[Gmod-ajax] Dataset selector not working in v1.11.0 if using the new jbrowse.conf format

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[Gmod-ajax] Dataset selector not working in v1.11.0 if using the new jbrowse.conf format

Richard Hayes
Hi,

The dataset selector is not working as expected if I use the new v1.11.0 jbrowse.conf format to specify datasets.

Moving dataset config back to JSON format in jbrowse_conf.json fixes this condition.

Non-working example:
Default installed config files
1) jbrowse_conf.json is just an empty { } data structure
2) datasets section of jbrowse.conf like:
[datasets/aquilegia]
url  = ?data=genomes/Acoerulea
name = Aquilegia coerulea v1.1

# [datasets/volvox]
# url  = ?data=sample_data/json/volvox
# name = Volvox Example

# [datasets/modencode]
# url  = ?data=sample_data/json/modencode
# name = MODEncode Example

# [datasets/yeast]
# url  = ?data=sample_data/json/yeast
# name = Yeast Example

3) dataset_id set to match in either of the config options below, in turn:
- in trackList.json
    "dataset_id" : "aquilegia"
- in tracks.conf
    [general]
    dataset_id = aquilegia

I get a drop down box for the three example datasets when viewing the Acoerulea dataset in both cases.

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net

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Re: Dataset selector not working in v1.11.0 if using the new jbrowse.conf format

Keiran Raine
Hi Richard,

I'm seeing the same problem so it's not just you,

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 28 Dec 2013, at 21:18, Richard Hayes <[hidden email]> wrote:

Hi,

The dataset selector is not working as expected if I use the new v1.11.0 jbrowse.conf format to specify datasets.

Moving dataset config back to JSON format in jbrowse_conf.json fixes this condition.

Non-working example:
Default installed config files
1) jbrowse_conf.json is just an empty { } data structure
2) datasets section of jbrowse.conf like:
[datasets/aquilegia]
url  = ?data=genomes/Acoerulea
name = Aquilegia coerulea v1.1

# [datasets/volvox]
# url  = ?data=sample_data/json/volvox
# name = Volvox Example

# [datasets/modencode]
# url  = ?data=sample_data/json/modencode
# name = MODEncode Example

# [datasets/yeast]
# url  = ?data=sample_data/json/yeast
# name = Yeast Example

3) dataset_id set to match in either of the config options below, in turn:
- in trackList.json
    "dataset_id" : "aquilegia"
- in tracks.conf
    [general]
    dataset_id = aquilegia

I get a drop down box for the three example datasets when viewing the Acoerulea dataset in both cases.

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net
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Re: Dataset selector not working in v1.11.0 if using the new jbrowse.conf format

Robert Buels-2
In reply to this post by Richard Hayes
Oh heck.  Those examples are wrong.

They should read:

# [datasets.volvox]
# url  = ?data=sample_data/json/volvox
# name = Volvox Example

# [datasets.modencode]
# url  = ?data=sample_data/json/modencode
# name = MODEncode Example

# [datasets.yeast]
# url  = ?data=sample_data/json/yeast
# name = Yeast Example


The separator is a ".", not a "/".

So if you do:

[datasets.aquilegia]
url  = ?data=genomes/Acoerulea
name = Aquilegia coerulea v1.1


Does it work?


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 12/28/2013 01:18 PM, Richard Hayes wrote:

> Hi,
>
> The dataset selector is not working as expected if I use the new v1.11.0
> jbrowse.conf format to specify datasets.
>
> Moving dataset config back to JSON format in jbrowse_conf.json fixes
> this condition.
>
> Non-working example:
> Default installed config files
> 1) jbrowse_conf.json is just an empty { } data structure
> 2) datasets section of jbrowse.conf like:
> [datasets/aquilegia]
> url  = ?data=genomes/Acoerulea
> name = Aquilegia coerulea v1.1
>
> # [datasets/volvox]
> # url  = ?data=sample_data/json/volvox
> # name = Volvox Example
>
> # [datasets/modencode]
> # url  = ?data=sample_data/json/modencode
> # name = MODEncode Example
>
> # [datasets/yeast]
> # url  = ?data=sample_data/json/yeast
> # name = Yeast Example
>
> 3) dataset_id set to match in either of the config options below, in turn:
> - in trackList.json
>      "dataset_id" : "aquilegia"
> - in tracks.conf
>      [general]
>      dataset_id = aquilegia
>
> I get a drop down box for the three example datasets when viewing the
> Acoerulea dataset in both cases.
>
> Richard D. Hayes, Ph.D.
> Joint Genome Institute / Lawrence Berkeley National Lab
> http://www.phytozome.net
>
>
> ------------------------------------------------------------------------------
> Rapidly troubleshoot problems before they affect your business. Most IT
> organizations don't have a clear picture of how application performance
> affects their revenue. With AppDynamics, you get 100% visibility into your
> Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
> http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

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Re: Dataset selector not working in v1.11.0 if using the new jbrowse.conf format

Keiran Raine
Hi Robert,

Yes, that works as expected now.

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 2 Jan 2014, at 05:49, Robert Buels <[hidden email]> wrote:

Oh heck.  Those examples are wrong.

They should read:

# [datasets.volvox]
# url  = ?data=sample_data/json/volvox
# name = Volvox Example

# [datasets.modencode]
# url  = ?data=sample_data/json/modencode
# name = MODEncode Example

# [datasets.yeast]
# url  = ?data=sample_data/json/yeast
# name = Yeast Example


The separator is a ".", not a "/".

So if you do:

[datasets.aquilegia]
url  = ?data=genomes/Acoerulea
name = Aquilegia coerulea v1.1


Does it work?


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 12/28/2013 01:18 PM, Richard Hayes wrote:
Hi,

The dataset selector is not working as expected if I use the new v1.11.0
jbrowse.conf format to specify datasets.

Moving dataset config back to JSON format in jbrowse_conf.json fixes
this condition.

Non-working example:
Default installed config files
1) jbrowse_conf.json is just an empty { } data structure
2) datasets section of jbrowse.conf like:
[datasets/aquilegia]
url  = ?data=genomes/Acoerulea
name = Aquilegia coerulea v1.1

# [datasets/volvox]
# url  = ?data=sample_data/json/volvox
# name = Volvox Example

# [datasets/modencode]
# url  = ?data=sample_data/json/modencode
# name = MODEncode Example

# [datasets/yeast]
# url  = ?data=sample_data/json/yeast
# name = Yeast Example

3) dataset_id set to match in either of the config options below, in turn:
- in trackList.json
    "dataset_id" : "aquilegia"
- in tracks.conf
    [general]
    dataset_id = aquilegia

I get a drop down box for the three example datasets when viewing the
Acoerulea dataset in both cases.

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


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-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

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