[Gmod-ajax] Regarding Jbrowse

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[Gmod-ajax] Regarding Jbrowse

Vijay Bhasker
Hi GMOD

Can anyone please tell me which file should I edit to change the names of the tracks in the left of my Jbrowse page. I have changed the key value in volvox.json in /JBrowse-1.11.0/docs/tutorial/conf_files. But when I refresh the page in the browser, the page remains the same. Please can anyone guide me resolve this.

Thanks.
Vijay.

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Re: Regarding Jbrowse

Scott Cain
You didn't show us the file you edited and what you changed.

You didn't tell us what browser you're using and what you're doing to prevent caching.

I doubt that changing a file in a "docs" directory is going to change the way JBrowse looks, since that would just be documentation.


On Thu, Aug 25, 2016 at 8:38 PM, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD

Can anyone please tell me which file should I edit to change the names of the tracks in the left of my Jbrowse page. I have changed the key value in volvox.json in /JBrowse-1.11.0/docs/tutorial/conf_files. But when I refresh the page in the browser, the page remains the same. Please can anyone guide me resolve this.

Thanks.
Vijay.

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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

Colin
Maybe if I can add a tip, the volvox sample data config files that you can try editing are located here:


sample_data/json/volvox/trackList.json

and/or

sample_data/json/volvox/tracks.conf

These both contain track configs, and if you modify them, your changes should be visible after refreshing the browser

The file that you are editing, docs/tutorial/conf_files/volvox.json, is a biodb-to-json.pl config file, not a final JBrowse config file used by the browser. If you did want your changes to docs/tutorial/conf_files/volvox.json to take place, you would have to re-run setup.sh which executes biodb-to-json.pl


Hope that helps
-Colin

On Fri, Aug 26, 2016 at 8:18 AM, Scott Cain <[hidden email]> wrote:
You didn't show us the file you edited and what you changed.

You didn't tell us what browser you're using and what you're doing to prevent caching.

I doubt that changing a file in a "docs" directory is going to change the way JBrowse looks, since that would just be documentation.


On Thu, Aug 25, 2016 at 8:38 PM, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD

Can anyone please tell me which file should I edit to change the names of the tracks in the left of my Jbrowse page. I have changed the key value in volvox.json in /JBrowse-1.11.0/docs/tutorial/conf_files. But when I refresh the page in the browser, the page remains the same. Please can anyone guide me resolve this.

Thanks.
Vijay.

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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

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Re: Regarding Jbrowse

Vijay Bhasker
In reply to this post by Scott Cain
Hi GMOD

I have just changed to the key valuesof some features to see if the changes works. I am adding the code that I have made changes. Also, to prevent caching I have seen a link which mentioned that ctrl+shift+del gives a pop-up which asks to clear cached data. That is how I cleared cache.

code:

         {
   "tracks" : [
      {
         "feature" : [
            "remark"
         ],
         "autocomplete" : "all",
         "track" : "ExampleFeatures",
         "class" : "transcript",
         "category": "Miscellaneous",
         "key" : "Example Features"
      },
      {
         "feature" : [
            "protein_coding_primary_transcript",
            "polypeptide"
         ],
         "track" : "NameTest",
         "class" : "feature2",
         "category": "Miscellaneous",
         "key" : "Name test track has a really long track label"
      },
      {
         "feature" : [
            "SNP"
         ],
         "track" : "snps",
         "class" : "triangle hgred",
         "category": "Miscellaneous",
         "key" : "HTMLFeatures - SNPs"
      },

When I refresh the browser it still doesn't change the name of the track. Please anyone help me.

Thanks.
Vijay.

On Fri, Aug 26, 2016 at 9:18 AM, Scott Cain <[hidden email]> wrote:
You didn't show us the file you edited and what you changed.

You didn't tell us what browser you're using and what you're doing to prevent caching.

I doubt that changing a file in a "docs" directory is going to change the way JBrowse looks, since that would just be documentation.


On Thu, Aug 25, 2016 at 8:38 PM, Vijay Bhasker <[hidden email]> wrote:
Hi GMOD

Can anyone please tell me which file should I edit to change the names of the tracks in the left of my Jbrowse page. I have changed the key value in volvox.json in /JBrowse-1.11.0/docs/tutorial/conf_files. But when I refresh the page in the browser, the page remains the same. Please can anyone guide me resolve this.

Thanks.
Vijay.

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--
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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


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