[Gmod-ajax] Regarding Jbrowse

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[Gmod-ajax] Regarding Jbrowse

Vijay Bhasker
Hi GMOD

I have changed the key name for some tracks in volvox.json but the track names remains the same in the browser even after refreshing it. Also, when I click on some tracks it shows the error message "Unable to fetch the ../.gff3". Could anyone please help me resolve this issue.

Thanks.

Regards
Vijay.

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Re: Regarding Jbrowse

nathandunn
Please post the full error and full tracks.conf and verify that the older tracks.conf is not cached.   You can do this under the networks developer tab under chrome or Firefox per Scott's earlier advice.  

> On Aug 21, 2016, at 8:13 AM, Vijay Bhasker <[hidden email]> wrote:
>
> Hi GMOD
>
> I have changed the key name for some tracks in volvox.json but the track names remains the same in the browser even after refreshing it. Also, when I click on some tracks it shows the error message "Unable to fetch the ../.gff3". Could anyone please help me resolve this issue.
>
> Thanks.
>
> Regards
> Vijay.
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

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Re: Regarding Jbrowse

Vijay Bhasker
Hi GMOD

In /bin/data/tracks.conf I have 

[tracks.alignments]
urlTemplate = FM.01.new.sorted.chr11.bam
type = Alignments2

And the tracks.conf in /data is empty.

In /bin/data/trackList.json I have

   "tracks" : [
      {
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "key" : "Reference sequence",
         "chunkSize" : 20000,
         "category" : "Reference sequence",
         "label" : "DNA",
         "type" : "SequenceTrack"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "key" : "dna",
         "label" : "dna",
         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$
         "urlTemplate" : "tracks/dna/{refseq}/trackData.json",
         "compress" : 0,
         "style" : {
           "className" : "feature",
            "color" : "function(feature) {return 'red'; }"
         },
         "type" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.js"
      },
      {
         "type" : "FeatureTrack",
         "style" : {
            "className" : "feature"
         },
         "compress" : 0,
         "urlTemplate" : "FM.01.new.sorted.chr11.bam",
         "trackType" : null,
         "label" : "vijay",
         "key" : "vijay",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM"
      }
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "formatVersion" : 1
}

This is my complete conf file. Now when I cleared the cache and refreshed the browser, I can only find the reference sequences track and all my previous tracks have been disappeared. Could anyone please help me bring back the tracks and how can I edit those tracks.

Thanks.

Regards
Vijay.

On Sun, Aug 21, 2016 at 11:54 AM, Lbl <[hidden email]> wrote:
Please post the full error and full tracks.conf and verify that the older tracks.conf is not cached.   You can do this under the networks developer tab under chrome or Firefox per Scott's earlier advice.

> On Aug 21, 2016, at 8:13 AM, Vijay Bhasker <[hidden email]> wrote:
>
> Hi GMOD
>
> I have changed the key name for some tracks in volvox.json but the track names remains the same in the browser even after refreshing it. Also, when I click on some tracks it shows the error message "Unable to fetch the ../.gff3". Could anyone please help me resolve this issue.
>
> Thanks.
>
> Regards
> Vijay.
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax


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Re: Regarding Jbrowse

nathandunn

The JSON is malformed.  Using:


1 - should start with an open {   (maybe just a copy and paste error)
2 - this is incorrect on the end:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$

should be:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView”,

This should show up in your javascript console as an error, as well,

Nathan

On Aug 22, 2016, at 7:23 AM, Vijay Bhasker <[hidden email]> wrote:

Hi GMOD

In /bin/data/tracks.conf I have 

[tracks.alignments]
urlTemplate = FM.01.new.sorted.chr11.bam
type = Alignments2

And the tracks.conf in /data is empty.

In /bin/data/trackList.json I have

   "tracks" : [
      {
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "key" : "Reference sequence",
         "chunkSize" : 20000,
         "category" : "Reference sequence",
         "label" : "DNA",
         "type" : "SequenceTrack"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "key" : "dna",
         "label" : "dna",
         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$
         "urlTemplate" : "tracks/dna/{refseq}/trackData.json",
         "compress" : 0,
         "style" : {
           "className" : "feature",
            "color" : "function(feature) {return 'red'; }"
         },
         "type" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.js"
      },
      {
         "type" : "FeatureTrack",
         "style" : {
            "className" : "feature"
         },
         "compress" : 0,
         "urlTemplate" : "FM.01.new.sorted.chr11.bam",
         "trackType" : null,
         "label" : "vijay",
         "key" : "vijay",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM"
      }
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "formatVersion" : 1
}

This is my complete conf file. Now when I cleared the cache and refreshed the browser, I can only find the reference sequences track and all my previous tracks have been disappeared. Could anyone please help me bring back the tracks and how can I edit those tracks.

Thanks.

Regards
Vijay.

On Sun, Aug 21, 2016 at 11:54 AM, Lbl <[hidden email]> wrote:
Please post the full error and full tracks.conf and verify that the older tracks.conf is not cached.   You can do this under the networks developer tab under chrome or Firefox per Scott's earlier advice.

> On Aug 21, 2016, at 8:13 AM, Vijay Bhasker <[hidden email]> wrote:
>
> Hi GMOD
>
> I have changed the key name for some tracks in volvox.json but the track names remains the same in the browser even after refreshing it. Also, when I click on some tracks it shows the error message "Unable to fetch the ../.gff3". Could anyone please help me resolve this issue.
>
> Thanks.
>
> Regards
> Vijay.
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax



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Re: Regarding Jbrowse

Vijay Bhasker
Hi

It was a copy paste error. It is as you mentioned it to be. Now what should I do to get back the tracks. Which file is responsible for the tracks. How can I edit those tracks? 

Regards.
Vijay.

On Monday, August 22, 2016, Nathan Dunn <[hidden email]> wrote:

The JSON is malformed.  Using:


1 - should start with an open {   (maybe just a copy and paste error)
2 - this is incorrect on the end:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$

should be:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView”,

This should show up in your javascript console as an error, as well,

Nathan

On Aug 22, 2016, at 7:23 AM, Vijay Bhasker <<a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;uday4vijay@gmail.com&#39;);" target="_blank">uday4vijay@...> wrote:

Hi GMOD

In /bin/data/tracks.conf I have 

[tracks.alignments]
urlTemplate = FM.01.new.sorted.chr11.bam
type = Alignments2

And the tracks.conf in /data is empty.

