[Gmod-ajax] Genome name not appearing

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[Gmod-ajax] Genome name not appearing

Sofia Robb
Hello,

I have a organisms.conf file and all my genomes are available in the "Genome" drop down menu and load like they should. The "name" of the genome that is assigned in my organisms.conf file is not displaying. I see "Genome" instead of the name for every organism. Am I missing a configuration detail?

Thanks,
Sofia


#### organisms.conf ########

[datasets.SmedSxl_v31]
name   = SmedSxl v3.1
url    = ?data=data/SmedSxl_v31

[datasets.SmedSxl_v42]
name   = SmedSxl v4.2
url    = ?data=data/SmedSxl_v42

[datasets.SmedSxl_v60]
name   = SmedSxl v6.0
url    = ?data=data/SmedSxl_v60

[datasets.Nvec_v10]
name   = Nematostella vectensis
url    = ?data=data/Nvec_v10

[datasets.Nfur_v10]
name   = Nothobranchius furzeri
url    = ?data=data/Nfur_v10

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
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Re: Genome name not appearing

Eric Yao
Hmm.... 
Try it in json or conf.
Make sure you define "dataset_id" in the dataset config either in trackList.json or tracks.conf

In trackList.json:

  "dataset_id": "volvox",

  "datasets": {
"volvox": {
"url":"?data=sample_data/json/volvox",
"name": "Ahoy Matey!"    
}
  },

In tracks.conf
[general] dataset_id = volvox

[datasets.volvox]
url  = ?data=sample_data/json/volvox
name = Ahoy Mate!


Seemed to work for me:





On Fri, Jun 3, 2016 at 10:26 AM, Sofia Robb <[hidden email]> wrote:
Hello,

I have a organisms.conf file and all my genomes are available in the "Genome" drop down menu and load like they should. The "name" of the genome that is assigned in my organisms.conf file is not displaying. I see "Genome" instead of the name for every organism. Am I missing a configuration detail?

Thanks,
Sofia


#### organisms.conf ########

[datasets.SmedSxl_v31]
name   = SmedSxl v3.1
url    = ?data=data/SmedSxl_v31

[datasets.SmedSxl_v42]
name   = SmedSxl v4.2
url    = ?data=data/SmedSxl_v42

[datasets.SmedSxl_v60]
name   = SmedSxl v6.0
url    = ?data=data/SmedSxl_v60

[datasets.Nvec_v10]
name   = Nematostella vectensis
url    = ?data=data/Nvec_v10

[datasets.Nfur_v10]
name   = Nothobranchius furzeri
url    = ?data=data/Nfur_v10

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
Gmod-ajax mailing list
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https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
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Re: Genome name not appearing

Sofia Robb-4
Hi Eric,
I have the dataset_id set and everything appears just like in your screen shot. I would like the genome name that is selected to be displayed as it is in wormbase, next to the drop down list, so that the user knows that they are looking at the correct genome.

Thanks for your help!
Sofia


Sent from my iPhone

On Jun 3, 2016, at 12:21 PM, Eric Yao <[hidden email]> wrote:

Hmm.... 
Try it in json or conf.
Make sure you define "dataset_id" in the dataset config either in trackList.json or tracks.conf

In trackList.json:

  "dataset_id": "volvox",

  "datasets": {
"volvox": {
"url":"?data=sample_data/json/volvox",
"name": "Ahoy Matey!"    
}
  },

In tracks.conf
[general] dataset_id = volvox

[datasets.volvox]
url  = ?data=sample_data/json/volvox
name = Ahoy Mate!


Seemed to work for me:
<Capture.PNG>




On Fri, Jun 3, 2016 at 10:26 AM, Sofia Robb <[hidden email]> wrote:
Hello,

I have a organisms.conf file and all my genomes are available in the "Genome" drop down menu and load like they should. The "name" of the genome that is assigned in my organisms.conf file is not displaying. I see "Genome" instead of the name for every organism. Am I missing a configuration detail?

