Suggestion: Let's create a new "Tools" menu item for BioViz where we can put links to tools where users can do stuff!

See IGBF-3188 for potential names for the trackhub page.

Unified trackhub web pages by adding the links to the Bioviz.org menu. Under the new menu dropdown, Data, View UCSC Trackhubs option will redirect user to the public trackhubs page. Under the tools menu dropdown, Tools, Trackhub-Quickload Converter will redirect the user to manual trackhub page. Help and Developers dropdowns are move under the About dropdown. Help is now Get help in the About options.

Trackhub-Quickload Converter redirects the user to translate.bioviz.org. It lacks the menu and social media links which needs to be fixed. See IGBF-3240
See commit: https://bitbucket.org/KarthikRavee91/bioviz/commits/555f2e8d71f83a7bde4d6523714c8f56335ef86c

I really like the new organization, I think it works very well.

Some comments and suggestions:

1. The text size for the About dropdown menu appears smaller than Data and Tools. I would think they should be the same size.
2. Under the About dropdown menu, the links under For Developers should be indented or highlighted in such a way to indicate that they are options specific to For Developers. Right now they are aligned with the links above For Developers, which may be confusing.
3. Under the Data dropdown menu, could we get rid of the word "View" in front of both options? It seems unnecessary.
4. On the trackhub-converter.html a lot of the text seems too large. This may just be my imagination, but it seems out of sync with the other bioviz.org pages.

I'm moving the ticket back to To Do in case Karthik would like to implement any of the above suggestions, but otherwise I think it is ready for pull request.

Changes are implemented. See Commit https://bitbucket.org/KarthikRavee91/bioviz/commits/3242489ba40da2806e354877e40ef6da9f3a3a68

I think the formatting looks much better.

Some final changes regarding links:

• Under Tools > Trackhub-Quickload Converter the link should go to bioviz.org/trackhub-converter.html instead of translate.bioviz.org.
• You can also provide just the html location for the public trackhubs (public-trackhubs.html) instead of the full URL in menu.html (and any other links that are served by bioviz.org, such as trackhub-conveter.html).

Changes are implemented. See Commit https://bitbucket.org/KarthikRavee91/bioviz/commits/712d39756914eff129901cf69cc327d6b1391698

Changes look good, recommend pull request.

Pull Request Submitted: https://bitbucket.org/KarthikRavee91/bioviz/pull-requests/2

Change requests for UI visible when users visit https://translate.bioviz.org :

• Change "Manual Track Hub Converter" to "Convert Track Hub URL to IGB Quickload URL"
• Remove text "This is a tool...Integrated Genome Browser"
• Change "Convert track hub to Quickload" to "Enter hub.txt URL for a Track Hub"
• Change "Convert" to "Do it"

I also have some concerns that changes to the production site https://bioviz.org might cause an unforeseen problem, so I would like for the new changes to be tested on a development/testing site.

Prior to merging, we need to deploy this on a testing site, using ansible playbooks.

Once that is done, need to test :

• genome dashboard (igb genomes link)
• apps.bioviz.org

Instructions on how to do this are available in the playbooks repository: https://bitbucket.org/lorainelab/bioviz-playbooks/src/master/

Server available for testing: https://bioviztest3.bioviz.org

Notes:

• It is configured with public keys for Karthik Raveendran and Nowlan Freese allowing you to run the playbooks and update the site.
• The site has the required authorization files to support https. You probably do not need these deployed on your local to run the playbooks. If the playbooks fail because you lack the required authorization files, let me know.

Changes are made. See Commit

Changes look good.

Karthik Raveendran - Ready for pull request.

PR Submitted https://bitbucket.org/lorainelab/bioviz/pull-requests/110

It doesn't look like the testing site has the new code deployed on it.

Note that I am mainly concerned about the changes to the menu.

