URL to specific organism and location

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URL to specific organism and location

Robin A. Ohm

Hi Nathan,

 

I would like to provide a URL to our users that leads them to a specific locus in a specific organism in Apollo. I know how to do this for public organisms in JBrowse, but I’m not sure how to translate this to non-public organisms in Apollo. In Apollo the URL in the browser doesn’t seem to change while navigating through a genome.

 

I found this section in the documentation, but it’s a bit too cryptic for me to know what to do:

https://genomearchitect.readthedocs.io/en/latest/Configure.html?highlight=url#url-modifications

 

Maybe I’m overlooking something obvious, but it would be helpful to see an example.

 

Thanks, best regards, Robin

 

Robin A. Ohm, PhD | Assistant Professor | Microbiology

Utrecht University | Kruyt Building | Room O409 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533041 | [hidden email]

 

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Re: URL to specific organism and location

nathandunn

I could probably me this easier, but let me know. 

At any address you can always click on the link icon, click on “Logged in URL” and then right-click the URL.  

I’ll try to change that so its always expanded next week, but for 2.6.0 (and prior) that is how you would do it. 

Nathan



On Jun 28, 2020, at 1:45 AM, Ohm, R.A. (Robin) <[hidden email]> wrote:

Hi Nathan,
 
I would like to provide a URL to our users that leads them to a specific locus in a specific organism in Apollo. I know how to do this for public organisms in JBrowse, but I’m not sure how to translate this to non-public organisms in Apollo. In Apollo the URL in the browser doesn’t seem to change while navigating through a genome.
 
I found this section in the documentation, but it’s a bit too cryptic for me to know what to do:
 
Maybe I’m overlooking something obvious, but it would be helpful to see an example.
 
Thanks, best regards, Robin
 
Robin A. Ohm, PhD | Assistant Professor | Microbiology
Utrecht University | Kruyt Building | Room O409 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533041 | [hidden email]

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RE: URL to specific organism and location

Robin A. Ohm

Hi Nathan,

 

Thanks, that’s exact what I needed! Looking at the URL, I now also understand what the docs said about loadLink. (Maybe an example can be added to that part of the documentation, to explain a bit more how to craft a URL in Apollo in the same style as JBrowse?)

 

Thanks again, best regards, Robin

 

Robin A. Ohm, PhD | Assistant Professor | Microbiology

Utrecht University | Kruyt Building | Room O409 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533041 | [hidden email]

 

From: Nathan Dunn <[hidden email]>
Sent: Sunday, June 28, 2020 19:13
To: Ohm, R.A. (Robin) <[hidden email]>
Cc: [hidden email]
Subject: Re: [apollo] URL to specific organism and location

 

 

I could probably me this easier, but let me know. 

 

At any address you can always click on the link icon, click on “Logged in URL” and then right-click the URL.  

 

I’ll try to change that so its always expanded next week, but for 2.6.0 (and prior) that is how you would do it. 

 

Nathan

 

 



On Jun 28, 2020, at 1:45 AM, Ohm, R.A. (Robin) <[hidden email]> wrote:

 

Hi Nathan,

 

I would like to provide a URL to our users that leads them to a specific locus in a specific organism in Apollo. I know how to do this for public organisms in JBrowse, but I’m not sure how to translate this to non-public organisms in Apollo. In Apollo the URL in the browser doesn’t seem to change while navigating through a genome.

 

I found this section in the documentation, but it’s a bit too cryptic for me to know what to do:

 

Maybe I’m overlooking something obvious, but it would be helpful to see an example.

 

Thanks, best regards, Robin

 

Robin A. Ohm, PhD | Assistant Professor | Microbiology

Utrecht University | Kruyt Building | Room O409 | Padualaan 8 | 3584 CH | Utrecht | The Netherlands | +31 30 2533041 | [hidden email]

 

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