Thanks,
Sofia


#### organisms.conf ########

[datasets.SmedSxl_v31]
name   = SmedSxl v3.1
url    = ?data=data/SmedSxl_v31

[datasets.SmedSxl_v42]
name   = SmedSxl v4.2
url    = ?data=data/SmedSxl_v42

[datasets.SmedSxl_v60]
name   = SmedSxl v6.0
url    = ?data=data/SmedSxl_v60

[datasets.Nvec_v10]
name   = Nematostella vectensis
url    = ?data=data/Nvec_v10

[datasets.Nfur_v10]
name   = Nothobranchius furzeri
url    = ?data=data/Nfur_v10

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
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Re: Genome name not appearing

Eric Yao
Oh, ok.  Sorry, I misunderstood.

I believe that is a customization that wormbase did, or perhaps it was a feature in an earlier version.

One way to achieve it would be to implement a small plugin.  You can take NeatHTMLFeatures as an example (under the plugins directory).
Steal this code in main.js in the plugin:

    constructor: function( args ) {

        var thisB = this;
        var browser = this.browser;

        // create function intercept after view initialization (because the view object doesn't exist before that)
        browser.afterMilestone( 'initView', function() {
               console.log(browser.config.dataset);
               console.log(browser.config.dataset_id);


From here you can extract the text from the config object and replace the text in the DIV element, replacing the word "Genome".


On Fri, Jun 3, 2016 at 12:53 PM, Sofia Robb <[hidden email]> wrote:
Hi Eric,
I have the dataset_id set and everything appears just like in your screen shot. I would like the genome name that is selected to be displayed as it is in wormbase, next to the drop down list, so that the user knows that they are looking at the correct genome.

Thanks for your help!
Sofia


Sent from my iPhone

On Jun 3, 2016, at 12:21 PM, Eric Yao <[hidden email]> wrote:

Hmm.... 
Try it in json or conf.
Make sure you define "dataset_id" in the dataset config either in trackList.json or tracks.conf

In trackList.json:

  "dataset_id": "volvox",

  "datasets": {
"volvox": {
"url":"?data=sample_data/json/volvox",
"name": "Ahoy Matey!"    
}
  },

In tracks.conf
[general] dataset_id = volvox

[datasets.volvox]
url  = ?data=sample_data/json/volvox
name = Ahoy Mate!


Seemed to work for me:
<Capture.PNG>




On Fri, Jun 3, 2016 at 10:26 AM, Sofia Robb <[hidden email]> wrote:
Hello,

I have a organisms.conf file and all my genomes are available in the "Genome" drop down menu and load like they should. The "name" of the genome that is assigned in my organisms.conf file is not displaying. I see "Genome" instead of the name for every organism. Am I missing a configuration detail?

Thanks,
Sofia


#### organisms.conf ########

[datasets.SmedSxl_v31]
name   = SmedSxl v3.1
url    = ?data=data/SmedSxl_v31

[datasets.SmedSxl_v42]
name   = SmedSxl v4.2
url    = ?data=data/SmedSxl_v42

[datasets.SmedSxl_v60]
name   = SmedSxl v6.0
url    = ?data=data/SmedSxl_v60

[datasets.Nvec_v10]
name   = Nematostella vectensis
url    = ?data=data/Nvec_v10

[datasets.Nfur_v10]
name   = Nothobranchius furzeri
url    = ?data=data/Nfur_v10

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
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Re: Genome name not appearing

Sofia Robb
Thanks Eric! I will try this out. If it works it will be my first plugin :)

Sofia



On Fri, Jun 3, 2016 at 4:22 PM, Eric Yao <[hidden email]> wrote:
Oh, ok.  Sorry, I misunderstood.

I believe that is a customization that wormbase did, or perhaps it was a feature in an earlier version.