My suggestion for how to proceed:

• Make a new branch specifically for the menu / banner change and cherrypick the commit onto the new branch
• Revert the cherry-picked change on this branch you're seeking to merge (PR will of course change since it points to the exact same branch)

I can then review the PR minus the menu change and probably merge it right away, since the the track-hub related code is still in beta.

Changes to trackhub-converter.html have been reverted and IGBF-3187 only has menu.html changes
PR Submitted. https://bitbucket.org/lorainelab/bioviz/pull-requests/111

I was able to test the bioviz playbooks on bioviztest3.bioviz.org. See additional comment in this ticket for notes on getting the playbook to work.
The menu changes were visible on the main site as well as the genome dashboard.

After discussion with Dr. Loraine we have a few last changes to the appearance of the menu.

• Move the For Developers links to a Developers dropdown.
• Move the Help link back to the menu bar.
• Put the links for View IGB Genomes and View UCSC Trackhubs under the Tools dropdown, then remove the Data dropdown.

Instructions for running the bioviz-playbooks for Loraine Lab members:
Make sure you have ansible running on your machine by running the following in your terminal:

ansible --version

Clone the bioviz-playbooks bitbucket repo:

git clone https://bitbucket.org/lorainelab/bioviz-playbooks.git

Navigate to the cloned repository directory on your machine.
Copy example_inventory.ini in the repository and rename the copy inventory.ini
Copy example_setup_vars.yml in the repository and rename the copy setup_vars.yml

In example_inventory.ini modify the following variables:
Change the example1 name to any name that makes sense to you (bioviztest3)
Set ansible_host to the public ip address of the EC2 host.
Set domain to the domain name (bioviztest3.bioviz.org)
Set stack to Develop if developing/testing.
Set bioviz_version to the bioviz branch (master or a specific branch, such as IGBF-3187)
Set bioviz_repo to the URL for the bioviz bitbucket repo (https://bitbucket.org/KarthikRavee91/bioviz.git)
Set igb_branch to the branch for IGB (release-9.1.10 though it is unclear if this is required)
Set igb_repository to the URL for the IGB bitbucket repo (https://bitbucket.org/lorainelab/integrated-genome-browser)

In setup_vars.yml:
Note: Need to get the ssl_chain_file, ssl_cert_key_file, and ssl_cert_file from Dr. Loraine. Then put them in the files directory of the bioviz_playbooks repo on your local machine.
Set ssl_chain_file to the name of the DigiCert certificate file.
Set ssl_cert_key_file to the name of the bioviz key file.
Set ssl_cert_file to the name of the bioviz certificate file.
Set igb_version to whatever version of IGB you are specifying (9.1.10)
Set genoviz_version to 1.1.9
Set igb_branch to the branch for IGB (release-9.1.10 though it is unclear if this is required)
Set igb_repository to the URL for the IGB bitbucket repo (https://bitbucket.org/lorainelab/integrated-genome-browser)
Set hub_facade_domain to translate.bioviz.org

In your terminal run

ansible-playbook -i inventory.ini setup.yml

Note:All of this assumes you have access to the EC2 host. If you do not, contact Dr. Loraine.

New changes are implemented. See commit

Tested most recent changes on bioviztest3.bioviz.org using the bioviz-playbooks. The menu looks good (see attached screenshot menu.png) and links work correctly. Genome Dashboard menu has the correct changes.

Ready for pull request.

PR Submitted. https://bitbucket.org/lorainelab/bioviz/pull-requests/113

PR merged. New code is deployed to https://bioiviz.org. Ready for testing.

Testing changes on Firefox and Safari.

• Menu appears correctly on bioviz.org and the genome dashboard.
• The new menu changes are not present on the App store, do we need to run the app store playbooks?
• Noticed something I had missed in earlier testing, the Get Help button is still present in the About dropdown. This leads to the same help page as the menu bar Help button. We could get rid of the Get Help button in the About dropdown, or leave it (extra chance for someone to find the help page?)

PR Submitted: https://bitbucket.org/lorainelab/bioviz/pull-requests/114

Testing completed, closing ticket.