In /bin/data/trackList.json I have

   "tracks" : [
      {
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "key" : "Reference sequence",
         "chunkSize" : 20000,
         "category" : "Reference sequence",
         "label" : "DNA",
         "type" : "SequenceTrack"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "key" : "dna",
         "label" : "dna",
         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$
         "urlTemplate" : "tracks/dna/{refseq}/trackData.json",
         "compress" : 0,
         "style" : {
           "className" : "feature",
            "color" : "function(feature) {return 'red'; }"
         },
         "type" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.js"
      },
      {
         "type" : "FeatureTrack",
         "style" : {
            "className" : "feature"
         },
         "compress" : 0,
         "urlTemplate" : "FM.01.new.sorted.chr11.bam",
         "trackType" : null,
         "label" : "vijay",
         "key" : "vijay",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM"
      }
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "formatVersion" : 1
}

This is my complete conf file. Now when I cleared the cache and refreshed the browser, I can only find the reference sequences track and all my previous tracks have been disappeared. Could anyone please help me bring back the tracks and how can I edit those tracks.

Thanks.

Regards
Vijay.

On Sun, Aug 21, 2016 at 11:54 AM, Lbl <<a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;nathandunn@lbl.gov&#39;);" target="_blank">nathandunn@...> wrote:
Please post the full error and full tracks.conf and verify that the older tracks.conf is not cached.   You can do this under the networks developer tab under chrome or Firefox per Scott's earlier advice.

> On Aug 21, 2016, at 8:13 AM, Vijay Bhasker <<a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;uday4vijay@gmail.com&#39;);" target="_blank">uday4vijay@...> wrote:
>
> Hi GMOD
>
> I have changed the key name for some tracks in volvox.json but the track names remains the same in the browser even after refreshing it. Also, when I click on some tracks it shows the error message "Unable to fetch the ../.gff3". Could anyone please help me resolve this issue.
>
> Thanks.
>
> Regards
> Vijay.
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-ajax mailing list
> <a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;Gmod-ajax@lists.sourceforge.net&#39;);" target="_blank">Gmod-ajax@...t
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax



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Re: Regarding Jbrowse

nathandunn

Can you post:

1 - the  javascript console in the developer tools window when you reload the page (with caching turned off - see the network tab) 
2 - the contents of the volvox directory so that we can see the file sizes
3 - the URL you are using to connect with
4 - the browser / OS you are using 
5 - a screenshot of what you are seeing 

Nathan

On Aug 22, 2016, at 7:42 AM, Vijay Bhasker <[hidden email]> wrote:

Hi

It was a copy paste error. It is as you mentioned it to be. Now what should I do to get back the tracks. Which file is responsible for the tracks. How can I edit those tracks? 

Regards.
Vijay.

On Monday, August 22, 2016, Nathan Dunn <[hidden email]> wrote:

The JSON is malformed.  Using:


1 - should start with an open {   (maybe just a copy and paste error)
2 - this is incorrect on the end:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$

should be:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView”,

This should show up in your javascript console as an error, as well,

Nathan

On Aug 22, 2016, at 7:23 AM, Vijay Bhasker <<a href="javascript:_e(%7B%7D,'cvml','uday4vijay@gmail.com');" target="_blank" class="">uday4vijay@...> wrote:

Hi GMOD

In /bin/data/tracks.conf I have 

[tracks.alignments]
urlTemplate = FM.01.new.sorted.chr11.bam
type = Alignments2

And the tracks.conf in /data is empty.

In /bin/data/trackList.json I have

   "tracks" : [
      {
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "key" : "Reference sequence",
         "chunkSize" : 20000,
         "category" : "Reference sequence",
         "label" : "DNA",
         "type" : "SequenceTrack"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "key" : "dna",
         "label" : "dna",
         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$
         "urlTemplate" : "tracks/dna/{refseq}/trackData.json",
         "compress" : 0,
         "style" : {
           "className" : "feature",
            "color" : "function(feature) {return 'red'; }"
         },
         "type" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.js"
      },
      {
         "type" : "FeatureTrack",
         "style" : {
            "className" : "feature"
         },
         "compress" : 0,
         "urlTemplate" : "FM.01.new.sorted.chr11.bam",
         "trackType" : null,
         "label" : "vijay",
         "key" : "vijay",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM"
      }
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "formatVersion" : 1
}

This is my complete conf file. Now when I cleared the cache and refreshed the browser, I can only find the reference sequences track and all my previous tracks have been disappeared. Could anyone please help me bring back the tracks and how can I edit those tracks.

Thanks.

Regards
Vijay.

On Sun, Aug 21, 2016 at 11:54 AM, Lbl <<a href="javascript:_e(%7B%7D,'cvml','nathandunn@lbl.gov');" target="_blank" class="">nathandunn@...> wrote:
Please post the full error and full tracks.conf and verify that the older tracks.conf is not cached.   You can do this under the networks developer tab under chrome or Firefox per Scott's earlier advice.

> On Aug 21, 2016, at 8:13 AM, Vijay Bhasker <<a href="javascript:_e(%7B%7D,'cvml','uday4vijay@gmail.com');" target="_blank" class="">uday4vijay@...> wrote:
>
> Hi GMOD
>
> I have changed the key name for some tracks in volvox.json but the track names remains the same in the browser even after refreshing it. Also, when I click on some tracks it shows the error message "Unable to fetch the ../.gff3". Could anyone please help me resolve this issue.
>
> Thanks.
>
> Regards
> Vijay.
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-ajax mailing list
> <a href="javascript:_e(%7B%7D,'cvml','Gmod-ajax@lists.sourceforge.net');" target="_blank" class="">Gmod-ajax@...t
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax




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Re: Regarding Jbrowse

Vijay Bhasker
Hi

I have attached the javascript console log, datafiles directory and the url i used to connect with in xubuntu in a virtualbox.

Thanks.

On Mon, Aug 22, 2016 at 10:45 AM, Nathan Dunn <[hidden email]> wrote:

Can you post:

1 - the  javascript console in the developer tools window when you reload the page (with caching turned off - see the network tab) 
2 - the contents of the volvox directory so that we can see the file sizes
3 - the URL you are using to connect with
4 - the browser / OS you are using 
5 - a screenshot of what you are seeing 

Nathan

On Aug 22, 2016, at 7:42 AM, Vijay Bhasker <[hidden email]> wrote:

Hi

It was a copy paste error. It is as you mentioned it to be. Now what should I do to get back the tracks. Which file is responsible for the tracks. How can I edit those tracks? 

Regards.
Vijay.

On Monday, August 22, 2016, Nathan Dunn <[hidden email]> wrote:

The JSON is malformed.  Using:


1 - should start with an open {   (maybe just a copy and paste error)
2 - this is incorrect on the end:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$

should be:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView”,

This should show up in your javascript console as an error, as well,

Nathan

On Aug 22, 2016, at 7:23 AM, Vijay Bhasker <[hidden email]> wrote:

Hi GMOD

In /bin/data/tracks.conf I have 

[tracks.alignments]
urlTemplate = FM.01.new.sorted.chr11.bam
type = Alignments2

And the tracks.conf in /data is empty.

