FW: [Gmod-gbrowse] GViewer questions..

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FW: [Gmod-gbrowse] GViewer questions..

Jayaraman, Pushkala

To clarify what ive written, I have a bunch of features that I would like to export to our Gbrowse as a track that is rendered on the fly.. so it will be different for each user.. but I do not want to make it into a file.. how do I do that?

Both Gbrowse and the other tool (read GViewer) are on the same server

I do not have DAS configured..

L

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala [mailto:[hidden email]]
Sent: Wednesday, January 19, 2011 10:14 AM
To: gmod-gbrowse
Subject: [Gmod-gbrowse] GViewer questions..

 

Hello, here is a few excerpts from my first email with responses form you guys:

 

 

3.       Is there any way in which Gviewer can be made compatible with the
>> Gbrowse? There were issues with compatibility with the older versions of
>> Gviewer and Gbrowse 1.68.
>>
>> 4.       We will soon be having SNPs and other sequence analysis data.
>> Would there be more sequence comparison tools integrated to Gbrowse?
>
> Can you give an example of some tools you would like to see integrated?

Right--I'm not sure what you mean by "integration with Gviewer;" I
could see Gviewer as an entryway for GBrowse.  In that case, Gviewer
would have to be configurable to have hyperlinks into GBrowse, but
that doesn't require GBrowse to do anything.  Are you envisioning
something more?

And for sequence comparison tools: what sorts of things are you
thinking about?  GBrowse does not do (much) analysis; it is a
visualization tool mostly.

 

 

 

I would like to know if there is a way in which we can send data from GViewer into Gbrowse?  The earlier Gbrowse 1.X could do that by sending in individual features from GViewer into Gbrowse.. can we do that with the new Gbrowse as well??  From a post on the gmod forum I found this from Lincoln:

 

 

In version 2.0 it is relatively easy. POST to the GBrowse URL (including the

datasource part of the URL) with the following parameters:

 

  - action="upload_file"

  - file=<a multipart/form-encoded file upload>

  - upload_id=<any numeric id of your choosing>

  - id=<the id of the user that you are uploading to>

 

Alternatively to providing the "file" argument you can provide a "data"

argument with the uploaded data provided directly.

 

The "id" argument indicates the id of the user that you are uploading for.

You can get this ID by bookmarking a page -- the "id" parameter records the

info. Alternatively, if you don't provide an ID, GBrowse will generate it

for you and return the ID in the response cookie, in an argument called

"gbrowse_sess".

 

If you have administrator's mode enabled, then you can provide the ID of the

administrator and the uploaded file will become part of the public set of

tracks.

 

Lincoln

 

 

 

Has someone gotten this to work.. could I get an example URL?

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 


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