Hello! Thanks for creating this tutorial. I’m trying to run through it and have some comments:
When I went to the starting page, I wasn’t sure if I should dive into the complete walkthough at the Preparing your data link or do the Quickstart. It seems like the Prepare your data link assumes you’ve installed auspice/auger since it refers to files in the example “data” directory. The Quickstart assumes you already understand running the analysis. A nice setup would be to have installation instructions, then a simple toy test case to make sure it works, then the rest of the tutorial (rather than Set up an dinstallation as step 2 when the files are needed for step 1). And I did the quick start, and did snakemake on the example directory, but it’s at step 58 of 106 steps and each step has a “Missing output files” error as it scrolls by on the screen…so a toy example would have been nice to check functionality.
Shouldn’t that say “snakemake --profile ./my_profiles/example” instead of my-analyses? Or should I have my-analyses and that’s why I got over 100 error messages?
Just running the example took quite a while (on a server with 32procs and 125GB RAM, maybe mention in the Quick Start the machine requirements). I thought I’d run through the tutorial since it was just an hour investment (Ph.D. in computer science, figured I could knock this right out), but it’s already been >45 minutes installing and waiting for that to run…and I’m not quite sure it installed correctly since I got so many errors.
nextstrain check-setup --set-default on the nextstrain.org installation instructions page, maybe add that to quickstart. Though that command hung for me on “Testing your setup…”.)