In /bin/data/trackList.json I have

   "tracks" : [
      {
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "key" : "Reference sequence",
         "chunkSize" : 20000,
         "category" : "Reference sequence",
         "label" : "DNA",
         "type" : "SequenceTrack"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "key" : "dna",
         "label" : "dna",
         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$
         "urlTemplate" : "tracks/dna/{refseq}/trackData.json",
         "compress" : 0,
         "style" : {
           "className" : "feature",
            "color" : "function(feature) {return 'red'; }"
         },
         "type" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.js"
      },
      {
         "type" : "FeatureTrack",
         "style" : {
            "className" : "feature"
         },
         "compress" : 0,
         "urlTemplate" : "FM.01.new.sorted.chr11.bam",
         "trackType" : null,
         "label" : "vijay",
         "key" : "vijay",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM"
      }
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "formatVersion" : 1
}

This is my complete conf file. Now when I cleared the cache and refreshed the browser, I can only find the reference sequences track and all my previous tracks have been disappeared. Could anyone please help me bring back the tracks and how can I edit those tracks.

Thanks.

Regards
Vijay.

On Sun, Aug 21, 2016 at 11:54 AM, Lbl <[hidden email]> wrote:
Please post the full error and full tracks.conf and verify that the older tracks.conf is not cached.   You can do this under the networks developer tab under chrome or Firefox per Scott's earlier advice.

> On Aug 21, 2016, at 8:13 AM, Vijay Bhasker <[hidden email]> wrote:
>
> Hi GMOD
>
> I have changed the key name for some tracks in volvox.json but the track names remains the same in the browser even after refreshing it. Also, when I click on some tracks it shows the error message "Unable to fetch the ../.gff3". Could anyone please help me resolve this issue.
>
> Thanks.
>
> Regards
> Vijay.
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]t
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax





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Re: Regarding Jbrowse

Vijay Bhasker
Hi 

Could anyone please tell me which file should I edit for the customization of features like pop-up boxes, mouse-over behavior etc.

Thanks.
Vijay.

On Mon, Aug 22, 2016 at 11:14 AM, Vijay Bhasker <[hidden email]> wrote:
Hi

I have attached the javascript console log, datafiles directory and the url i used to connect with in xubuntu in a virtualbox.

Thanks.

On Mon, Aug 22, 2016 at 10:45 AM, Nathan Dunn <[hidden email]> wrote:

Can you post:

1 - the  javascript console in the developer tools window when you reload the page (with caching turned off - see the network tab) 
2 - the contents of the volvox directory so that we can see the file sizes
3 - the URL you are using to connect with
4 - the browser / OS you are using 
5 - a screenshot of what you are seeing 

Nathan

On Aug 22, 2016, at 7:42 AM, Vijay Bhasker <[hidden email]> wrote:

Hi

It was a copy paste error. It is as you mentioned it to be. Now what should I do to get back the tracks. Which file is responsible for the tracks. How can I edit those tracks? 

Regards.
Vijay.

On Monday, August 22, 2016, Nathan Dunn <[hidden email]> wrote:

The JSON is malformed.  Using:


1 - should start with an open {   (maybe just a copy and paste error)
2 - this is incorrect on the end:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$

should be:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView”,

This should show up in your javascript console as an error, as well,

Nathan

On Aug 22, 2016, at 7:23 AM, Vijay Bhasker <[hidden email]> wrote:

Hi GMOD

In /bin/data/tracks.conf I have 

[tracks.alignments]
urlTemplate = FM.01.new.sorted.chr11.bam
type = Alignments2

And the tracks.conf in /data is empty.

In /bin/data/trackList.json I have

   "tracks" : [
      {
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "key" : "Reference sequence",
         "chunkSize" : 20000,
         "category" : "Reference sequence",
         "label" : "DNA",
         "type" : "SequenceTrack"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "key" : "dna",
         "label" : "dna",
         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$
         "urlTemplate" : "tracks/dna/{refseq}/trackData.json",
         "compress" : 0,
         "style" : {
           "className" : "feature",
            "color" : "function(feature) {return 'red'; }"
         },
         "type" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.js"
      },
      {
         "type" : "FeatureTrack",
         "style" : {
            "className" : "feature"
         },
         "compress" : 0,
         "urlTemplate" : "FM.01.new.sorted.chr11.bam",
         "trackType" : null,
         "label" : "vijay",
         "key" : "vijay",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM"
      }
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "formatVersion" : 1
}

This is my complete conf file. Now when I cleared the cache and refreshed the browser, I can only find the reference sequences track and all my previous tracks have been disappeared. Could anyone please help me bring back the tracks and how can I edit those tracks.

Thanks.

Regards
Vijay.

On Sun, Aug 21, 2016 at 11:54 AM, Lbl <[hidden email]> wrote:
Please post the full error and full tracks.conf and verify that the older tracks.conf is not cached.   You can do this under the networks developer tab under chrome or Firefox per Scott's earlier advice.

> On Aug 21, 2016, at 8:13 AM, Vijay Bhasker <[hidden email]> wrote:
>
> Hi GMOD
>
> I have changed the key name for some tracks in volvox.json but the track names remains the same in the browser even after refreshing it. Also, when I click on some tracks it shows the error message "Unable to fetch the ../.gff3". Could anyone please help me resolve this issue.
>
> Thanks.
>
> Regards
> Vijay.
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]t
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax






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Re: Regarding Jbrowse

Scott Cain
My recollection is that browsers generally don't behave the same when you are looking at a file via a "file:///" versus a "http://" url.  You should really be accessing this page via a web browser.

Scott

On Mon, Aug 22, 2016 at 11:20 AM, Vijay Bhasker <[hidden email]> wrote:
Hi 

Could anyone please tell me which file should I edit for the customization of features like pop-up boxes, mouse-over behavior etc.

Thanks.
Vijay.

On Mon, Aug 22, 2016 at 11:14 AM, Vijay Bhasker <[hidden email]> wrote:
Hi

I have attached the javascript console log, datafiles directory and the url i used to connect with in xubuntu in a virtualbox.

Thanks.

On Mon, Aug 22, 2016 at 10:45 AM, Nathan Dunn <[hidden email]> wrote:

Can you post:

1 - the  javascript console in the developer tools window when you reload the page (with caching turned off - see the network tab) 
2 - the contents of the volvox directory so that we can see the file sizes
3 - the URL you are using to connect with
4 - the browser / OS you are using 
5 - a screenshot of what you are seeing 

Nathan

On Aug 22, 2016, at 7:42 AM, Vijay Bhasker <[hidden email]> wrote:

Hi

It was a copy paste error. It is as you mentioned it to be. Now what should I do to get back the tracks. Which file is responsible for the tracks. How can I edit those tracks? 

Regards.
Vijay.

