Error installing dependencies for WazyAlphaFold2.ipynb

[nkiely]

When I try to run WazyAlphaFold2.ipynb it is giving me a "resolutionimpossible" error during the "Install dependencies" step

Expected Behavior: install dependencies

Current Behavior: "resolutionimpossible" error

Steps to Reproduce (for bugs)

I don't know how to "Factory Reset" in latest Colab version I was running in the high RAM paid account, now I let the subscription stop so I don't know if that's what's causing the error. But before I upgraded to pro it never had this problem Input: VLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILMKMWTFGNFWCEFWTSIDVLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYANETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLQKIDKSEGRFHVQNLSQVEQDGRTGHGLRRSSKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIY Then all defaults

ColabFold Output (for bugs)

https://colab.research.google.com/github/ur-whitelab/wazy/blob/master/colab/WazyAlphaFold2.ipynb#scrollTo=iccGdbe_Pmt9 ERROR: Cannot install ERROR: ResolutionImpossible

Context

Never experiences this error using both free and Colab Pro high RAM environment

Your Environment

Colab free version online Python 3 Google Compute Engine backend (GPU)

[sokrypton]

replace:

if [ ! -f COLABFOLD_READY ]; then
  # install dependencies
  # We have to use "--no-warn-conflicts" because colab already has a lot preinstalled with requirements different to ours
  pip install -q --no-warn-conflicts "colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold"
  # high risk high gain
  pip install -q "jax[cuda11_cudnn805]>=0.3.8,<0.4" wazy MDAnalysis -f https://storage.googleapis.com/jax-releases/jax_releases.html  
  touch COLABFOLD_READY
fi

with

if [ ! -f COLABFOLD_READY ]; then
  echo "installing colabfold..."
  # install dependencies
  # We have to use "--no-warn-conflicts" because colab already has a lot preinstalled with requirements different to ours
  pip install -q --no-warn-conflicts "colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold" "tensorflow-cpu==2.11.0"
  pip uninstall -yq jax jaxlib
  pip install -q "jax[cuda]==0.3.25" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
  pip install -q wazy MDAnalysis
  touch COLABFOLD_READY
fi

[nkiely]

Thank you so much! That worked. It could install the dependencies. But now on the next step (Set-up AlphaFold) I am getting this error:

If you have any idea what could solve this I'm also so grateful, thank you