Update tutorials to use `nextstrain run`

[joverlee521]

Existing tutorials to include steps for downloading the zika-tutorial or zika repositories using git. The big win for nextstrain run is removing the need for git, so let's use it in our intro tutorials!

We can already update the "Running an ingest workflow" tutorial which uses the zika repo that already supports nextstrain run.
The "Running a phylogenetic workflow" tutorial is blocked on nextstrain/zika-tutorial#18.

[tsibley]

For "Running a phylo workflow", it seems it'd make sense to switch to nextstrain setup and nextstrain run instead of git clone and nextstrain build.

For "Creating a phylo workflow", we probably (?) want to 1) stick with git clone (instead of nextstrain setup) and add explanation about how/why version control is used and 2) switch to nextstrain run and/or discuss (briefly!) nextstrain build vs. nextstrain run (or link out to such an explanation).