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Update Conda in Colab and fix dependency issues
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PiperOrigin-RevId: 549256996
Change-Id: I1c5fb68a1abe6016a89740cab1e033876c248c56
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Jane333 authored and copybara-github committed Jul 19, 2023
1 parent 6c4d833 commit 6cb85e9
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Showing 3 changed files with 9 additions and 9 deletions.
4 changes: 2 additions & 2 deletions docker/Dockerfile
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Expand Up @@ -53,13 +53,13 @@ RUN wget -q -P /tmp \

# Install conda packages.
ENV PATH="/opt/conda/bin:$PATH"
RUN conda install -qy conda==4.13.0 \
RUN conda install -qy conda==23.5.2 \
&& conda install -y -c conda-forge \
openmm=7.7.0 \
cudatoolkit==${CUDA_VERSION} \
pdbfixer \
pip \
python=3.8 \
python=3.10 \
&& conda clean --all --force-pkgs-dirs --yes

COPY . /app/alphafold
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2 changes: 1 addition & 1 deletion notebooks/AlphaFold.ipynb
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Expand Up @@ -109,7 +109,7 @@
"\n",
" PATH=%env PATH\n",
" %env PATH=/opt/conda/bin:{PATH}\n",
" %shell conda install -qy conda==4.13.0 \\\n",
" %shell conda install -qy conda==23.5.2 \\\n",
" \u0026\u0026 conda install -qy -c conda-forge \\\n",
" python=3.10 \\\n",
" openmm=7.7.0 \\\n",
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12 changes: 6 additions & 6 deletions requirements.txt
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Expand Up @@ -2,12 +2,12 @@ absl-py==1.0.0
biopython==1.79
chex==0.0.7
dm-haiku==0.0.9
dm-tree==0.1.6
dm-tree==0.1.8
docker==5.0.0
immutabledict==2.0.0
jax==0.3.25
jax==0.4.13
ml-collections==0.1.0
numpy==1.21.6
pandas==1.3.4
scipy==1.7.3
tensorflow-cpu==2.11.0
numpy==1.24.3
pandas==2.0.3
scipy==1.11.1
tensorflow-cpu==2.13.0

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