            Description

            Support to deploy IGB directly from Galaxy has been implemented.
            To test the feature we need to
            *load an annotation file to galaxy
            *request to view the file using IGB.
            Do "scientific" things with the data to make sure the communication between galaxy and IGB does not break
            the same should be done with:
            *bam
            *bigbed
            *bed
            *bigwig
            *wig

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                jfvillal jfvillal created issue -
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                jfvillal jfvillal added a comment -

                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.

                Show
                jfvillal jfvillal added a comment - 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.
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                alyssa Alyssa Gulledge (Inactive) added a comment -

                atlas.transvar.org/galaxy

                Show
                alyssa Alyssa Gulledge (Inactive) added a comment - atlas.transvar.org/galaxy
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                alyssa Alyssa Gulledge (Inactive) added a comment -

                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...

                Show
                alyssa Alyssa Gulledge (Inactive) added a comment - 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...
                alyssa Alyssa Gulledge (Inactive) made changes -
                Field Original Value New Value
                Assignee Alyssa Gulledge [ alyssa ] Hiral Vora [ hiralv ]
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                hiralv Hiral Vora (Inactive) added a comment -

                Checked bam and bed. Seems to be working fine.

                Could you test it out?

                Show
                hiralv Hiral Vora (Inactive) added a comment - Checked bam and bed. Seems to be working fine. Could you test it out?
                hiralv Hiral Vora (Inactive) made changes -
                Assignee Hiral Vora [ hiralv ] David Norris [ david ]
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                david David Norris (Inactive) added a comment -

                This seems to work as expected.

                Show
                david David Norris (Inactive) added a comment - This seems to work as expected.
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                david David Norris (Inactive) added a comment -

                I wasn't able to reproduce the error Alyssa experienced.

                Show
                david David Norris (Inactive) added a comment - I wasn't able to reproduce the error Alyssa experienced.
                david David Norris (Inactive) made changes -
                Assignee David Norris [ david ] Alyssa Gulledge [ alyssa ]
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                alyssa Alyssa Gulledge (Inactive) added a comment -

                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.

                Show
                alyssa Alyssa Gulledge (Inactive) added a comment - 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.
                alyssa Alyssa Gulledge (Inactive) made changes -
                Assignee Alyssa Gulledge [ alyssa ] David Norris [ david ]
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                david David Norris (Inactive) added a comment -

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

                Show
                david David Norris (Inactive) added a comment - Next Tuesday I'll try to remember to come by and take a look.
                hiralv Hiral Vora (Inactive) made changes -
                Assignee David Norris [ david ] Alyssa Gulledge [ alyssa ]
                hiralv Hiral Vora (Inactive) made changes -
                Environment 6.6 6.7
                Description Support to deploy IGB directly from Galaxy has been implemented.
                To test the feature we need to
                *load an annotation file to galaxy
                *request to view the file using IGB.
                Do "scientific" things with the data to make sure the communication between galaxy and IGB does not break
                the same should be done with:
                *bam
                *bigbed
                *bed
                *bigwig

                		 Support to deploy IGB directly from Galaxy has been implemented.
                To test the feature we need to
                *load an annotation file to galaxy
                *request to view the file using IGB.
                Do "scientific" things with the data to make sure the communication between galaxy and IGB does not break
                the same should be done with:
                *bam
                *bigbed
                *bed
                *bigwig
                *wig
                Hide
                Permalink
                alyssa Alyssa Gulledge (Inactive) added a comment -

                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)

                Show
                alyssa Alyssa Gulledge (Inactive) added a comment - 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)
                alyssa Alyssa Gulledge (Inactive) made changes -
                Assignee Alyssa Gulledge [ alyssa ] Hiral Vora [ hiralv ]
                Hide
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                hiralv Hiral Vora (Inactive) added a comment -

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

                Show
                hiralv Hiral Vora (Inactive) added a comment - Always use http://atlas.transvar.org/galaxy and not http://atlas.transvar.org:8080
                hiralv Hiral Vora (Inactive) made changes -
                Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
                alyssa Alyssa Gulledge (Inactive) made changes -
                Status Open [ 1 ] Resolved [ 5 ]
                Assignee Alyssa Gulledge [ alyssa ]
                Resolution Fixed [ 1 ]
                alyssa Alyssa Gulledge (Inactive) made changes -
                Status Resolved [ 5 ] Closed [ 6 ]
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                hiralv Hiral Vora (Inactive) added a comment -

                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.