On Monday, August 22, 2016, Nathan Dunn <[hidden email]> wrote:

The JSON is malformed.  Using:


1 - should start with an open {   (maybe just a copy and paste error)
2 - this is incorrect on the end:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$

should be:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView”,

This should show up in your javascript console as an error, as well,

Nathan

On Aug 22, 2016, at 7:23 AM, Vijay Bhasker <[hidden email]> wrote:

Hi GMOD

In /bin/data/tracks.conf I have 

[tracks.alignments]
urlTemplate = FM.01.new.sorted.chr11.bam
type = Alignments2

And the tracks.conf in /data is empty.

In /bin/data/trackList.json I have

   "tracks" : [
      {
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "key" : "Reference sequence",
         "chunkSize" : 20000,
         "category" : "Reference sequence",
         "label" : "DNA",
         "type" : "SequenceTrack"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "key" : "dna",
         "label" : "dna",
         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$
         "urlTemplate" : "tracks/dna/{refseq}/trackData.json",
         "compress" : 0,
         "style" : {
           "className" : "feature",
            "color" : "function(feature) {return 'red'; }"
         },
         "type" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.js"
      },
      {
         "type" : "FeatureTrack",
         "style" : {
            "className" : "feature"
         },
         "compress" : 0,
         "urlTemplate" : "FM.01.new.sorted.chr11.bam",
         "trackType" : null,
         "label" : "vijay",
         "key" : "vijay",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM"
      }
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "formatVersion" : 1
}

This is my complete conf file. Now when I cleared the cache and refreshed the browser, I can only find the reference sequences track and all my previous tracks have been disappeared. Could anyone please help me bring back the tracks and how can I edit those tracks.

Thanks.

Regards
Vijay.

On Sun, Aug 21, 2016 at 11:54 AM, Lbl <[hidden email]> wrote:
Please post the full error and full tracks.conf and verify that the older tracks.conf is not cached.   You can do this under the networks developer tab under chrome or Firefox per Scott's earlier advice.

> On Aug 21, 2016, at 8:13 AM, Vijay Bhasker <[hidden email]> wrote:
>
> Hi GMOD
>
> I have changed the key name for some tracks in volvox.json but the track names remains the same in the browser even after refreshing it. Also, when I click on some tracks it shows the error message "Unable to fetch the ../.gff3". Could anyone please help me resolve this issue.
>
> Thanks.
>
> Regards
> Vijay.
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]t
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax






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

_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Regarding Jbrowse

Vijay Bhasker
Hi

I have moved jbrowse folder to/var/www/html and typed in the url localhost/jbrowse/JBrowse-1.11.0/index.html. I got the Jbrowse page but again with a single reference sequence.

Thanks.
Vijay.

On Mon, Aug 22, 2016 at 11:36 AM, Scott Cain <[hidden email]> wrote:
My recollection is that browsers generally don't behave the same when you are looking at a file via a "file:///" versus a "http://" url.  You should really be accessing this page via a web browser.

Scott

On Mon, Aug 22, 2016 at 11:20 AM, Vijay Bhasker <[hidden email]> wrote:
Hi 

Could anyone please tell me which file should I edit for the customization of features like pop-up boxes, mouse-over behavior etc.

Thanks.
Vijay.

On Mon, Aug 22, 2016 at 11:14 AM, Vijay Bhasker <[hidden email]> wrote:
Hi

I have attached the javascript console log, datafiles directory and the url i used to connect with in xubuntu in a virtualbox.

Thanks.

On Mon, Aug 22, 2016 at 10:45 AM, Nathan Dunn <[hidden email]> wrote:

Can you post:

1 - the  javascript console in the developer tools window when you reload the page (with caching turned off - see the network tab) 
2 - the contents of the volvox directory so that we can see the file sizes
3 - the URL you are using to connect with
4 - the browser / OS you are using 
5 - a screenshot of what you are seeing 

Nathan

On Aug 22, 2016, at 7:42 AM, Vijay Bhasker <[hidden email]> wrote:

Hi

It was a copy paste error. It is as you mentioned it to be. Now what should I do to get back the tracks. Which file is responsible for the tracks. How can I edit those tracks? 

Regards.
Vijay.

On Monday, August 22, 2016, Nathan Dunn <[hidden email]> wrote:

The JSON is malformed.  Using:


1 - should start with an open {   (maybe just a copy and paste error)
2 - this is incorrect on the end:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$

should be:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView”,

This should show up in your javascript console as an error, as well,

Nathan

On Aug 22, 2016, at 7:23 AM, Vijay Bhasker <[hidden email]> wrote:

Hi GMOD

In /bin/data/tracks.conf I have 

[tracks.alignments]
urlTemplate = FM.01.new.sorted.chr11.bam
type = Alignments2

And the tracks.conf in /data is empty.

In /bin/data/trackList.json I have

   "tracks" : [
      {
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "key" : "Reference sequence",
         "chunkSize" : 20000,
         "category" : "Reference sequence",
         "label" : "DNA",
         "type" : "SequenceTrack"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "key" : "dna",
         "label" : "dna",
         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$
         "urlTemplate" : "tracks/dna/{refseq}/trackData.json",
         "compress" : 0,
         "style" : {
           "className" : "feature",
            "color" : "function(feature) {return 'red'; }"
         },
         "type" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.js"
      },
      {
         "type" : "FeatureTrack",
         "style" : {
            "className" : "feature"
         },
         "compress" : 0,
         "urlTemplate" : "FM.01.new.sorted.chr11.bam",
         "trackType" : null,
         "label" : "vijay",
         "key" : "vijay",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM"
      }
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "formatVersion" : 1
}

This is my complete conf file. Now when I cleared the cache and refreshed the browser, I can only find the reference sequences track and all my previous tracks have been disappeared. Could anyone please help me bring back the tracks and how can I edit those tracks.

Thanks.

Regards
Vijay.

On Sun, Aug 21, 2016 at 11:54 AM, Lbl <[hidden email]> wrote:
Please post the full error and full tracks.conf and verify that the older tracks.conf is not cached.   You can do this under the networks developer tab under chrome or Firefox per Scott's earlier advice.

> On Aug 21, 2016, at 8:13 AM, Vijay Bhasker <[hidden email]> wrote:
>
> Hi GMOD
>
> I have changed the key name for some tracks in volvox.json but the track names remains the same in the browser even after refreshing it. Also, when I click on some tracks it shows the error message "Unable to fetch the ../.gff3". Could anyone please help me resolve this issue.
>
> Thanks.
>
> Regards
> Vijay.
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]t
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax






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

_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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

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Re: Regarding Jbrowse

nathandunn

Can you provide screen shots that include the new page with the URL and the track list on the left? 

Nathan

On Aug 22, 2016, at 9:06 AM, Vijay Bhasker <[hidden email]> wrote:

Hi

I have moved jbrowse folder to/var/www/html and typed in the url localhost/jbrowse/JBrowse-1.11.0/index.html. I got the Jbrowse page but again with a single reference sequence.

Thanks.
Vijay.

