[Gmod-ajax] Questions about configuration keys of tracks

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[Gmod-ajax] Questions about configuration keys of tracks

Kenta Sato
Hi all,

I'm really new to JBrowse and planning to use it in the next project. I read JBrowse Configuration Guide (http://gmod.org/wiki/JBrowse_Configuration_Guide) but some keys don't have explanation. So, let me ask here.

In the following example, what "urlTemplate", "storeClass" and "type" exactly mean? Also, what values are supposed to be? The value looks separated by slash but I have no idea what these separated values mean.
{
 "tracks": [
   {
     "urlTemplate" : "volvox-sorted.bam",
     "storeClass"  : "JBrowse/Store/SeqFeature/BAM",
     "type"        : "JBrowse/View/Track/Alignments2",
     "label"       : "BAM_track",
     "key"         : "My BAM track"
     "style": { "color": "red" }
   }
 ]
}

Thank you in advance!


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Name : 佐藤建太(Sato Kenta)
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Re: Questions about configuration keys of tracks

Raymond Wan-2
Hi Kenta,


On Thu, May 26, 2016 at 8:26 PM, Kenta Sato <[hidden email]> wrote:

> I'm really new to JBrowse and planning to use it in the next project. I read
> JBrowse Configuration Guide
> (http://gmod.org/wiki/JBrowse_Configuration_Guide) but some keys don't have
> explanation. So, let me ask here.
>
> In the following example, what "urlTemplate", "storeClass" and "type"
> exactly mean? Also, what values are supposed to be? The value looks
> separated by slash but I have no idea what these separated values mean.
>
> {
>  "tracks": [
>    {
>      "urlTemplate" : "volvox-sorted.bam",
>      "storeClass"  : "JBrowse/Store/SeqFeature/BAM",
>      "type"        : "JBrowse/View/Track/Alignments2",
>      "label"       : "BAM_track",
>      "key"         : "My BAM track"
>      "style": { "color": "red" }
>    }
>  ]
> }


* urlTemplate is the name of the BAM file that you want displayed.
This is mentioned in the section "BAM Data Configuration Options" of
that link you mentioned.

* storeClass is the type of data.  So, this basically means that
volvox-sorted.bam is a BAM file.

* type is the type of the track.  See the "Alignments2" section in
that link you mentioned.

Perhaps the information could be organized as more of a reference
manual with explanations, but generally, all of the information is on
that page.  Other pages you might want to look at are tutorial pages
such as this one:  http://gmod.org/wiki/JBrowse_Tutorial_2013 .  It
shows some configuration values for BAM, BigWig, VCF, etc. so you can
compare and contrast them to see what you need.

For me, I started out with the sample data set that comes with a
default JBrowse installation and modified the configuration files
until I understood what I was doing.  Of course, I got it wrong many
times, so I kept an eye on the web server's log files for any helpful
error messages.  I suggest you play with this a bit before attempting
to apply JBrowse to your own data.

Ray

------------------------------------------------------------------------------
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bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
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Re: Questions about configuration keys of tracks

Eric Yao
I'll just add that those values with slashes are class references to specific files under the under the src directory.
for example, 
 "storeClass"  : "JBrowse/Store/SeqFeature/BAM",

is referring to a file <your jbrowse dir>/src/JBrowse/Store/SeqFeature/BAM.js where the class is implemented.

On Thu, May 26, 2016 at 8:16 AM, Raymond Wan <[hidden email]> wrote:
Hi Kenta,


On Thu, May 26, 2016 at 8:26 PM, Kenta Sato <[hidden email]> wrote:
> I'm really new to JBrowse and planning to use it in the next project. I read
> JBrowse Configuration Guide
> (http://gmod.org/wiki/JBrowse_Configuration_Guide) but some keys don't have
> explanation. So, let me ask here.
>
> In the following example, what "urlTemplate", "storeClass" and "type"
> exactly mean? Also, what values are supposed to be? The value looks
> separated by slash but I have no idea what these separated values mean.
>
> {
>  "tracks": [
>    {
>      "urlTemplate" : "volvox-sorted.bam",
>      "storeClass"  : "JBrowse/Store/SeqFeature/BAM",
>      "type"        : "JBrowse/View/Track/Alignments2",
>      "label"       : "BAM_track",
>      "key"         : "My BAM track"
>      "style": { "color": "red" }
>    }
>  ]
> }


* urlTemplate is the name of the BAM file that you want displayed.
This is mentioned in the section "BAM Data Configuration Options" of
that link you mentioned.

* storeClass is the type of data.  So, this basically means that
volvox-sorted.bam is a BAM file.

* type is the type of the track.  See the "Alignments2" section in
that link you mentioned.

Perhaps the information could be organized as more of a reference
manual with explanations, but generally, all of the information is on
that page.  Other pages you might want to look at are tutorial pages
such as this one:  http://gmod.org/wiki/JBrowse_Tutorial_2013 .  It
shows some configuration values for BAM, BigWig, VCF, etc. so you can
compare and contrast them to see what you need.

For me, I started out with the sample data set that comes with a
default JBrowse installation and modified the configuration files
until I understood what I was doing.  Of course, I got it wrong many
times, so I kept an eye on the web server's log files for any helpful
error messages.  I suggest you play with this a bit before attempting
to apply JBrowse to your own data.

Ray

------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
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