[Gmod-ajax] Add two Bam tracks failed problem

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[Gmod-ajax] Add two Bam tracks failed problem

hitim
HI

I want to add two BAM tracks into the Jbrowse. But only one sample can be show in the page.

My trackList.json file is below:

{
   "tracks" : [
      {
         "chunkSize" : 20000,
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "category" : "Reference sequence",
         "type" : "SequenceTrack",
         "label" : "DNA",
         "key" : "Reference sequence"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",
         "urlTemplate" : "vcf/Cosmic_format_v68.vcf.gz",
           "category" : "Reference DB",
         "label" : "Cosmic SNV",
         "type" : "JBrowse/View/Track/CanvasVariants"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",
         "urlTemplate" : "vcf/dbsnp_137.hg19.vcf.gz",
         "label" : "dbSNP",
           "category" : "Reference DB",
         "type" : "JBrowse/View/Track/CanvasVariants"
      },
      {
         "style" : {
            "className" : "feature"
         },
         "key" : "miRNA",
         "category" : "Reference DB",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : null,
         "urlTemplate" : "tracks/miRNA/{refseq}/trackData.json",
         "compress" : 0,
         "type" : "FeatureTrack",
         "label" : "miRNA"
      },
      {
         "style" : {
            "className" : "feature"
         },
         "key" : "Cytogenetic Ideogra",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : null,
         "urlTemplate" : "tracks/Cytogenetic Ideogra/{refseq}/trackData.json",
         "compress" : 0,
         "category" : "Reference DB",
         "type" : "FeatureTrack",
         "label" : "Cytogenetic Ideogra"
      },
     {
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "urlTemplate" : "xdxm/xdau1/run1/Preprocess/GATK/587329_output.fix.rg.sort.mkdup.realn.recal.bam",
         "label" : "SNP Coverage",
         "category" : "Project Xiandao",
         "type" : "JBrowse/View/Track/SNPCoverage",
         "baiUrlTemplate" : "xdxm/xdau1/run1/Preprocess/GATK/587329_output.fix.rg.sort.mkdup.realn.recal.bai",
         "key" : "Coverage_587329_normal"
      },
       {
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "urlTemplate" : "xdxm/xdau1/run1/Preprocess/GATK/587329_output.fix.rg.sort.mkdup.realn.recal.bam",
         "label" : "Aligments",
         "category" : "Project Xiandao",
         "type" : "JBrowse/View/Track/Alignments2",
         "baiUrlTemplate" : "xdxm/xdau1/run1/Preprocess/GATK/587329_output.fix.rg.sort.mkdup.realn.recal.bai",
         "key" : "Aligments_587329_normal"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "urlTemplate" : "xdxm/xdau1/run2/Preprocess/GATK/587328_output.fix.rg.sort.mkdup.realn.recal.bam",
         "label" : "SNP Coverage",
         "type" : "JBrowse/View/Track/SNPCoverage",
         "baiUrlTemplate" : "xdxm/xdau1/run2/Preprocess/GATK/587328_output.fix.rg.sort.mkdup.realn.recal.bai",
         "key" : "Coverage_587328_tumor"
      },
       {
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "urlTemplate" : "xdxm/xdau1/run2/Preprocess/GATK/587328_output.fix.rg.sort.mkdup.realn.recal.bam",
         "label" : "Aligments",
         "type" : "JBrowse/View/Track/Alignments2",
         "baiUrlTemplate" : "xdxm/xdau1/run2/Preprocess/GATK/587328_output.fix.rg.sort.mkdup.realn.recal.bai",
         "key" : "Aligments_587328_tumor"
      }
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "formatVersion" : 1
}


Only 587329 track was OK

Can any one can help?  Thanks!!  *0*



Tim
[hidden email]




------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
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Re: Add two Bam tracks failed problem

Colin
Hi there,
Can you clarify what is happening on your instance? You say only one of the BAM files is OK, but what happens to the other one?