One way to achieve it would be to implement a small plugin.  You can take NeatHTMLFeatures as an example (under the plugins directory).
Steal this code in main.js in the plugin:

    constructor: function( args ) {

        var thisB = this;
        var browser = this.browser;

        // create function intercept after view initialization (because the view object doesn't exist before that)
        browser.afterMilestone( 'initView', function() {
               console.log(browser.config.dataset);
               console.log(browser.config.dataset_id);


From here you can extract the text from the config object and replace the text in the DIV element, replacing the word "Genome".


On Fri, Jun 3, 2016 at 12:53 PM, Sofia Robb <[hidden email]> wrote:
Hi Eric,
I have the dataset_id set and everything appears just like in your screen shot. I would like the genome name that is selected to be displayed as it is in wormbase, next to the drop down list, so that the user knows that they are looking at the correct genome.

Thanks for your help!
Sofia


Sent from my iPhone

On Jun 3, 2016, at 12:21 PM, Eric Yao <[hidden email]> wrote:

Hmm.... 
Try it in json or conf.
Make sure you define "dataset_id" in the dataset config either in trackList.json or tracks.conf

In trackList.json:

  "dataset_id": "volvox",

  "datasets": {
"volvox": {
"url":"?data=sample_data/json/volvox",
"name": "Ahoy Matey!"    
}
  },

In tracks.conf
[general] dataset_id = volvox

[datasets.volvox]
url  = ?data=sample_data/json/volvox
name = Ahoy Mate!


Seemed to work for me:
<Capture.PNG>




On Fri, Jun 3, 2016 at 10:26 AM, Sofia Robb <[hidden email]> wrote:
Hello,

I have a organisms.conf file and all my genomes are available in the "Genome" drop down menu and load like they should. The "name" of the genome that is assigned in my organisms.conf file is not displaying. I see "Genome" instead of the name for every organism. Am I missing a configuration detail?

Thanks,
Sofia


#### organisms.conf ########

[datasets.SmedSxl_v31]
name   = SmedSxl v3.1
url    = ?data=data/SmedSxl_v31

[datasets.SmedSxl_v42]
name   = SmedSxl v4.2
url    = ?data=data/SmedSxl_v42

[datasets.SmedSxl_v60]
name   = SmedSxl v6.0
url    = ?data=data/SmedSxl_v60

[datasets.Nvec_v10]
name   = Nematostella vectensis
url    = ?data=data/Nvec_v10

[datasets.Nfur_v10]
name   = Nothobranchius furzeri
url    = ?data=data/Nfur_v10

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax





------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
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Re: Genome name not appearing

Scott Cain
In reply to this post by Eric Yao
We certainly didn't do that as a plugin, though we are still using 1.11.6.  I think it should be the default behavior when using multiple genomes.

Scott


On Fri, Jun 3, 2016 at 6:22 PM, Eric Yao <[hidden email]> wrote:
Oh, ok.  Sorry, I misunderstood.

I believe that is a customization that wormbase did, or perhaps it was a feature in an earlier version.

One way to achieve it would be to implement a small plugin.  You can take NeatHTMLFeatures as an example (under the plugins directory).
Steal this code in main.js in the plugin:

    constructor: function( args ) {

        var thisB = this;
        var browser = this.browser;

        // create function intercept after view initialization (because the view object doesn't exist before that)
        browser.afterMilestone( 'initView', function() {
               console.log(browser.config.dataset);
               console.log(browser.config.dataset_id);


From here you can extract the text from the config object and replace the text in the DIV element, replacing the word "Genome".


On Fri, Jun 3, 2016 at 12:53 PM, Sofia Robb <[hidden email]> wrote:
Hi Eric,
I have the dataset_id set and everything appears just like in your screen shot. I would like the genome name that is selected to be displayed as it is in wormbase, next to the drop down list, so that the user knows that they are looking at the correct genome.

Thanks for your help!
Sofia


Sent from my iPhone

On Jun 3, 2016, at 12:21 PM, Eric Yao <[hidden email]> wrote:

Hmm.... 
Try it in json or conf.
Make sure you define "dataset_id" in the dataset config either in trackList.json or tracks.conf

In trackList.json:

  "dataset_id": "volvox",

  "datasets": {
"volvox": {
"url":"?data=sample_data/json/volvox",
"name": "Ahoy Matey!"    
}
  },

In tracks.conf
[general] dataset_id = volvox

[datasets.volvox]
url  = ?data=sample_data/json/volvox
name = Ahoy Mate!


