cannot find guppy_6 branch

[bjaysheel]

Hi, I am following install guide to install boss-runs and readfish for adaptive sampling, but when trying to install readfish using the command

pip install git+https://github.com/LooseLab/readfish@guppy_6

I get an error

Cloning https://github.com/LooseLab/readfish (to revision guppy_6) to /tmp/pip-req-build-ghi3ob0f
Running command git clone --filter=blob:none --quiet https://github.com/LooseLab/readfish /tmp/pip-req-build-ghi3ob0f
WARNING: Did not find branch or tag 'guppy_6', assuming revision or ref.
Running command git checkout -q guppy_6
error: pathspec 'guppy_6' did not match any file(s) known to git
error: subprocess-exited-with-error

Looks like the branch no long exists, wonder if the is a recent change as I ran the same install process about a month ago and everything seem to have worked at that time.

Thank you

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[Adoni5]

Hi @bjaysheel - we indeed removed that branch, as we have majorly refactored readfish. A BOSS-RUNS plugin is on our roadmap (somewhere).

You should be able to find working code that is compatible with BOSS-RUNS under our releases here.

This is just source code, but you can extract the source code folder, cd into it and run either

pip install -e . to install into the current python environment or equally python setup install should work. All the other requirements (ont-pyguppy-client-lib and read-until) should be installed according to the instructions you were following.

Let me know if this doesn't work
Rory

[bjaysheel]

Hi Rory, thank you for the reply. I was able install readfish based on the link above. Let you know if I run into any other issues with adaptive sampling.

Thank you
Jaysheel