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Commit 410e8294 authored by Vaclav Hanzl's avatar Vaclav Hanzl
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Fix Colab: Install all conda packages together 

Later on the conda setup is likely broken by pip.
parent 1f9270cb
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notebooks/OpenFold.ipynb
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...@@ -129,6 +129,8 @@ ...@@ -129,6 +129,8 @@
" kalign2=2.04 \\\n", " kalign2=2.04 \\\n",
" hhsuite=3.3.0 \\\n", " hhsuite=3.3.0 \\\n",
" python={python_version} \\\n", " python={python_version} \\\n",
" openmm=7.7.0 \\\n",
" pdbfixer \\\n",
" 2>&1 1>/dev/null\n", " 2>&1 1>/dev/null\n",
" %shell pip install -q \\\n", " %shell pip install -q \\\n",
" ml-collections==0.1.0 \\\n", " ml-collections==0.1.0 \\\n",
...@@ -185,9 +187,6 @@ ...@@ -185,9 +187,6 @@
" %shell cp -f /content/stereo_chemical_props.txt /content/openfold/openfold/resources\n", " %shell cp -f /content/stereo_chemical_props.txt /content/openfold/openfold/resources\n",
" %shell /usr/bin/python3 -m pip install -q ./openfold\n", " %shell /usr/bin/python3 -m pip install -q ./openfold\n",
"\n", "\n",
" %shell conda install -y -q -c conda-forge openmm=7.7.0\n",
" %shell conda install -y -q -c conda-forge pdbfixer\n",
"\n",
" if(weight_set == 'AlphaFold'):\n", " if(weight_set == 'AlphaFold'):\n",
" %shell mkdir --parents \"{ALPHAFOLD_PARAMS_DIR}\"\n", " %shell mkdir --parents \"{ALPHAFOLD_PARAMS_DIR}\"\n",
" %shell wget -O {ALPHAFOLD_PARAMS_PATH} {ALPHAFOLD_PARAM_SOURCE_URL}\n", " %shell wget -O {ALPHAFOLD_PARAMS_PATH} {ALPHAFOLD_PARAM_SOURCE_URL}\n",
......
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