Tripal JBrowse API

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Tripal JBrowse API

Nick Booher
Hello,

I wanted to let everyone know about a new module I just released: Tripal JBrowse API. This module automatically turns your Chado features table into a JBrowse compatible REST API!

The module is available here on GitHub and setup is just three easy steps:
  1. Download and install the module on your Tripal site
  2. Visit admin/people/permissions on your site and give the Use JBrowse API permission to all roles.
  3. Go to http://jbrowse.org/code/JBrowse-1.12.1/?data=http://yourtripalsite.com/api/jbrowse/YourOrganismsCommonName to see all the tracks that were automatically created from your Chado features table!
This module is based on the work of the Chado-JBrowse Connector project and would not have been possible without their help. In addition to writing the SQL queries that make everything work, they also agreed to provide the queries under a GPLv3 license so this module could keep the standard GPL license of most Drupal modules.. Thanks guys!

-Nick

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Re: Tripal JBrowse API

Kucheran, Lacey Sanderson
This looks Awesome Nick! Thanks for the contribution -I can’t wait to give it a try :-)

~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On Aug 24, 2016, at 1:49 PM, Nick Booher <[hidden email]> wrote:

Hello,

I wanted to let everyone know about a new module I just released: Tripal JBrowse API. This module automatically turns your Chado features table into a JBrowse compatible REST API!

The module is available here on GitHub and setup is just three easy steps:
  1. Download and install the module on your Tripal site
  2. Visit admin/people/permissions on your site and give the Use JBrowse API permission to all roles.
  3. Go to http://jbrowse.org/code/JBrowse-1.12.1/?data=http://yourtripalsite.com/api/jbrowse/YourOrganismsCommonName to see all the tracks that were automatically created from your Chado features table!
This module is based on the work of the Chado-JBrowse Connector project and would not have been possible without their help. In addition to writing the SQL queries that make everything work, they also agreed to provide the queries under a GPLv3 license so this module could keep the standard GPL license of most Drupal modules.. Thanks guys!

-Nick
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Re: Tripal JBrowse API

Nick Booher
In reply to this post by Nick Booher
Hello,

Just a note that the latest version (7.x-1.3, released today) provides a single URL that will expose all available organisms on the site at a single URL and lets you switch between them in the Genome menu on JBrowse.

E. g.


-Nick

On Wed, Aug 24, 2016 at 2:49 PM, Nick Booher <[hidden email]> wrote:
Hello,

I wanted to let everyone know about a new module I just released: Tripal JBrowse API. This module automatically turns your Chado features table into a JBrowse compatible REST API!

The module is available here on GitHub and setup is just three easy steps:
  1. Download and install the module on your Tripal site
  2. Visit admin/people/permissions on your site and give the Use JBrowse API permission to all roles.
  3. Go to http://jbrowse.org/code/JBrowse-1.12.1/?data=http://yourtripalsite.com/api/jbrowse/YourOrganismsCommonName to see all the tracks that were automatically created from your Chado features table!
This module is based on the work of the Chado-JBrowse Connector project and would not have been possible without their help. In addition to writing the SQL queries that make everything work, they also agreed to provide the queries under a GPLv3 license so this module could keep the standard GPL license of most Drupal modules.. Thanks guys!

-Nick


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Re: Tripal JBrowse API

Nick Booher
As of 7.x-1.5, this module now outputs gene models like a GFF3 track instead of the track per feature type it output before. It also supports searching for features by name.

-Nick

On Tue, Aug 30, 2016 at 3:21 PM, Nick Booher <[hidden email]> wrote:
Hello,

Just a note that the latest version (7.x-1.3, released today) provides a single URL that will expose all available organisms on the site at a single URL and lets you switch between them in the Genome menu on JBrowse.

E. g.


-Nick

On Wed, Aug 24, 2016 at 2:49 PM, Nick Booher <[hidden email]> wrote:
Hello,

I wanted to let everyone know about a new module I just released: Tripal JBrowse API. This module automatically turns your Chado features table into a JBrowse compatible REST API!

The module is available here on GitHub and setup is just three easy steps:
  1. Download and install the module on your Tripal site
  2. Visit admin/people/permissions on your site and give the Use JBrowse API permission to all roles.
  3. Go to http://jbrowse.org/code/JBrowse-1.12.1/?data=http://yourtripalsite.com/api/jbrowse/YourOrganismsCommonName to see all the tracks that were automatically created from your Chado features table!
This module is based on the work of the Chado-JBrowse Connector project and would not have been possible without their help. In addition to writing the SQL queries that make everything work, they also agreed to provide the queries under a GPLv3 license so this module could keep the standard GPL license of most Drupal modules.. Thanks guys!

-Nick



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