On Mon, Aug 22, 2016 at 11:36 AM, Scott Cain <[hidden email]> wrote:
My recollection is that browsers generally don't behave the same when you are looking at a file via a "file:///" versus a "http://" url.  You should really be accessing this page via a web browser.

Scott

On Mon, Aug 22, 2016 at 11:20 AM, Vijay Bhasker <[hidden email]> wrote:
Hi 

Could anyone please tell me which file should I edit for the customization of features like pop-up boxes, mouse-over behavior etc.

Thanks.
Vijay.

On Mon, Aug 22, 2016 at 11:14 AM, Vijay Bhasker <[hidden email]> wrote:
Hi

I have attached the javascript console log, datafiles directory and the url i used to connect with in xubuntu in a virtualbox.

Thanks.

On Mon, Aug 22, 2016 at 10:45 AM, Nathan Dunn <[hidden email]> wrote:

Can you post:

1 - the  javascript console in the developer tools window when you reload the page (with caching turned off - see the network tab) 
2 - the contents of the volvox directory so that we can see the file sizes
3 - the URL you are using to connect with
4 - the browser / OS you are using 
5 - a screenshot of what you are seeing 

Nathan

On Aug 22, 2016, at 7:42 AM, Vijay Bhasker <[hidden email]> wrote:

Hi

It was a copy paste error. It is as you mentioned it to be. Now what should I do to get back the tracks. Which file is responsible for the tracks. How can I edit those tracks? 

Regards.
Vijay.

On Monday, August 22, 2016, Nathan Dunn <[hidden email]> wrote:

The JSON is malformed.  Using:


1 - should start with an open {   (maybe just a copy and paste error)
2 - this is incorrect on the end:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$

should be:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView”,

This should show up in your javascript console as an error, as well,

Nathan

On Aug 22, 2016, at 7:23 AM, Vijay Bhasker <[hidden email]> wrote:

Hi GMOD

In /bin/data/tracks.conf I have 

[tracks.alignments]
urlTemplate = FM.01.new.sorted.chr11.bam
type = Alignments2

And the tracks.conf in /data is empty.

In /bin/data/trackList.json I have

   "tracks" : [
      {
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "key" : "Reference sequence",
         "chunkSize" : 20000,
         "category" : "Reference sequence",
         "label" : "DNA",
         "type" : "SequenceTrack"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "key" : "dna",
         "label" : "dna",
         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$
         "urlTemplate" : "tracks/dna/{refseq}/trackData.json",
         "compress" : 0,
         "style" : {
           "className" : "feature",
            "color" : "function(feature) {return 'red'; }"
         },
         "type" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.js"
      },
      {
         "type" : "FeatureTrack",
         "style" : {
            "className" : "feature"
         },
         "compress" : 0,
         "urlTemplate" : "FM.01.new.sorted.chr11.bam",
         "trackType" : null,
         "label" : "vijay",
         "key" : "vijay",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM"
      }
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "formatVersion" : 1
}

This is my complete conf file. Now when I cleared the cache and refreshed the browser, I can only find the reference sequences track and all my previous tracks have been disappeared. Could anyone please help me bring back the tracks and how can I edit those tracks.

Thanks.

Regards
Vijay.

On Sun, Aug 21, 2016 at 11:54 AM, Lbl <[hidden email]> wrote:
Please post the full error and full tracks.conf and verify that the older tracks.conf is not cached.   You can do this under the networks developer tab under chrome or Firefox per Scott's earlier advice.

> On Aug 21, 2016, at 8:13 AM, Vijay Bhasker <[hidden email]> wrote:
>
> Hi GMOD
>
> I have changed the key name for some tracks in volvox.json but the track names remains the same in the browser even after refreshing it. Also, when I click on some tracks it shows the error message "Unable to fetch the ../.gff3". Could anyone please help me resolve this issue.
>
> Thanks.
>
> Regards
> Vijay.
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]t
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax






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

_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank" class="">216-392-3087
Ontario Institute for Cancer Research



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

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Re: Regarding Jbrowse

Vijay Bhasker
Hi

Sure Nathan. I have attached the latest page here.

Thanks.
Vijay.

On Mon, Aug 22, 2016 at 12:22 PM, Nathan Dunn <[hidden email]> wrote:

Can you provide screen shots that include the new page with the URL and the track list on the left? 

Nathan

On Aug 22, 2016, at 9:06 AM, Vijay Bhasker <[hidden email]> wrote:

Hi

I have moved jbrowse folder to/var/www/html and typed in the url localhost/jbrowse/JBrowse-1.11.0/index.html. I got the Jbrowse page but again with a single reference sequence.

Thanks.
Vijay.

On Mon, Aug 22, 2016 at 11:36 AM, Scott Cain <[hidden email]> wrote:
My recollection is that browsers generally don't behave the same when you are looking at a file via a "file:///" versus a "http://" url.  You should really be accessing this page via a web browser.

Scott

On Mon, Aug 22, 2016 at 11:20 AM, Vijay Bhasker <[hidden email]> wrote:
Hi 

Could anyone please tell me which file should I edit for the customization of features like pop-up boxes, mouse-over behavior etc.

Thanks.
Vijay.

On Mon, Aug 22, 2016 at 11:14 AM, Vijay Bhasker <[hidden email]> wrote:
Hi

I have attached the javascript console log, datafiles directory and the url i used to connect with in xubuntu in a virtualbox.

Thanks.

On Mon, Aug 22, 2016 at 10:45 AM, Nathan Dunn <[hidden email]> wrote:

Can you post:

1 - the  javascript console in the developer tools window when you reload the page (with caching turned off - see the network tab) 
2 - the contents of the volvox directory so that we can see the file sizes
3 - the URL you are using to connect with
4 - the browser / OS you are using 
5 - a screenshot of what you are seeing 

Nathan

On Aug 22, 2016, at 7:42 AM, Vijay Bhasker <[hidden email]> wrote:

Hi

It was a copy paste error. It is as you mentioned it to be. Now what should I do to get back the tracks. Which file is responsible for the tracks. How can I edit those tracks? 

Regards.
Vijay.

On Monday, August 22, 2016, Nathan Dunn <[hidden email]> wrote:

The JSON is malformed.  Using:


1 - should start with an open {   (maybe just a copy and paste error)
2 - this is incorrect on the end:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$

should be:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView”,

This should show up in your javascript console as an error, as well,

Nathan

On Aug 22, 2016, at 7:23 AM, Vijay Bhasker <[hidden email]> wrote:

Hi GMOD

In /bin/data/tracks.conf I have 

[tracks.alignments]
urlTemplate = FM.01.new.sorted.chr11.bam
type = Alignments2

And the tracks.conf in /data is empty.

