diff --git a/batch/AlphaFold2_batch.ipynb b/batch/AlphaFold2_batch.ipynb index 6dd66cb7..910d3858 100644 --- a/batch/AlphaFold2_batch.ipynb +++ b/batch/AlphaFold2_batch.ipynb @@ -127,9 +127,11 @@ "if [ ! -f COLABFOLD_READY ]; then\n", " # install dependencies\n", " # We have to use \"--no-warn-conflicts\" because colab already has a lot preinstalled with requirements different to ours\n", - " pip install -q --no-warn-conflicts \"colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold\" \"tensorflow-cpu==2.11.0\"\n", - " pip uninstall -yq jax jaxlib\n", - " pip install -q \"jax[cuda]==0.3.25\" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html\n", + " pip install -q --no-warn-conflicts \"colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold\"\n", + " pip install --upgrade dm-haiku\n", + " ln -s /usr/local/lib/python3.*/dist-packages/colabfold colabfold\n", + " ln -s /usr/local/lib/python3.*/dist-packages/alphafold alphafold\n", + " sed -i 's/weights = jax.nn.softmax(logits)/logits=jnp.clip(logits,-1e8,1e8);weights=jax.nn.softmax(logits)/g' alphafold/model/modules.py\n", " touch COLABFOLD_READY\n", "fi\n", "\n",