This tutorial will walk you through how to embed an example JBrowse instance using this module. All steps shown here take place on the Tripal 4 site directly. As new functionality is added to the module, this tutorial should also be updated. If you need clarification of any steps or have any suggestions to improve this tutorial, please reach out to us through the Issues tab and create an issue!
Please follow the instructions from the README on how to either:
- Setup a Docker environment with Tripal 4 + Tripal JBrowse
- How to install Tripal JBrowse on a pre-existing Tripal 4 site
Make sure you are logged in as an administrator. If you are using the tripaldocker environment, log in as an administrator using the credentials found here
We've sourced an example JBrowse configuration file from the repository for JBrowse2 here and included it in this repository for convenience as example_config.json.
Your first task is to make sure you have an organism page for the organism of your JBrowse instance. From the Administration toolbar at the top of the page, click on Tripal, then Content in the toolbar that drops down. Then click on the button +Add Tripal Content and select Organism under General.
Our example JBrowse is of a human genome assembly, so in Genus put "Homo" and in Species put "sapiens". You can fill out the other fields if you'd like but they aren't required, then hit Save at the bottom.
You will be directed to an organism page for Homo sapiens - yay!
Just as with creating an organism, navigate to the Add Tripal Content page. Under the Genomic heading, click on Genome Assembly. Though not required, I recommend giving a name to your genome assembly to make it easy to recognize. In this case: hg19. Then fill out the required fields with the following (or really, whatever you'd like!):
- Program, Pipeline, Workflow or Method Name:
My pipeline - Program Version:
1.0
And hit Save. You are now at your newly created Genome Assembly page for the hg19 assembly!
Now return to Tripal then Content. Above the blue buttons, you'll see multiple tabs and you should currently be on the Tripal Content tab. Click on the JBrowse Instances tab and then on the blue button +Add jbrowse instance.
Give your JBrowse instance a title and optional description.
-
JBrowse2 Configuration URL: http://localhost/modules/contrib/tripal_jbrowse/Tutorial/example_config.json NOTE: If you set up your docker container on a different port than 80, then your URL will include that port number after
localhost:. For example, for port 9000, it will be: http://localhost:9000/modules/contrib/tripal_jbrowse/Tutorial/example_config.json Here, you are essentially hosting the example config file on your docker directly through localhost! If you wanted to try this with a valid configuration file hosted elsewhere, you can add that URL instead. You will want to ensure the host server has cross origin resource sharing (CORS) enabled in order for this to work. Refer to the JBrowse documentation here for more information -
Default Start Location: This can be left empty, or you can set it using this format:
<chr>:<start pos>..<end pos>For example,1:1..100,000,000will start the JBrowse session at chromosome 1 between the 1st and 100,000,000 nucelotide. -
Organism: Begin typing "Homo sapiens" and choose it from the dropdown (it may take a second or more to appear). It's important to select it rather than just typing it out, otherwise you'll encounter an error when submitting the form.
-
Genome Assembly: Begin typing "hg19" and select it from the dropdown.
Here is an example of the form filled out:
Now click Save.
Hopefully, you will be rewarded with a JBrowse2 instance like the one below:
