[Gmod-ajax] organizing a project in JBrowse

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[Gmod-ajax] organizing a project in JBrowse

Abhishek Pratap
Hey

I am getting started to using JBrowse for our datasets and have few
questions. If some of them happen to be listed as FAQs somewhere
please do let me know.

I want to understand a good practice of creating and managing
project/s data on Jbrowse. Suppose we have 3-4 projects which use the
same reference and gene features (hg19)

1. Is it needed to load ref and genes for each one of them separately
? I guess not but not sure how they could share sequences and some
tracks but display different datasets

2. How can we keep the projects/data separated into separate folders ?
An example would be very handy. I did look at volvox / yeast but they
all had different ref/ features.

3. Suppose we want to display more than few (for eg. 20 bigwig files
on the browser) is there a way to add multiple files to the track list
in single block

In essence if I could get a peek at well organized project in Jbrowse
I think I would be able to help myself. Any example codebase you can
point me to ?


Thanks!
-Abhi

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Re: organizing a project in JBrowse

Robert Buels-2
Other tools that can be used for organizing things:

- JBrowse config files support an "include" statement that can load and
include other config files.  The configuration in an included file is
merged into the file that includes it, with the values in the included
file taking precedence.  This is the same kind of cascading merging
that's done in most other systems, like CSS.

- From the server's perspective, JBrowse is all static files, and can
live just in a single directory, so there's no reason you can't have a
whole copy of JBrowse for each project.

- Or, JBrowse has a dataset selector that can be used to switch among
different projects in a single JBrowse instance, see
http://gmod.org/wiki/JBrowse_Configuration_Guide#Dataset_Selector

- JBrowse 1.11.0, probably coming out early next week, will support
templating in its configuration, meaning that you can interpolate the
values of some configuration variables into other configuration
variables.  This could be used for managing large numbers of projects.
JBrowse ignores configuration variables that it doesn't understand, so
you can put your own stuff in JSON configurations with no problem.

Lots of tools that can be used in different ways.


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

On 12/09/2013 05:58 PM, Abhishek Pratap wrote:

> Hey
>
> I am getting started to using JBrowse for our datasets and have few
> questions. If some of them happen to be listed as FAQs somewhere
> please do let me know.
>
> I want to understand a good practice of creating and managing
> project/s data on Jbrowse. Suppose we have 3-4 projects which use the
> same reference and gene features (hg19)
>
> 1. Is it needed to load ref and genes for each one of them separately
> ? I guess not but not sure how they could share sequences and some
> tracks but display different datasets
>
> 2. How can we keep the projects/data separated into separate folders ?
> An example would be very handy. I did look at volvox / yeast but they
> all had different ref/ features.
>
> 3. Suppose we want to display more than few (for eg. 20 bigwig files
> on the browser) is there a way to add multiple files to the track list
> in single block
>
> In essence if I could get a peek at well organized project in Jbrowse
> I think I would be able to help myself. Any example codebase you can
> point me to ?
>
>
> Thanks!
> -Abhi
>
> ------------------------------------------------------------------------------
> Sponsored by Intel(R) XDK
> Develop, test and display web and hybrid apps with a single code base.
> Download it for free now!
> http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

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Re: organizing a project in JBrowse

Richard Hayes

On Thu, Dec 12, 2013 at 1:02 PM, Robert Buels <[hidden email]> wrote:
Other tools that can be used for organizing things:

- JBrowse config files support an "include" statement that can load and
include other config files.  The configuration in an included file is
merged into the file that includes it, with the values in the included
file taking precedence.  This is the same kind of cascading merging
that's done in most other systems, like CSS.


Will this support external javascript files that declare functions for custom callbacks (like customized left-click behavior, color selection based on attributes, etc.)? I'm using these extensively, and having to smoosh a full function into a single line of JSON config is currently a nightmare for debugging.
 
- From the server's perspective, JBrowse is all static files, and can
live just in a single directory, so there's no reason you can't have a
whole copy of JBrowse for each project.

- Or, JBrowse has a dataset selector that can be used to switch among
different projects in a single JBrowse instance, see
http://gmod.org/wiki/JBrowse_Configuration_Guide#Dataset_Selector

- JBrowse 1.11.0, probably coming out early next week, will support
templating in its configuration, meaning that you can interpolate the
values of some configuration variables into other configuration
variables.  This could be used for managing large numbers of projects.
JBrowse ignores configuration variables that it doesn't understand, so
you can put your own stuff in JSON configurations with no problem.


This will also be useful. Looking forward to it!
 
Lots of tools that can be used in different ways.


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

On 12/09/2013 05:58 PM, Abhishek Pratap wrote:
> Hey
>
> I am getting started to using JBrowse for our datasets and have few
> questions. If some of them happen to be listed as FAQs somewhere
> please do let me know.
>
> I want to understand a good practice of creating and managing
> project/s data on Jbrowse. Suppose we have 3-4 projects which use the
> same reference and gene features (hg19)
>
> 1. Is it needed to load ref and genes for each one of them separately
> ? I guess not but not sure how they could share sequences and some
> tracks but display different datasets
>
> 2. How can we keep the projects/data separated into separate folders ?
> An example would be very handy. I did look at volvox / yeast but they
> all had different ref/ features.
>
> 3. Suppose we want to display more than few (for eg. 20 bigwig files
> on the browser) is there a way to add multiple files to the track list
> in single block
>
> In essence if I could get a peek at well organized project in Jbrowse
> I think I would be able to help myself. Any example codebase you can
> point me to ?
>
>
> Thanks!
> -Abhi
>
> ------------------------------------------------------------------------------
> Sponsored by Intel(R) XDK
> Develop, test and display web and hybrid apps with a single code base.
> Download it for free now!
> http://pubads.g.doubleclick.net/gampad/clk?id=111408631&iu=/4140/ostg.clktrk
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

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Re: organizing a project in JBrowse

Keiran Raine
In reply to this post by Robert Buels-2
Hi Robert,

On the subject of releases are there any plans to move on to the 2.x branches soon?  For me to make JBrowse more than just a demonstration system for out group I need semantic zooming (#327) from BAM to bigwig and potentially to ability for the user to be able to use a toggle to switch between alignment and SNPcoverge rather than have this as 3 separate tracks.