-Colin


On Mon, Jul 7, 2014 at 10:24 PM, Tim <[hidden email]> wrote:
HI

I want to add two BAM tracks into the Jbrowse. But only one sample can be show in the page.

My trackList.json file is below:

{
   "tracks" : [
      {
         "chunkSize" : 20000,
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "category" : "Reference sequence",
         "type" : "SequenceTrack",
         "label" : "DNA",
         "key" : "Reference sequence"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",
         "urlTemplate" : "vcf/Cosmic_format_v68.vcf.gz",
           "category" : "Reference DB",
         "label" : "Cosmic SNV",
         "type" : "JBrowse/View/Track/CanvasVariants"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",
         "urlTemplate" : "vcf/dbsnp_137.hg19.vcf.gz",
         "label" : "dbSNP",
           "category" : "Reference DB",
         "type" : "JBrowse/View/Track/CanvasVariants"
      },
      {
         "style" : {
            "className" : "feature"
         },
         "key" : "miRNA",
         "category" : "Reference DB",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : null,
         "urlTemplate" : "tracks/miRNA/{refseq}/trackData.json",
         "compress" : 0,
         "type" : "FeatureTrack",
         "label" : "miRNA"
      },
      {
         "style" : {
            "className" : "feature"
         },
         "key" : "Cytogenetic Ideogra",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : null,
         "urlTemplate" : "tracks/Cytogenetic Ideogra/{refseq}/trackData.json",
         "compress" : 0,
         "category" : "Reference DB",
         "type" : "FeatureTrack",
         "label" : "Cytogenetic Ideogra"
      },
     {
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "urlTemplate" : "xdxm/xdau1/run1/Preprocess/GATK/587329_output.fix.rg.sort.mkdup.realn.recal.bam",
         "label" : "SNP Coverage",
         "category" : "Project Xiandao",
         "type" : "JBrowse/View/Track/SNPCoverage",
         "baiUrlTemplate" : "xdxm/xdau1/run1/Preprocess/GATK/587329_output.fix.rg.sort.mkdup.realn.recal.bai",
         "key" : "Coverage_587329_normal"
      },
       {
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "urlTemplate" : "xdxm/xdau1/run1/Preprocess/GATK/587329_output.fix.rg.sort.mkdup.realn.recal.bam",
         "label" : "Aligments",
         "category" : "Project Xiandao",
         "type" : "JBrowse/View/Track/Alignments2",
         "baiUrlTemplate" : "xdxm/xdau1/run1/Preprocess/GATK/587329_output.fix.rg.sort.mkdup.realn.recal.bai",
         "key" : "Aligments_587329_normal"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "urlTemplate" : "xdxm/xdau1/run2/Preprocess/GATK/587328_output.fix.rg.sort.mkdup.realn.recal.bam",
         "label" : "SNP Coverage",
         "type" : "JBrowse/View/Track/SNPCoverage",
         "baiUrlTemplate" : "xdxm/xdau1/run2/Preprocess/GATK/587328_output.fix.rg.sort.mkdup.realn.recal.bai",
         "key" : "Coverage_587328_tumor"
      },
       {
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "urlTemplate" : "xdxm/xdau1/run2/Preprocess/GATK/587328_output.fix.rg.sort.mkdup.realn.recal.bam",
         "label" : "Aligments",
         "type" : "JBrowse/View/Track/Alignments2",
         "baiUrlTemplate" : "xdxm/xdau1/run2/Preprocess/GATK/587328_output.fix.rg.sort.mkdup.realn.recal.bai",
         "key" : "Aligments_587328_tumor"
      }
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "formatVersion" : 1
}


Only 587329 track was OK

Can any one can help?  Thanks!!  *0*



Tim
[hidden email]




------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
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Re: Add two Bam tracks failed problem

Colin
Sorry I didn't see it in my last post but you need to change the label parameters for your BAM files so that each one has a unique "label".
the label is actually a internal identifier. The key parameter is what is actually displayed in the track list.

