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Once we upgrade the site from galaxy version 18.09 to version 19.01 we can add in the branch selection viz (This commit removed it: 8d604fb). We can't add it in now because we need Sam's code for saving the annotated tree as a history dataset which is in 19.01 but not 18.09.

Relates to veg/tools-iuc#45.

Current status:

• The code that is currently live on galaxy.hyphy.org is the dynamics-patch_live branch which is three commits ahead and ~5,000 commits behind galaxyproject/galaxy/dev
• veg/galaxy/dev is ~3,000 commits behind galaxyproject/galaxy/dev
• veg/galaxy/master is ~4,000 commits behind galaxyproject/galaxy/master

Things to keep in mind:

• We may eventually want to have some of our changes merged into the main galaxyproject repo so that our tools (thinking especially of our visualizations) can be used on other galaxy instances
• I think any changes we make that will be specific to our instance would be made in config files that wouldn't be tracked by revision control but I'm not certain that this is the case

I opened example PRs ( rdvelazquez#1 and rdvelazquez#2) in my fork to see what conflicts could exist if we were to open a PR from veg/galaxy/dynamics-patch or veg/galaxy/dynamics-pathc_live into galaxyproject/galaxy/dev or maser. There are quite a few conflicts.

I believe we have had each of these vizs working at one point in time but the list below is the current state on galaxy.hyphy.org.

• HIV-TRACE-Viz
• Phylotree (See #7)
• HyPhy-Vision
• MMVC (We may eventually want to add this back in but it will likely require re-implementing the tool as alignment.js has changed since the original viz was wrapped)