Thanks,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

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

On 12 Dec 2013, at 21:02, Robert Buels <[hidden email]> wrote:

Other tools that can be used for organizing things:

- JBrowse config files support an "include" statement that can load and
include other config files.  The configuration in an included file is
merged into the file that includes it, with the values in the included
file taking precedence.  This is the same kind of cascading merging
that's done in most other systems, like CSS.

- From the server's perspective, JBrowse is all static files, and can
live just in a single directory, so there's no reason you can't have a
whole copy of JBrowse for each project.

- Or, JBrowse has a dataset selector that can be used to switch among
different projects in a single JBrowse instance, see
http://gmod.org/wiki/JBrowse_Configuration_Guide#Dataset_Selector

- JBrowse 1.11.0, probably coming out early next week, will support
templating in its configuration, meaning that you can interpolate the
values of some configuration variables into other configuration
variables.  This could be used for managing large numbers of projects.
JBrowse ignores configuration variables that it doesn't understand, so
you can put your own stuff in JSON configurations with no problem.

Lots of tools that can be used in different ways.


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

On 12/09/2013 05:58 PM, Abhishek Pratap wrote:
Hey

I am getting started to using JBrowse for our datasets and have few
questions. If some of them happen to be listed as FAQs somewhere
please do let me know.

I want to understand a good practice of creating and managing
project/s data on Jbrowse. Suppose we have 3-4 projects which use the
same reference and gene features (hg19)

1. Is it needed to load ref and genes for each one of them separately
? I guess not but not sure how they could share sequences and some
tracks but display different datasets

2. How can we keep the projects/data separated into separate folders ?
An example would be very handy. I did look at volvox / yeast but they
all had different ref/ features.

3. Suppose we want to display more than few (for eg. 20 bigwig files
on the browser) is there a way to add multiple files to the track list
in single block

In essence if I could get a peek at well organized project in Jbrowse
I think I would be able to help myself. Any example codebase you can
point me to ?


Thanks!
-Abhi

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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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Re: organizing a project in JBrowse

Robert Buels-2
On 12/12/2013 06:21 PM, Keiran Raine wrote:
> On the subject of releases are there any plans to move on to the 2.x
> branches soon?  For me to make JBrowse more than just a demonstration

It's probably going to be at least a couple more months.

> system for out group I need semantic zooming (#327) from BAM to bigwig

Support for this limited case of semantic zooming is coming out next
week in 1.11.0.

> and potentially to ability for the user to be able to use a toggle to
> switch between alignment and SNPcoverge rather than have this as 3
> separate tracks.

I'll look into whether I can do something about this sooner than 2.0.


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

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Re: organizing a project in JBrowse

Keiran Raine
>
>> system for out group I need semantic zooming (#327) from BAM to bigwig
>
> Support for this limited case of semantic zooming is coming out next week in 1.11.0.

That's fantastic, if we can semantic zoom from BAM alignment to BigWig coverage that's equivalent to what we have under GBrowse.



--
 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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Re: organizing a project in JBrowse

Robert Buels-2
In reply to this post by Richard Hayes
On 12/12/2013 04:34 PM, Richard Hayes wrote:

>
> On Thu, Dec 12, 2013 at 1:02 PM, Robert Buels <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Other tools that can be used for organizing things:
>
>     - JBrowse config files support an "include" statement that can load and
>     include other config files.  The configuration in an included file is
>     merged into the file that includes it, with the values in the included
>     file taking precedence.  This is the same kind of cascading merging
>     that's done in most other systems, like CSS.
>
>
> Will this support external javascript files that declare functions for
> custom callbacks (like customized left-click behavior, color selection
> based on attributes, etc.)? I'm using these extensively, and having to
> smoosh a full function into a single line of JSON config is currently a
> nightmare for debugging.

I did some work on a new configuration system for 1.11.0 that should
make this less painful.  Have a look at the 1.11.0-pre3 prerelease I
just sent you and Keiran.  The config variable templating and the new
optional GBrowse-like config syntax should make it easier to maintain
large numbers of JS callbacks.

Rob

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Re: organizing a project in JBrowse

Keiran Raine
Hi Robert,

Am I missing an email or link?  I don't seem to have anything as indicated here.

Keiran

> I did some work on a new configuration system for 1.11.0 that should
> make this less painful.  Have a look at the 1.11.0-pre3 prerelease I
> just sent you and Keiran.  The config variable templating and the new
> optional GBrowse-like config syntax should make it easier to maintain
> large numbers of JS callbacks.
>
> Rob



--
 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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Re: organizing a project in JBrowse

Robert Buels-2
Weird.  I guess I didn't actually send it.  Sent again.

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

On 12/13/2013 11:16 AM, Keiran Raine wrote:

> Hi Robert,
>
> Am I missing an email or link?  I don't seem to have anything as indicated here.
>
> Keiran
>
>> I did some work on a new configuration system for 1.11.0 that should
>> make this less painful.  Have a look at the 1.11.0-pre3 prerelease I
>> just sent you and Keiran.  The config variable templating and the new
>> optional GBrowse-like config syntax should make it easier to maintain
>> large numbers of JS callbacks.
>>
>> Rob
>
>
>

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