In /bin/data/trackList.json I have

   "tracks" : [
      {
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "key" : "Reference sequence",
         "chunkSize" : 20000,
         "category" : "Reference sequence",
         "label" : "DNA",
         "type" : "SequenceTrack"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "key" : "dna",
         "label" : "dna",
         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$
         "urlTemplate" : "tracks/dna/{refseq}/trackData.json",
         "compress" : 0,
         "style" : {
           "className" : "feature",
            "color" : "function(feature) {return 'red'; }"
         },
         "type" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.js"
      },
      {
         "type" : "FeatureTrack",
         "style" : {
            "className" : "feature"
         },
         "compress" : 0,
         "urlTemplate" : "FM.01.new.sorted.chr11.bam",
         "trackType" : null,
         "label" : "vijay",
         "key" : "vijay",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM"
      }
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "formatVersion" : 1
}

This is my complete conf file. Now when I cleared the cache and refreshed the browser, I can only find the reference sequences track and all my previous tracks have been disappeared. Could anyone please help me bring back the tracks and how can I edit those tracks.

Thanks.

Regards
Vijay.

On Sun, Aug 21, 2016 at 11:54 AM, Lbl <[hidden email]> wrote:
Please post the full error and full tracks.conf and verify that the older tracks.conf is not cached.   You can do this under the networks developer tab under chrome or Firefox per Scott's earlier advice.

> On Aug 21, 2016, at 8:13 AM, Vijay Bhasker <[hidden email]> wrote:
>
> Hi GMOD
>
> I have changed the key name for some tracks in volvox.json but the track names remains the same in the browser even after refreshing it. Also, when I click on some tracks it shows the error message "Unable to fetch the ../.gff3". Could anyone please help me resolve this issue.
>
> Thanks.
>
> Regards
> Vijay.
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]t
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax






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

_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




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

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Re: Regarding Jbrowse

Scott Cain
Hi Vijay,

Let's back up a little.  I few emails ago, you wrote that your config files (tracks.conf and trackList.json) are in /bin/data.  That is an odd place for them to be, even if I assume you didn't intend to have that leading slash and it isn't really in the system /bin directory, rather in the jbrowse bin/ directory.  Typically, configuration files like this would be in the data directory directly under the jbrowse directory, so for example here:

  /var/www/jbrowse/JBrowse-1.11.0/data

(I'm guessing from other thing that you've written that this is where it should be).  If those files aren't there, then you almost certainly have to edit the jbrowse.conf or jbrowse_conf.json files so that JBrowse can find them.  In jbrowse.conf, you'd need to look for the dataRoot option.

Finally, as a fairly minor side note: are you really using JBrowse 1.11.0?  It's quite old; the newest release is 1.12.2.

Scott


On Mon, Aug 22, 2016 at 12:46 PM, Vijay Bhasker <[hidden email]> wrote:
Hi

Sure Nathan. I have attached the latest page here.

Thanks.
Vijay.

On Mon, Aug 22, 2016 at 12:22 PM, Nathan Dunn <[hidden email]> wrote:

Can you provide screen shots that include the new page with the URL and the track list on the left? 

Nathan

On Aug 22, 2016, at 9:06 AM, Vijay Bhasker <[hidden email]> wrote:

Hi

I have moved jbrowse folder to/var/www/html and typed in the url localhost/jbrowse/JBrowse-1.11.0/index.html. I got the Jbrowse page but again with a single reference sequence.

Thanks.
Vijay.

On Mon, Aug 22, 2016 at 11:36 AM, Scott Cain <[hidden email]> wrote:
My recollection is that browsers generally don't behave the same when you are looking at a file via a "file:///" versus a "http://" url.  You should really be accessing this page via a web browser.

Scott

On Mon, Aug 22, 2016 at 11:20 AM, Vijay Bhasker <[hidden email]> wrote:
Hi 

Could anyone please tell me which file should I edit for the customization of features like pop-up boxes, mouse-over behavior etc.

Thanks.
Vijay.

On Mon, Aug 22, 2016 at 11:14 AM, Vijay Bhasker <[hidden email]> wrote:
Hi

I have attached the javascript console log, datafiles directory and the url i used to connect with in xubuntu in a virtualbox.

Thanks.

On Mon, Aug 22, 2016 at 10:45 AM, Nathan Dunn <[hidden email]> wrote:

Can you post:

1 - the  javascript console in the developer tools window when you reload the page (with caching turned off - see the network tab) 
2 - the contents of the volvox directory so that we can see the file sizes
3 - the URL you are using to connect with
4 - the browser / OS you are using 
5 - a screenshot of what you are seeing 

Nathan

On Aug 22, 2016, at 7:42 AM, Vijay Bhasker <[hidden email]> wrote:

Hi

It was a copy paste error. It is as you mentioned it to be. Now what should I do to get back the tracks. Which file is responsible for the tracks. How can I edit those tracks? 

Regards.
Vijay.

On Monday, August 22, 2016, Nathan Dunn <[hidden email]> wrote:

The JSON is malformed.  Using:


1 - should start with an open {   (maybe just a copy and paste error)
2 - this is incorrect on the end:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$

should be:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView”,

This should show up in your javascript console as an error, as well,

Nathan

On Aug 22, 2016, at 7:23 AM, Vijay Bhasker <[hidden email]> wrote:

Hi GMOD

In /bin/data/tracks.conf I have 

[tracks.alignments]
urlTemplate = FM.01.new.sorted.chr11.bam
type = Alignments2

And the tracks.conf in /data is empty.

In /bin/data/trackList.json I have

   "tracks" : [
      {
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "key" : "Reference sequence",
         "chunkSize" : 20000,
         "category" : "Reference sequence",
         "label" : "DNA",
         "type" : "SequenceTrack"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "key" : "dna",
         "label" : "dna",
         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$
         "urlTemplate" : "tracks/dna/{refseq}/trackData.json",
         "compress" : 0,
         "style" : {
           "className" : "feature",
            "color" : "function(feature) {return 'red'; }"
         },
         "type" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.js"
      },
      {
         "type" : "FeatureTrack",
         "style" : {
            "className" : "feature"
         },
         "compress" : 0,
         "urlTemplate" : "FM.01.new.sorted.chr11.bam",
         "trackType" : null,
         "label" : "vijay",
         "key" : "vijay",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM"
      }
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "formatVersion" : 1
}

This is my complete conf file. Now when I cleared the cache and refreshed the browser, I can only find the reference sequences track and all my previous tracks have been disappeared. Could anyone please help me bring back the tracks and how can I edit those tracks.

Thanks.

Regards
Vijay.

On Sun, Aug 21, 2016 at 11:54 AM, Lbl <[hidden email]> wrote:
Please post the full error and full tracks.conf and verify that the older tracks.conf is not cached.   You can do this under the networks developer tab under chrome or Firefox per Scott's earlier advice.

