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Commit 4494af84 authored by Hamish Tomlinson's avatar Hamish Tomlinson
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Bump python in colab to 3.8

parent 8537f51d
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notebooks/AlphaFold.ipynb
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......@@ -106,7 +106,7 @@
" %env PATH=/opt/conda/bin:{PATH}\n",
" %shell conda install -qy conda==4.13.0 \\\n",
" \u0026\u0026 conda install -qy -c conda-forge \\\n",
" python=3.7 \\\n",
" python=3.8 \\\n",
" openmm=7.5.1 \\\n",
" pdbfixer\n",
" pbar.update(80)\n",
......@@ -157,15 +157,15 @@
" pbar.update(10)\n",
"\n",
" # Apply OpenMM patch.\n",
" %shell pushd /opt/conda/lib/python3.7/site-packages/ \u0026\u0026 \\\n",
" %shell pushd /opt/conda/lib/python3.8/site-packages/ \u0026\u0026 \\\n",
" patch -p0 \u003c /content/alphafold/docker/openmm.patch \u0026\u0026 \\\n",
" popd\n",
"\n",
" # Make sure stereo_chemical_props.txt is in all locations where it could be searched for.\n",
" %shell mkdir -p /content/alphafold/alphafold/common\n",
" %shell cp -f /content/stereo_chemical_props.txt /content/alphafold/alphafold/common\n",
" %shell mkdir -p /opt/conda/lib/python3.7/site-packages/alphafold/common/\n",
" %shell cp -f /content/stereo_chemical_props.txt /opt/conda/lib/python3.7/site-packages/alphafold/common/\n",
" %shell mkdir -p /opt/conda/lib/python3.8/site-packages/alphafold/common/\n",
" %shell cp -f /content/stereo_chemical_props.txt /opt/conda/lib/python3.8/site-packages/alphafold/common/\n",
"\n",
" %shell mkdir --parents \"{PARAMS_DIR}\"\n",
" %shell wget -O \"{PARAMS_PATH}\" \"{SOURCE_URL}\"\n",
......@@ -189,7 +189,7 @@
"\n",
"# Make sure everything we need is on the path.\n",
"import sys\n",
"sys.path.append('/opt/conda/lib/python3.7/site-packages')\n",
"sys.path.append('/opt/conda/lib/python3.8/site-packages')\n",
"sys.path.append('/content/alphafold')\n",
"\n",
"# Make sure all necessary environment variables are set.\n",
......
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