                Show
                hiralv Hiral Vora (Inactive) added a comment - 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.
                hiralv Hiral Vora (Inactive) made changes -
                Resolution Fixed [ 1 ]
                Status Closed [ 6 ] Reopened [ 4 ]
                Assignee Alyssa Gulledge [ alyssa ]
                alyssa Alyssa Gulledge (Inactive) made changes -
                Assignee Alyssa Gulledge [ alyssa ]
                hiralv Hiral Vora (Inactive) made changes -
                Assignee Alyssa Gulledge [ alyssa ]
                alyssa Alyssa Gulledge (Inactive) made changes -
                Assignee Alyssa Gulledge [ alyssa ] Kyle Suttlemyre [ kyle ]
                alyssa Alyssa Gulledge (Inactive) made changes -
                Reporter Jeremy Villalobos [ jfvillal ] Alyssa Gulledge [ alyssa ]
                kyle Kyle Suttlemyre (Inactive) made changes -
                Project Data servers and Data bases [ 10042 ] Testing [ 10741 ]
                Key DATA-11 TEST-5
                Issue Type New Feature [ 2 ] Bug [ 1 ]
                Hide
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                kyle Kyle Suttlemyre (Inactive) added a comment -

                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
                ----------------------------------------

                Show
                kyle Kyle Suttlemyre (Inactive) added a comment - 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 ----------------------------------------
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                ann.loraine Ann Loraine added a comment -

                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.

                Show
                ann.loraine Ann Loraine added a comment - 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.
                Hide
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                kyle Kyle Suttlemyre (Inactive) added a comment -

                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

                Show
                kyle Kyle Suttlemyre (Inactive) added a comment - 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
                ann.loraine Ann Loraine made changes -
                Project Testing [ 10741 ] IGB 8.1 [ 10640 ]
                Key TEST-5 IGBE-91
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                ann.loraine Ann Loraine added a comment -

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

                Show
                ann.loraine Ann Loraine added a comment - link labeled "local" in UseGalaxy.org for BA1 reads file (a BAM file)
                ann.loraine Ann Loraine made changes -
                Attachment igblocallink [ 12351 ]
                Hide
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                ann.loraine Ann Loraine added a comment -

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

                Show
                ann.loraine Ann Loraine added a comment - What wget printed when we tried to access the link (see attached) when IGB r16004 branch was running and showing A_thaliana_Jun_2009.
                ann.loraine Ann Loraine made changes -
                Attachment firstrequest.txt [ 12352 ]
                Hide
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                kyle Kyle Suttlemyre (Inactive) added a comment -

                David Norris is changing how Galaxy and IGB interact.

                Show
                kyle Kyle Suttlemyre (Inactive) added a comment - David Norris is changing how Galaxy and IGB interact.
                kyle Kyle Suttlemyre (Inactive) made changes -
                Status Reopened [ 4 ] Resolved [ 5 ]
                Assignee Kyle Suttlemyre [ kyle ]
                Resolution Fixed [ 1 ]
                ann.loraine Ann Loraine made changes -
                Epic Link IGBF-1880 [ 17970 ]
                ann.loraine Ann Loraine made changes -
                Story Points 0.25
                Sprint Fall 7 : 11 Nov to 22 Nov [ 78 ]
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                ann.loraine Ann Loraine added a comment - - edited

                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.

                Show
                ann.loraine Ann Loraine added a comment - - edited 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.
                ann.loraine Ann Loraine made changes -
                Assignee Philip Badzuh [ pbadzuh ]
                ann.loraine Ann Loraine made changes -
                Resolution Fixed [ 1 ]
                Status Resolved [ 5 ] Reopened [ 4 ]

                  People

                  • Assignee:
                    pbadzuh Philip Badzuh (Inactive)
                    Reporter:
                    alyssa Alyssa Gulledge (Inactive)
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    1 Start watching this issue

                    Dates

                    • Created:
                      Updated: