search

LooseLab / readfish

CLI tool for flexible and fast adaptive sampling on ONT sequencers
https://looselab.github.io/readfish/
GNU General Public License v3.0
163 stars 31 forks source link

cannot find guppy_6 branch #318

Closed bjaysheel closed 7 months ago

bjaysheel commented 7 months ago

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

github-actions[bot] commented 7 months ago

Thank you for your issue. Give us a little time to review it.

PS. You might want to check the FAQ if you haven't done so already.

This is an automated reply, generated by FAQtory

Adoni5 commented 7 months ago

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 commented 7 months ago

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