> On Aug 21, 2016, at 8:13 AM, Vijay Bhasker <[hidden email]> wrote:
>
> Hi GMOD
>
> I have changed the key name for some tracks in volvox.json but the track names remains the same in the browser even after refreshing it. Also, when I click on some tracks it shows the error message "Unable to fetch the ../.gff3". Could anyone please help me resolve this issue.
>
> Thanks.
>
> Regards
> Vijay.
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]t
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax






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GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research






--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Regarding Jbrowse

Vijay Bhasker
Hi Scott 

Just to clarify the tracks.conf and trackList.json are present in both JBrowse-1.11.0/bin/data and JBrowse-1.11.0/data. But tracks.conf in JBrowse-1.11.0/data is empty. tracks.conf in JBrowse-1.11.0/bin/data has [tracks.alignments]
urlTemplate = FM.01.new.chr11.bam
type = Alignments2

On Monday, August 22, 2016, Scott Cain <[hidden email]> wrote:
Hi Vijay,

Let's back up a little.  I few emails ago, you wrote that your config files (tracks.conf and trackList.json) are in /bin/data.  That is an odd place for them to be, even if I assume you didn't intend to have that leading slash and it isn't really in the system /bin directory, rather in the jbrowse bin/ directory.  Typically, configuration files like this would be in the data directory directly under the jbrowse directory, so for example here:

  /var/www/jbrowse/JBrowse-1.11.0/data

(I'm guessing from other thing that you've written that this is where it should be).  If those files aren't there, then you almost certainly have to edit the jbrowse.conf or jbrowse_conf.json files so that JBrowse can find them.  In jbrowse.conf, you'd need to look for the dataRoot option.

Finally, as a fairly minor side note: are you really using JBrowse 1.11.0?  It's quite old; the newest release is 1.12.2.

Scott


On Mon, Aug 22, 2016 at 12:46 PM, Vijay Bhasker <<a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;uday4vijay@gmail.com&#39;);" target="_blank">uday4vijay@...> wrote:
Hi

Sure Nathan. I have attached the latest page here.

Thanks.
Vijay.

On Mon, Aug 22, 2016 at 12:22 PM, Nathan Dunn <<a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;nathandunn@lbl.gov&#39;);" target="_blank">nathandunn@...> wrote:

Can you provide screen shots that include the new page with the URL and the track list on the left? 

Nathan

On Aug 22, 2016, at 9:06 AM, Vijay Bhasker <<a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;uday4vijay@gmail.com&#39;);" target="_blank">uday4vijay@...> wrote:

Hi

I have moved jbrowse folder to/var/www/html and typed in the url localhost/jbrowse/JBrowse-1.11.0/index.html. I got the Jbrowse page but again with a single reference sequence.

Thanks.
Vijay.

On Mon, Aug 22, 2016 at 11:36 AM, Scott Cain <<a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;scott@scottcain.net&#39;);" target="_blank">scott@...> wrote:
My recollection is that browsers generally don't behave the same when you are looking at a file via a "file:///" versus a "http://" url.  You should really be accessing this page via a web browser.

Scott

On Mon, Aug 22, 2016 at 11:20 AM, Vijay Bhasker <<a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;uday4vijay@gmail.com&#39;);" target="_blank">uday4vijay@...> wrote:
Hi 

Could anyone please tell me which file should I edit for the customization of features like pop-up boxes, mouse-over behavior etc.

Thanks.
Vijay.

On Mon, Aug 22, 2016 at 11:14 AM, Vijay Bhasker <<a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;uday4vijay@gmail.com&#39;);" target="_blank">uday4vijay@...> wrote:
Hi

I have attached the javascript console log, datafiles directory and the url i used to connect with in xubuntu in a virtualbox.

Thanks.

On Mon, Aug 22, 2016 at 10:45 AM, Nathan Dunn <<a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;nathandunn@lbl.gov&#39;);" target="_blank">nathandunn@...> wrote:

Can you post:

1 - the  javascript console in the developer tools window when you reload the page (with caching turned off - see the network tab) 
2 - the contents of the volvox directory so that we can see the file sizes
3 - the URL you are using to connect with
4 - the browser / OS you are using 
5 - a screenshot of what you are seeing 

Nathan

On Aug 22, 2016, at 7:42 AM, Vijay Bhasker <<a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;uday4vijay@gmail.com&#39;);" target="_blank">uday4vijay@...> wrote:

Hi

It was a copy paste error. It is as you mentioned it to be. Now what should I do to get back the tracks. Which file is responsible for the tracks. How can I edit those tracks? 

Regards.
Vijay.

On Monday, August 22, 2016, Nathan Dunn <<a href="javascript:_e(%7B%7D,&#39;cvml&#39;,&#39;nathandunn@lbl.gov&#39;);" target="_blank">nathandunn@...> wrote:

The JSON is malformed.  Using:


1 - should start with an open {   (maybe just a copy and paste error)
2 - this is incorrect on the end:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$

should be:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView”,

This should show up in your javascript console as an error, as well,

Nathan

On Aug 22, 2016, at 7:23 AM, Vijay Bhasker <[hidden email]> wrote:

Hi GMOD

In /bin/data/tracks.conf I have 

[tracks.alignments]
urlTemplate = FM.01.new.sorted.chr11.bam
type = Alignments2

And the tracks.conf in /data is empty.

In /bin/data/trackList.json I have

   "tracks" : [
      {
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "key" : "Reference sequence",
         "chunkSize" : 20000,
         "category" : "Reference sequence",
         "label" : "DNA",
         "type" : "SequenceTrack"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "key" : "dna",
         "label" : "dna",
         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$
         "urlTemplate" : "tracks/dna/{refseq}/trackData.json",
         "compress" : 0,
         "style" : {
           "className" : "feature",
            "color" : "function(feature) {return 'red'; }"
         },
         "type" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.js"
      },
      {
         "type" : "FeatureTrack",
         "style" : {
            "className" : "feature"
         },
         "compress" : 0,
         "urlTemplate" : "FM.01.new.sorted.chr11.bam",
         "trackType" : null,
         "label" : "vijay",
         "key" : "vijay",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM"
      }
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "formatVersion" : 1
}

This is my complete conf file. Now when I cleared the cache and refreshed the browser, I can only find the reference sequences track and all my previous tracks have been disappeared. Could anyone please help me bring back the tracks and how can I edit those tracks.

Thanks.

Regards
Vijay.

On Sun, Aug 21, 2016 at 11:54 AM, Lbl <[hidden email]> wrote:
Please post the full error and full tracks.conf and verify that the older tracks.conf is not cached.   You can do this under the networks developer tab under chrome or Firefox per Scott's earlier advice.