Seemed to work for me:
<Capture.PNG>




On Fri, Jun 3, 2016 at 10:26 AM, Sofia Robb <[hidden email]> wrote:
Hello,

I have a organisms.conf file and all my genomes are available in the "Genome" drop down menu and load like they should. The "name" of the genome that is assigned in my organisms.conf file is not displaying. I see "Genome" instead of the name for every organism. Am I missing a configuration detail?

Thanks,
Sofia


#### organisms.conf ########

[datasets.SmedSxl_v31]
name   = SmedSxl v3.1
url    = ?data=data/SmedSxl_v31

[datasets.SmedSxl_v42]
name   = SmedSxl v4.2
url    = ?data=data/SmedSxl_v42

[datasets.SmedSxl_v60]
name   = SmedSxl v6.0
url    = ?data=data/SmedSxl_v60

[datasets.Nvec_v10]
name   = Nematostella vectensis
url    = ?data=data/Nvec_v10

[datasets.Nfur_v10]
name   = Nothobranchius furzeri
url    = ?data=data/Nfur_v10

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
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

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
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Re: Genome name not appearing

Colin
You can add classicMenu=true in jbrowse.conf to get it to display the dataset names on the menubar "a la wormbase"

The option was added in the 1.12 versions of jbrowse

-Colin

On Sat, Jun 11, 2016 at 9:04 AM, Scott Cain <[hidden email]> wrote:
We certainly didn't do that as a plugin, though we are still using 1.11.6.  I think it should be the default behavior when using multiple genomes.

Scott


On Fri, Jun 3, 2016 at 6:22 PM, Eric Yao <[hidden email]> wrote:
Oh, ok.  Sorry, I misunderstood.

I believe that is a customization that wormbase did, or perhaps it was a feature in an earlier version.

One way to achieve it would be to implement a small plugin.  You can take NeatHTMLFeatures as an example (under the plugins directory).
Steal this code in main.js in the plugin:

    constructor: function( args ) {

        var thisB = this;
        var browser = this.browser;

        // create function intercept after view initialization (because the view object doesn't exist before that)
        browser.afterMilestone( 'initView', function() {
               console.log(browser.config.dataset);
               console.log(browser.config.dataset_id);


From here you can extract the text from the config object and replace the text in the DIV element, replacing the word "Genome".


On Fri, Jun 3, 2016 at 12:53 PM, Sofia Robb <[hidden email]> wrote:
Hi Eric,
I have the dataset_id set and everything appears just like in your screen shot. I would like the genome name that is selected to be displayed as it is in wormbase, next to the drop down list, so that the user knows that they are looking at the correct genome.

Thanks for your help!
Sofia


Sent from my iPhone

On Jun 3, 2016, at 12:21 PM, Eric Yao <[hidden email]> wrote:

Hmm.... 
Try it in json or conf.
Make sure you define "dataset_id" in the dataset config either in trackList.json or tracks.conf

In trackList.json:

  "dataset_id": "volvox",

  "datasets": {
"volvox": {
"url":"?data=sample_data/json/volvox",
"name": "Ahoy Matey!"    
}
  },

In tracks.conf
[general] dataset_id = volvox

[datasets.volvox]
url  = ?data=sample_data/json/volvox
name = Ahoy Mate!


Seemed to work for me:
<Capture.PNG>




On Fri, Jun 3, 2016 at 10:26 AM, Sofia Robb <[hidden email]> wrote:
Hello,

I have a organisms.conf file and all my genomes are available in the "Genome" drop down menu and load like they should. The "name" of the genome that is assigned in my organisms.conf file is not displaying. I see "Genome" instead of the name for every organism. Am I missing a configuration detail?