Hope that helps

-Colin


On Tue, Jul 8, 2014 at 12:49 PM, Colin <[hidden email]> wrote:
Hi there,
Can you clarify what is happening on your instance? You say only one of the BAM files is OK, but what happens to the other one?

-Colin


On Mon, Jul 7, 2014 at 10:24 PM, Tim <[hidden email]> wrote:
HI

I want to add two BAM tracks into the Jbrowse. But only one sample can be show in the page.

My trackList.json file is below:

{
   "tracks" : [
      {
         "chunkSize" : 20000,
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "category" : "Reference sequence",
         "type" : "SequenceTrack",
         "label" : "DNA",
         "key" : "Reference sequence"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",
         "urlTemplate" : "vcf/Cosmic_format_v68.vcf.gz",
           "category" : "Reference DB",
         "label" : "Cosmic SNV",
         "type" : "JBrowse/View/Track/CanvasVariants"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/VCFTabix",
         "urlTemplate" : "vcf/dbsnp_137.hg19.vcf.gz",
         "label" : "dbSNP",
           "category" : "Reference DB",
         "type" : "JBrowse/View/Track/CanvasVariants"
      },
      {
         "style" : {
            "className" : "feature"
         },
         "key" : "miRNA",
         "category" : "Reference DB",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : null,
         "urlTemplate" : "tracks/miRNA/{refseq}/trackData.json",
         "compress" : 0,
         "type" : "FeatureTrack",
         "label" : "miRNA"
      },
      {
         "style" : {
            "className" : "feature"
         },
         "key" : "Cytogenetic Ideogra",
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "trackType" : null,
         "urlTemplate" : "tracks/Cytogenetic Ideogra/{refseq}/trackData.json",
         "compress" : 0,
         "category" : "Reference DB",
         "type" : "FeatureTrack",
         "label" : "Cytogenetic Ideogra"
      },
     {
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "urlTemplate" : "xdxm/xdau1/run1/Preprocess/GATK/587329_output.fix.rg.sort.mkdup.realn.recal.bam",
         "label" : "SNP Coverage",
         "category" : "Project Xiandao",
         "type" : "JBrowse/View/Track/SNPCoverage",
         "baiUrlTemplate" : "xdxm/xdau1/run1/Preprocess/GATK/587329_output.fix.rg.sort.mkdup.realn.recal.bai",
         "key" : "Coverage_587329_normal"
      },
       {
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "urlTemplate" : "xdxm/xdau1/run1/Preprocess/GATK/587329_output.fix.rg.sort.mkdup.realn.recal.bam",
         "label" : "Aligments",
         "category" : "Project Xiandao",
         "type" : "JBrowse/View/Track/Alignments2",
         "baiUrlTemplate" : "xdxm/xdau1/run1/Preprocess/GATK/587329_output.fix.rg.sort.mkdup.realn.recal.bai",
         "key" : "Aligments_587329_normal"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "urlTemplate" : "xdxm/xdau1/run2/Preprocess/GATK/587328_output.fix.rg.sort.mkdup.realn.recal.bam",
         "label" : "SNP Coverage",
         "type" : "JBrowse/View/Track/SNPCoverage",
         "baiUrlTemplate" : "xdxm/xdau1/run2/Preprocess/GATK/587328_output.fix.rg.sort.mkdup.realn.recal.bai",
         "key" : "Coverage_587328_tumor"
      },
       {
         "storeClass" : "JBrowse/Store/SeqFeature/BAM",
         "urlTemplate" : "xdxm/xdau1/run2/Preprocess/GATK/587328_output.fix.rg.sort.mkdup.realn.recal.bam",
         "label" : "Aligments",
         "type" : "JBrowse/View/Track/Alignments2",
         "baiUrlTemplate" : "xdxm/xdau1/run2/Preprocess/GATK/587328_output.fix.rg.sort.mkdup.realn.recal.bai",
         "key" : "Aligments_587328_tumor"
      }
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "formatVersion" : 1
}


Only 587329 track was OK

Can any one can help?  Thanks!!  *0*



Tim
[hidden email]




------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax