Automated Screenshots

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Automated Screenshots

abhijit.synl@gmail.com
Hello,

I was wondering whether there was some script/module that one could run, on the command line, to capture screenshots in an automated fashion from Apollo. Using screen capture is too cumbersome since I have a lot of image captures to do.

Thanks
Abhijit




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Re: Automated Screenshots

nathandunn
Abhijit,

There are quite a few options.  

What is the purpose of the screen shots?  

Nathan

> On May 9, 2018, at 9:50 AM, Abhijit Sanyal <[hidden email]> wrote:
>
> Hello,
>
> I was wondering whether there was some script/module that one could run, on the command line, to capture screenshots in an automated fashion from Apollo. Using screen capture is too cumbersome since I have a lot of image captures to do.
>
> Thanks
> Abhijit
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>




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Re: Automated Screenshots

abhijit.synl@gmail.com
Hi Nathan,

I want to capture screenshots around particular reference genes (gene and flanking 5 kb) in a way that I can see all the tracks with evidences for that gene in one screenshot. Purpose is to do some image analytics

-Abhijit

On Wed, May 9, 2018 at 10:22 PM, Nathan Dunn <[hidden email]> wrote:
Abhijit,

There are quite a few options. 

What is the purpose of the screen shots? 

Nathan

> On May 9, 2018, at 9:50 AM, Abhijit Sanyal <[hidden email]> wrote:
>
> Hello,
>
> I was wondering whether there was some script/module that one could run, on the command line, to capture screenshots in an automated fashion from Apollo. Using screen capture is too cumbersome since I have a lot of image captures to do.
>
> Thanks
> Abhijit
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Automated Screenshots

nathandunn

That sounds fascinating! 

I’m cross-posting to the gmod-ajax list.  I think the easiest solution might be to integrate a JBrowse plugin that does this out of the box such as this one:



I’ve also run the Manet npm server: https://www.npmjs.com/package/manet against JBrowse / Apollo URLs to create screenshots.  

Nathan


On May 9, 2018, at 10:30 AM, Abhijit Sanyal <[hidden email]> wrote:

Hi Nathan,

I want to capture screenshots around particular reference genes (gene and flanking 5 kb) in a way that I can see all the tracks with evidences for that gene in one screenshot. Purpose is to do some image analytics

-Abhijit

On Wed, May 9, 2018 at 10:22 PM, Nathan Dunn <[hidden email]> wrote:
Abhijit,

There are quite a few options. 

What is the purpose of the screen shots? 

Nathan

> On May 9, 2018, at 9:50 AM, Abhijit Sanyal <[hidden email]> wrote:
>
> Hello,
>
> I was wondering whether there was some script/module that one could run, on the command line, to capture screenshots in an automated fashion from Apollo. Using screen capture is too cumbersome since I have a lot of image captures to do.
>
> Thanks
> Abhijit
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Automated Screenshots

jim.hu.biobio
In reply to this post by abhijit.synl@gmail.com
I would add that having something like this would be important for mods that want to have small genomic context views on gene pages. Gbrowse had this capability. I haven’t kept up on how to do it with jbrowse.

I know apollo != jbrowse, but it would be useful for both. 

Jim

On May 9, 2018, at 12:30 PM, Abhijit Sanyal <[hidden email]> wrote:

Hi Nathan,

I want to capture screenshots around particular reference genes (gene and flanking 5 kb) in a way that I can see all the tracks with evidences for that gene in one screenshot. Purpose is to do some image analytics

-Abhijit

On Wed, May 9, 2018 at 10:22 PM, Nathan Dunn <[hidden email]> wrote:
Abhijit,

There are quite a few options. 

What is the purpose of the screen shots? 

Nathan

> On May 9, 2018, at 9:50 AM, Abhijit Sanyal <[hidden email]> wrote:
>
> Hello,
>
> I was wondering whether there was some script/module that one could run, on the command line, to capture screenshots in an automated fashion from Apollo. Using screen capture is too cumbersome since I have a lot of image captures to do.
>
> Thanks
> Abhijit
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Automated Screenshots

nathandunn

If you are already using Apollo (in master), you can use the track services web services to represent JSON for the tracks you are interested in:



And sort of hacked in here: 


In theory we have a componetized version (vanilla js + d3) of the source here, but I have not tested the integration yet.  I would start here if possible and fork it to how you want it:


All of the data is coming through the original JBrowse / Apollo (and cached).   I think in master, there is a way to load variant data as well, which we plan to pull into the next version of some of these.


Also, Scott as a way to do this with straight JBrowse via some sort of JavaScript voodoo.


Nathan

(Track services web service)



On May 9, 2018, at 11:10 AM, Jim Hu <[hidden email]> wrote:

I would add that having something like this would be important for mods that want to have small genomic context views on gene pages. Gbrowse had this capability. I haven’t kept up on how to do it with jbrowse.

I know apollo != jbrowse, but it would be useful for both. 

Jim

On May 9, 2018, at 12:30 PM, Abhijit Sanyal <[hidden email]> wrote:

Hi Nathan,

I want to capture screenshots around particular reference genes (gene and flanking 5 kb) in a way that I can see all the tracks with evidences for that gene in one screenshot. Purpose is to do some image analytics

-Abhijit

On Wed, May 9, 2018 at 10:22 PM, Nathan Dunn <[hidden email]> wrote:
Abhijit,

There are quite a few options. 

What is the purpose of the screen shots? 

Nathan

> On May 9, 2018, at 9:50 AM, Abhijit Sanyal <[hidden email]> wrote:
>
> Hello,
>
> I was wondering whether there was some script/module that one could run, on the command line, to capture screenshots in an automated fashion from Apollo. Using screen capture is too cumbersome since I have a lot of image captures to do.
>
> Thanks
> Abhijit
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.