Thanks,
Sofia


#### organisms.conf ########

[datasets.SmedSxl_v31]
name   = SmedSxl v3.1
url    = ?data=data/SmedSxl_v31

[datasets.SmedSxl_v42]
name   = SmedSxl v4.2
url    = ?data=data/SmedSxl_v42

[datasets.SmedSxl_v60]
name   = SmedSxl v6.0
url    = ?data=data/SmedSxl_v60

[datasets.Nvec_v10]
name   = Nematostella vectensis
url    = ?data=data/Nvec_v10

[datasets.Nfur_v10]
name   = Nothobranchius furzeri
url    = ?data=data/Nfur_v10

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
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[hidden email]
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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

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
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Re: Genome name not appearing

Sofia Robb-4
Yea! That worked! Thank you!!!

On Mon, Jun 13, 2016 at 6:22 AM, Colin <[hidden email]> wrote:
You can add classicMenu=true in jbrowse.conf to get it to display the dataset names on the menubar "a la wormbase"

The option was added in the 1.12 versions of jbrowse

-Colin

On Sat, Jun 11, 2016 at 9:04 AM, Scott Cain <[hidden email]> wrote:
We certainly didn't do that as a plugin, though we are still using 1.11.6.  I think it should be the default behavior when using multiple genomes.

Scott


On Fri, Jun 3, 2016 at 6:22 PM, Eric Yao <[hidden email]> wrote:
Oh, ok.  Sorry, I misunderstood.

I believe that is a customization that wormbase did, or perhaps it was a feature in an earlier version.

One way to achieve it would be to implement a small plugin.  You can take NeatHTMLFeatures as an example (under the plugins directory).
Steal this code in main.js in the plugin:

    constructor: function( args ) {

        var thisB = this;
        var browser = this.browser;

        // create function intercept after view initialization (because the view object doesn't exist before that)
        browser.afterMilestone( 'initView', function() {
               console.log(browser.config.dataset);
               console.log(browser.config.dataset_id);


From here you can extract the text from the config object and replace the text in the DIV element, replacing the word "Genome".


On Fri, Jun 3, 2016 at 12:53 PM, Sofia Robb <[hidden email]> wrote:
Hi Eric,
I have the dataset_id set and everything appears just like in your screen shot. I would like the genome name that is selected to be displayed as it is in wormbase, next to the drop down list, so that the user knows that they are looking at the correct genome.

Thanks for your help!
Sofia


Sent from my iPhone

On Jun 3, 2016, at 12:21 PM, Eric Yao <[hidden email]> wrote:

Hmm.... 
Try it in json or conf.
Make sure you define "dataset_id" in the dataset config either in trackList.json or tracks.conf

In trackList.json:

  "dataset_id": "volvox",

  "datasets": {
"volvox": {
"url":"?data=sample_data/json/volvox",
"name": "Ahoy Matey!"    
}
  },

In tracks.conf
[general] dataset_id = volvox

[datasets.volvox]
url  = ?data=sample_data/json/volvox
name = Ahoy Mate!


Seemed to work for me:
<Capture.PNG>




On Fri, Jun 3, 2016 at 10:26 AM, Sofia Robb <[hidden email]> wrote:
Hello,

I have a organisms.conf file and all my genomes are available in the "Genome" drop down menu and load like they should. The "name" of the genome that is assigned in my organisms.conf file is not displaying. I see "Genome" instead of the name for every organism. Am I missing a configuration detail?

Thanks,
Sofia


#### organisms.conf ########

[datasets.SmedSxl_v31]
name   = SmedSxl v3.1
url    = ?data=data/SmedSxl_v31

[datasets.SmedSxl_v42]
name   = SmedSxl v4.2
url    = ?data=data/SmedSxl_v42

[datasets.SmedSxl_v60]
name   = SmedSxl v6.0
url    = ?data=data/SmedSxl_v60

[datasets.Nvec_v10]
name   = Nematostella vectensis
url    = ?data=data/Nvec_v10

[datasets.Nfur_v10]
name   = Nothobranchius furzeri
url    = ?data=data/Nfur_v10

------------------------------------------------------------------------------
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What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
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consuming the most bandwidth. Provides multi-vendor support for NetFlow,
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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

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
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------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
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Re: Genome name not appearing

nathandunn

Thanks . . Just noticed it here:


I’ll close the bugs I had opened for this.  

