[Gmod-ajax] Dataset selector showing all tracks

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

[Gmod-ajax] Dataset selector showing all tracks

vaneet

Hello,

 

I’m new to JBrowse and started by adding 2 Xenopus genomes (Laevis and Tropicalis) and 1 gene model track for each (GFF).  I tried to follow the basic instructions to setup the dataset selector in order to have the option to view the other genome tracks when looking at one of them.  It does successfully add the genomes to the drop down bar of Genome however no matter which genome species I’m looking at it lists all of the tracks from both species in the left pane of ‘Available Tracks’.  How do I get it to only list the tracks belonging to that genome species which I’m viewing.

 

These are the lines I’ve added in my main jbrowse.conf file in root JBrowse directory:

 

[datasets.xl9_2]

url  = ?data=data/xl9_2

name = Xenopus Laevis 9.2 JGI

 

[datasets.xt9_1]

url  = ?data=data/xt9_1

name = Xenopus Tropicalis 9.1 JGI

 

I also added include statements for the ‘trackList.json’ and ‘tracks.conf’ belonging to each species as well.

 

In each of the directories referenced above I added lines to ‘tracks.conf’ file to map to the corresponding dataset. For example in data/xl9_2/tracks.conf I added this:

 

[general]

dataset_id = xl9_2

 

Can you think of what I did wrong or what I need to add in order to only show the tracks for a given genome?  I tried the “defaultTracks” attribute as well but it doesn’t seem to work, it still shows both species’ tracks.

 

Any help you can provide is appreciated, I’m new to JBrowse and trying to get familiar with it as best as I can.

 

Thanks,


Vaneet

 

Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW

Calgary AB T2N 1N4

CANADA

 


------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: Dataset selector showing all tracks

Colin
This setup seems basically correct.

The dataset selector is pretty conceptually simple, it is literally just making a link to a URL such as this using the url attribute of your dataset config




If you manually visit these links, are they the same data? That would be a different config issue rather than dataset selector :)

-Colin

On Tue, May 2, 2017 at 6:27 PM, Vaneet Lotay <[hidden email]> wrote:

Hello,

 

I’m new to JBrowse and started by adding 2 Xenopus genomes (Laevis and Tropicalis) and 1 gene model track for each (GFF).  I tried to follow the basic instructions to setup the dataset selector in order to have the option to view the other genome tracks when looking at one of them.  It does successfully add the genomes to the drop down bar of Genome however no matter which genome species I’m looking at it lists all of the tracks from both species in the left pane of ‘Available Tracks’.  How do I get it to only list the tracks belonging to that genome species which I’m viewing.

 

These are the lines I’ve added in my main jbrowse.conf file in root JBrowse directory:

 

[datasets.xl9_2]

url  = ?data=data/xl9_2

name = Xenopus Laevis 9.2 JGI

 

[datasets.xt9_1]

url  = ?data=data/xt9_1

name = Xenopus Tropicalis 9.1 JGI

 

I also added include statements for the ‘trackList.json’ and ‘tracks.conf’ belonging to each species as well.

 

In each of the directories referenced above I added lines to ‘tracks.conf’ file to map to the corresponding dataset. For example in data/xl9_2/tracks.conf I added this:

 

[general]

dataset_id = xl9_2

 

Can you think of what I did wrong or what I need to add in order to only show the tracks for a given genome?  I tried the “defaultTracks” attribute as well but it doesn’t seem to work, it still shows both species’ tracks.

 

Any help you can provide is appreciated, I’m new to JBrowse and trying to get familiar with it as best as I can.

 

Thanks,


Vaneet

 

Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW

Calgary AB T2N 1N4

CANADA

 


------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: Dataset selector showing all tracks

vaneet

When I visit the URL for both genomes it does successfully switch the reference sequence to the correct genome but it still leaves both my gene model tracks selectable in the left pane under ‘Available tracks’.  I tried to set ‘defaultTracks’ for each genome but it doesn’t even move the checkmark to the correct gene model track which I’ve set it just stays with the one that was previously checked, so I have to manually uncheck that track and check the other correct one for the right genome.

 

Is there something wrong with how I organized my data folders?  I noticed when I add the ‘volvox’ example data to all configs the same thing happens, all tracks from the 3 genomes are always shown under ‘Available tracks’.

 

Is this the default behavior for JBrowse?

 

I can send you the direct link to my JBrowse server in a separate e-mail if you want to take a closer look.

 

Thanks,

 

Vaneet

 

Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW

Calgary AB T2N 1N4

CANADA

 

From: Colin [mailto:[hidden email]]
Sent: Wednesday, May 03, 2017 1:22 PM
To: Vaneet Lotay <[hidden email]>
Cc: [hidden email]
Subject: Re: [Gmod-ajax] Dataset selector showing all tracks

 

This setup seems basically correct.

 

The dataset selector is pretty conceptually simple, it is literally just making a link to a URL such as this using the url attribute of your dataset config

 

 

 

 

If you manually visit these links, are they the same data? That would be a different config issue rather than dataset selector :)

 

-Colin

 

On Tue, May 2, 2017 at 6:27 PM, Vaneet Lotay <[hidden email]> wrote:

Hello,

 

I’m new to JBrowse and started by adding 2 Xenopus genomes (Laevis and Tropicalis) and 1 gene model track for each (GFF).  I tried to follow the basic instructions to setup the dataset selector in order to have the option to view the other genome tracks when looking at one of them.  It does successfully add the genomes to the drop down bar of Genome however no matter which genome species I’m looking at it lists all of the tracks from both species in the left pane of ‘Available Tracks’.  How do I get it to only list the tracks belonging to that genome species which I’m viewing.

 

These are the lines I’ve added in my main jbrowse.conf file in root JBrowse directory:

 

[datasets.xl9_2]

url  = ?data=data/xl9_2

name = Xenopus Laevis 9.2 JGI

 

[datasets.xt9_1]

url  = ?data=data/xt9_1

name = Xenopus Tropicalis 9.1 JGI

 

I also added include statements for the ‘trackList.json’ and ‘tracks.conf’ belonging to each species as well.

 

In each of the directories referenced above I added lines to ‘tracks.conf’ file to map to the corresponding dataset. For example in data/xl9_2/tracks.conf I added this:

 

[general]

dataset_id = xl9_2

 

Can you think of what I did wrong or what I need to add in order to only show the tracks for a given genome?  I tried the “defaultTracks” attribute as well but it doesn’t seem to work, it still shows both species’ tracks.

 

Any help you can provide is appreciated, I’m new to JBrowse and trying to get familiar with it as best as I can.

 

Thanks,


Vaneet

 

Vaneet Lotay

Xenbase Bioinformatician

716 ICT Building - University of Calgary

2500 University Drive NW

Calgary AB T2N 1N4

CANADA

 


------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

 


------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax