The workflow implemented in the Galaxy Bridge page - with URL https://bioviz.org/galaxy.html - is not working as expected. A re-design of the code may be needed!

Here is what should happen:

If a user clicks a "display in IGB ( View )" link for a Galaxy dataset and IGB is not yet running, a message is supposed to appear letting the user know that they need to start IGB to see the data. This works fine if a dataset dbkey is set.

However, if a dataset is lacking a dbkey and IGB is not running, then another message appears that does not make a lot of sense if IGB is not running. That message says:

The file you are trying to view does not have a genome version associated with it. Please return to Galaxy and associate a genome version with the file and try again.

Thus, the business logic of the page appears to be messed up. Here is what ideally should happen whenever a user clicks the "view in IGB" link for a Galaxy History dataset:

First, the page code should check: Is IGB running?

• Yes -> go to A
• No -> go to B

A: Check: is there a "dbkey" for the dataset?

• Yes -> go to C
• No -> go to D

B: Display a message that tells the user to start IGB and then refresh the page. Upon refresh, do A.

C: At this point, we know that Galaxy History dataset dbkey value is set and also that IGB is running. Now tell the user to check IGB. IGB should have opened a new empty track for the dataset. They should zoom in on a gene or a group of genes, and click Load Data button to load the Galaxy History dataset's data into the new track.

D. At this point, we know that Galaxy History dataset dbkey value is NOT set and also that IGB is running. This means that IGB may or may not be showing a genome version appropriate for the dataset to be shown on top of. Tell the user that if they have not already done so, go to IGB and open the genome of corresponding to the Galaxy History dataset they are trying to view. Let them know that once they do that, they can refresh the page to send the data to a new track in IGB.

Note that we have set up Google Analytics for this page. We are tracking a number of the steps in the workflow, and we need to take this into account when making any changes. Ideally, we would not lose our ability to track any of these key "milestones" when viewing data from Galaxy History data files.

For this task, please:

• Attempt to reproduce the bug, e.g., when IGB is not running and you click a "view in IGB" link from a Galaxy History dataset, you see the message from above:

The file you are trying to view does not have a genome version associated with it. Please return to Galaxy and associate a genome version with the file and try again.

• Propose a new structure for the underlying code that will correctly guide an astute user through the steps they need to perform in order to view the data from a Galaxy History dataset in IGB.