Nathan

On Jun 13, 2016, at 9:11 AM, Sofia Robb <[hidden email]> wrote:

Yea! That worked! Thank you!!!

On Mon, Jun 13, 2016 at 6:22 AM, Colin <[hidden email]> wrote:
You can add classicMenu=true in jbrowse.conf to get it to display the dataset names on the menubar "a la wormbase"

The option was added in the 1.12 versions of jbrowse

-Colin

On Sat, Jun 11, 2016 at 9:04 AM, Scott Cain <[hidden email]> wrote:
We certainly didn't do that as a plugin, though we are still using 1.11.6.  I think it should be the default behavior when using multiple genomes.

Scott


On Fri, Jun 3, 2016 at 6:22 PM, Eric Yao <[hidden email]> wrote:
Oh, ok.  Sorry, I misunderstood.

I believe that is a customization that wormbase did, or perhaps it was a feature in an earlier version.

One way to achieve it would be to implement a small plugin.  You can take NeatHTMLFeatures as an example (under the plugins directory).
Steal this code in main.js in the plugin:

    constructor: function( args ) {

        var thisB = this;
        var browser = this.browser;

        // create function intercept after view initialization (because the view object doesn't exist before that)
        browser.afterMilestone( 'initView', function() {
               console.log(browser.config.dataset);
               console.log(browser.config.dataset_id);


From here you can extract the text from the config object and replace the text in the DIV element, replacing the word "Genome".


On Fri, Jun 3, 2016 at 12:53 PM, Sofia Robb <[hidden email]> wrote:
Hi Eric,
I have the dataset_id set and everything appears just like in your screen shot. I would like the genome name that is selected to be displayed as it is in wormbase, next to the drop down list, so that the user knows that they are looking at the correct genome.

Thanks for your help!
Sofia


Sent from my iPhone

On Jun 3, 2016, at 12:21 PM, Eric Yao <[hidden email]> wrote:

Hmm.... 
Try it in json or conf.
Make sure you define "dataset_id" in the dataset config either in trackList.json or tracks.conf

In trackList.json:

  "dataset_id": "volvox",

  "datasets": {
"volvox": {
"url":"?data=sample_data/json/volvox",
"name": "Ahoy Matey!"    
}
  },

In tracks.conf
[general] dataset_id = volvox

[datasets.volvox]
url  = ?data=sample_data/json/volvox
name = Ahoy Mate!


Seemed to work for me:
<Capture.PNG>




On Fri, Jun 3, 2016 at 10:26 AM, Sofia Robb <[hidden email]> wrote:
Hello,

I have a organisms.conf file and all my genomes are available in the "Genome" drop down menu and load like they should. The "name" of the genome that is assigned in my organisms.conf file is not displaying. I see "Genome" instead of the name for every organism. Am I missing a configuration detail?

Thanks,
Sofia


#### organisms.conf ########

[datasets.SmedSxl_v31]
name   = SmedSxl v3.1
url    = ?data=data/SmedSxl_v31

[datasets.SmedSxl_v42]
name   = SmedSxl v4.2
url    = ?data=data/SmedSxl_v42

[datasets.SmedSxl_v60]
name   = SmedSxl v6.0
url    = ?data=data/SmedSxl_v60

[datasets.Nvec_v10]
name   = Nematostella vectensis
url    = ?data=data/Nvec_v10

[datasets.Nfur_v10]
name   = Nothobranchius furzeri
url    = ?data=data/Nfur_v10

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax




------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
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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" class="">216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
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------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e_______________________________________________
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------------------------------------------------------------------------------
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
_______________________________________________
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