Private builds: run the app on your own computer

You need

• A Mac, or Windows with WSL (Windows Subsystem for Linux).
• Conda (Miniconda is fine).
• A nextstrain.org account that is a member of the lab's private Nextstrain group. Ask the lab's Nextstrain group owner to add you. Without it you can still run the app with the public builds.

Set up once

1. Get the app

   Open a terminal and download the app folder:

   git clone https://github.com/<owner>/flu-freq-compare.git
   cd flu-freq-compare

   The app's code is at this website's GitHub repository.

2. Install it

   This creates a separate environment with everything the app needs, including the Nextstrain command-line tool:

   conda env create -f environment.yml
   conda activate flu-freq-compare

Run it

1. Start the guided setup

   conda activate flu-freq-compare
   ffc start

   It asks a few questions. Press Enter to accept a suggested answer.

2. Choose where the JHH builds come from

   Pick 1) Private PekoszLab group. The other choices are the public builds, a copy from the lab's pipeline folder, or builds you downloaded before.

3. Sign in to Nextstrain

   If you are not signed in, the app offers to run nextstrain login. That is Nextstrain's own sign-in: it opens your web browser, and this app never sees your password. The app then checks that your account belongs to the lab's private group.

   No access? The app tells you, and offers to continue with the public builds instead.

4. Pick the builds, then wait

   Choose the subtypes and the global Nextstrain builds (6 months to 12 years), or keep the defaults. The app downloads them, processes them, and opens the dashboard in your browser at http://127.0.0.1:8050.

   Leave the terminal open while you use it. Press Ctrl+C to stop.

What it looks like

$ ffc start
Flu Frequency Compare: guided start

[1/5] Checking your setup
  ✓ Nextstrain CLI found
[2/5] Where should the JHH builds come from?
    1) Private PekoszLab group on nextstrain.org (needs a Nextstrain login with group access) (default)
    2) Public PekoszLab-Public group on nextstrain.org (no login)
  Choose: [1]
[3/5] Nextstrain access
  You are not logged in to nextstrain.org.
  Log in now? (opens Nextstrain's own sign-in; this app never sees your password) [Y/n]
  ✓ Logged in, with access to the PekoszLab group
[4/5] Which builds?
  Subtypes (space-separated): [h1n1pdm h3n2 vic]
  Global Nextstrain builds to compare with: [6m 2y 3y 6y 12y]
[5/5] Download, process and open
  ...
  ✓ Dashboard ready at http://127.0.0.1:8050  (only this computer can open it; Ctrl+C to stop)

Next time

Run ffc start again to get the latest builds, or choose Use the builds already downloaded to open the dashboard without downloading. ffc serve --open opens the dashboard directly.

Keeping the data private

• Downloaded builds and the processed data stay in the app folder (data/ and store/), which git ignores, and a safety check blocks committing them.
• The dashboard only listens on 127.0.0.1: other computers cannot open it.
• Exported figures and tables contain frequencies and counts, never strain names. Treat them like any unpublished lab result.

Troubleshooting

ffc: command not found

Activate the environment first: conda activate flu-freq-compare.

"Your account is not a member of the PekoszLab group"

Ask the lab's Nextstrain group owner to add your nextstrain.org account, then run ffc start again. Until then, continue with the public builds.

Some builds say "could not download … 404"

That build doesn't exist on nextstrain.org (for example a resolution Nextstrain doesn't publish). The others still work.

The page doesn't open

Copy the address printed in the terminal into your browser. If port 8050 is busy, the app picks the next free one and prints it.