> On Aug 21, 2016, at 8:13 AM, Vijay Bhasker <[hidden email]> wrote:
>
> Hi GMOD
>
> I have changed the key name for some tracks in volvox.json but the track names remains the same in the browser even after refreshing it. Also, when I click on some tracks it shows the error message "Unable to fetch the ../.gff3". Could anyone please help me resolve this issue.
>
> Thanks.
>
> Regards
> Vijay.
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]t
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax






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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research






--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Regarding Jbrowse

Vijay Bhasker
Hi GMOD

As I told in the previous e-mail about the tracks.conf and trackList.json but I have not yet seen any tracks in the JBrowse page. Can anyone please help me with this. I am in real need of it. Can anyone respond quick?

Thanks in advance.

Regards
Vijay.

On Mon, Aug 22, 2016 at 2:15 PM, Vijay Bhasker <[hidden email]> wrote:
Hi Scott 

Just to clarify the tracks.conf and trackList.json are present in both JBrowse-1.11.0/bin/data and JBrowse-1.11.0/data. But tracks.conf in JBrowse-1.11.0/data is empty. tracks.conf in JBrowse-1.11.0/bin/data has [tracks.alignments]
urlTemplate = FM.01.new.chr11.bam
type = Alignments2


On Monday, August 22, 2016, Scott Cain <[hidden email]> wrote:
Hi Vijay,

Let's back up a little.  I few emails ago, you wrote that your config files (tracks.conf and trackList.json) are in /bin/data.  That is an odd place for them to be, even if I assume you didn't intend to have that leading slash and it isn't really in the system /bin directory, rather in the jbrowse bin/ directory.  Typically, configuration files like this would be in the data directory directly under the jbrowse directory, so for example here:

  /var/www/jbrowse/JBrowse-1.11.0/data

(I'm guessing from other thing that you've written that this is where it should be).  If those files aren't there, then you almost certainly have to edit the jbrowse.conf or jbrowse_conf.json files so that JBrowse can find them.  In jbrowse.conf, you'd need to look for the dataRoot option.

Finally, as a fairly minor side note: are you really using JBrowse 1.11.0?  It's quite old; the newest release is 1.12.2.

Scott


On Mon, Aug 22, 2016 at 12:46 PM, Vijay Bhasker <[hidden email]> wrote:
Hi

Sure Nathan. I have attached the latest page here.

Thanks.
Vijay.

On Mon, Aug 22, 2016 at 12:22 PM, Nathan Dunn <[hidden email]> wrote:

Can you provide screen shots that include the new page with the URL and the track list on the left? 

Nathan

On Aug 22, 2016, at 9:06 AM, Vijay Bhasker <[hidden email]> wrote:

Hi

I have moved jbrowse folder to/var/www/html and typed in the url localhost/jbrowse/JBrowse-1.11.0/index.html. I got the Jbrowse page but again with a single reference sequence.

Thanks.
Vijay.

On Mon, Aug 22, 2016 at 11:36 AM, Scott Cain <[hidden email]> wrote:
My recollection is that browsers generally don't behave the same when you are looking at a file via a "file:///" versus a "http://" url.  You should really be accessing this page via a web browser.

Scott

On Mon, Aug 22, 2016 at 11:20 AM, Vijay Bhasker <[hidden email]> wrote:
Hi 

Could anyone please tell me which file should I edit for the customization of features like pop-up boxes, mouse-over behavior etc.

Thanks.
Vijay.

On Mon, Aug 22, 2016 at 11:14 AM, Vijay Bhasker <[hidden email]> wrote:
Hi

I have attached the javascript console log, datafiles directory and the url i used to connect with in xubuntu in a virtualbox.

Thanks.

On Mon, Aug 22, 2016 at 10:45 AM, Nathan Dunn <[hidden email]> wrote:

Can you post:

1 - the  javascript console in the developer tools window when you reload the page (with caching turned off - see the network tab) 
2 - the contents of the volvox directory so that we can see the file sizes
3 - the URL you are using to connect with
4 - the browser / OS you are using 
5 - a screenshot of what you are seeing 

Nathan

On Aug 22, 2016, at 7:42 AM, Vijay Bhasker <[hidden email]> wrote:

Hi

It was a copy paste error. It is as you mentioned it to be. Now what should I do to get back the tracks. Which file is responsible for the tracks. How can I edit those tracks? 

Regards.
Vijay.

On Monday, August 22, 2016, Nathan Dunn <[hidden email]> wrote:

The JSON is malformed.  Using:


1 - should start with an open {   (maybe just a copy and paste error)
2 - this is incorrect on the end:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$

should be:

         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView”,

This should show up in your javascript console as an error, as well,

Nathan

On Aug 22, 2016, at 7:23 AM, Vijay Bhasker <[hidden email]> wrote:

Hi GMOD

In /bin/data/tracks.conf I have 

[tracks.alignments]
urlTemplate = FM.01.new.sorted.chr11.bam
type = Alignments2

And the tracks.conf in /data is empty.

In /bin/data/trackList.json I have

   "tracks" : [
      {
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "key" : "Reference sequence",
         "chunkSize" : 20000,
         "category" : "Reference sequence",
         "label" : "DNA",
         "type" : "SequenceTrack"
      },
      {
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "key" : "dna",
         "label" : "dna",
         "trackType" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.$
         "urlTemplate" : "tracks/dna/{refseq}/trackData.json",
         "compress" : 0,
         "style" : {
           "className" : "feature",
            "color" : "function(feature) {return 'red'; }"
         },
         "type" : "/var/www/jbrowse/JBrowse-1.11.0/src/JBrowse/GenomeView.js"
      },
      {
         "type" : "FeatureTrack",
         "style" : {
            "className" : "feature"
         },
         "compress" : 0,
         "urlTemplate" : "FM.01.new.sorted.chr11.bam",
         "trackType" : null,
         "label" : "vijay",
         "key" : "vijay",
         "storeClass" : "JBrowse/Store/SeqFeature/BAM"
      }
   ],
   "names" : {
      "url" : "names/",
      "type" : "Hash"
   },
   "formatVersion" : 1
}

This is my complete conf file. Now when I cleared the cache and refreshed the browser, I can only find the reference sequences track and all my previous tracks have been disappeared. Could anyone please help me bring back the tracks and how can I edit those tracks.

Thanks.

Regards
Vijay.

On Sun, Aug 21, 2016 at 11:54 AM, Lbl <[hidden email]> wrote:
Please post the full error and full tracks.conf and verify that the older tracks.conf is not cached.   You can do this under the networks developer tab under chrome or Firefox per Scott's earlier advice.

> On Aug 21, 2016, at 8:13 AM, Vijay Bhasker <[hidden email]> wrote:
>
> Hi GMOD
>
> I have changed the key name for some tracks in volvox.json but the track names remains the same in the browser even after refreshing it. Also, when I click on some tracks it shows the error message "Unable to fetch the ../.gff3". Could anyone please help me resolve this issue.
>
> Thanks.
>
> Regards
> Vijay.
> ------------------------------------------------------------------------------
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]t
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax






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

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Gmod-ajax mailing list
[hidden email]t
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research






--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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