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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| #!/bin/bash | ||
|
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| # check commands | ||
| type wget || { echo "wget command is not installed. Please install it at first using Homebrew." ; exit 1 ; } | ||
| type gsed || { echo "gnu-sed command is not installed. Please install it at first using Homebrew." ; exit 1 ; } | ||
| type hhsearch || { echo "hhsearch command is not installed. Please install it at first using Homebrew." ; exit 1 ; } | ||
| type kalign || { echo "kalign command is not installed. Please install it at first using Homebrew." ; exit 1 ; } | ||
|
|
||
| # check whether Apple Silicon (M1 mac) or Intel Mac | ||
| arch_name="$(uname -m)" | ||
|
|
||
| if [ "${arch_name}" = "x86_64" ]; then | ||
| if [ "$(sysctl -in sysctl.proc_translated)" = "1" ]; then | ||
| echo "Running on Rosetta 2" | ||
| else | ||
| echo "Running on native Intel" | ||
| fi | ||
| elif [ "${arch_name}" = "arm64" ]; then | ||
| echo "Running on Apple Silicon (M1 mac)" | ||
| echo "This installer is only for intel Mac. Use install_colabfold_M1mac.sh to install on this Mac." | ||
| exit 1 | ||
| else | ||
| echo "Unknown architecture: ${arch_name}" | ||
| exit 1 | ||
| fi | ||
|
|
||
| CURRENTPATH=`pwd` | ||
| COLABFOLDDIR="${CURRENTPATH}/colabfold_batch" | ||
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| mkdir -p ${COLABFOLDDIR} | ||
| cd ${COLABFOLDDIR} | ||
| wget https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt --no-check-certificate | ||
| wget -q -P . https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh | ||
| bash ./Miniconda3-latest-MacOSX-x86_64.sh -b -p ${COLABFOLDDIR}/conda | ||
| rm Miniconda3-latest-MacOSX-x86_64.sh | ||
| . "${COLABFOLDDIR}/conda/etc/profile.d/conda.sh" | ||
| export PATH="${COLABFOLDDIR}/conda/condabin:${PATH}" | ||
| conda create -p $COLABFOLDDIR/colabfold-conda python=3.7 -y | ||
| conda activate $COLABFOLDDIR/colabfold-conda | ||
| conda update -n base conda -y | ||
| conda install -c conda-forge python=3.7 openmm==7.5.1 pdbfixer -y | ||
| # patch to openmm | ||
| wget -qnc https://raw.githubusercontent.com/deepmind/alphafold/main/docker/openmm.patch --no-check-certificate | ||
| (cd ${COLABFOLDDIR}/colabfold-conda/lib/python3.7/site-packages; patch -s -p0 < ${COLABFOLDDIR}/openmm.patch) | ||
| rm openmm.patch | ||
| # install ColabFold and Jaxlib | ||
| colabfold-conda/bin/python3.7 -m pip install "colabfold[alphafold] @ git+https://github.com/sokrypton/ColabFold" | ||
| colabfold-conda/bin/python3.7 -m pip install https://storage.googleapis.com/jax-releases/mac/jaxlib-0.1.74-cp37-none-macosx_10_9_x86_64.whl | ||
|
|
||
| # bin directory to run | ||
| mkdir -p $COLABFOLDDIR/bin | ||
| cd $COLABFOLDDIR/bin | ||
| cat << EOF > colabfold_batch | ||
| #!/bin/sh | ||
| $COLABFOLDDIR/colabfold-conda/bin/colabfold_batch --cpu \$@ | ||
| EOF | ||
| chmod +x colabfold_batch | ||
|
|
||
| # hack to share the parameter files in a workstation. | ||
| gsed -i -e "s#props_path = \"stereo_chemical_props.txt\"#props_path = \"${COLABFOLDDIR}/stereo_chemical_props.txt\"#" ${COLABFOLDDIR}/colabfold-conda/lib/python3.7/site-packages/colabfold/batch.py | ||
| gsed -i -e "s#kalign_binary_path=\"kalign\"#kalign_binary_path=\"/usr/local/bin/kalign\"#g" ${COLABFOLDDIR}/colabfold-conda/lib/python3.7/site-packages/colabfold/batch.py | ||
| gsed -i -e "s#binary_path=\"hhsearch\"#binary_path=\"/usr/local/bin/hhsearch\"#g" ${COLABFOLDDIR}/colabfold-conda/lib/python3.7/site-packages/colabfold/batch.py | ||
| gsed -i -e "s#Path(appdirs.user_cache_dir(__package__ or \"colabfold\"))#${COLABFOLDDIR}#g" ${COLABFOLDDIR}/colabfold-conda/lib/python3.7/site-packages/colabfold/download.py | ||
|
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| echo "Installation of colabFold_batch finished." | ||
| echo "Note: AlphaFold2 weight parameters will be donwloaded at ${COLABFOLDDIR}/params directory in the first run." | ||
| echo "Please set your PATH to ${COLABFOLDDIR}/bin to run 'colabfold_batch'." | ||
| echo "i.e. For Bash, export PATH=\"${COLABFOLDDIR}/bin:\$PATH\"" | ||
| echo "For more details, please type 'colabfold_batch --help'." |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| #!/bin/bash | ||
|
|
||
| type wget || { echo "wget command is not installed. Please install it at first using apt or yum." ; exit 1 ; } | ||
| type curl || { echo "curl command is not installed. Please install it at first using apt or yum. " ; exit 1 ; } | ||
|
|
||
| CURRENTPATH=`pwd` | ||
| COLABFOLDDIR="${CURRENTPATH}/colabfold_batch" | ||
|
|
||
| mkdir -p ${COLABFOLDDIR} | ||
| cd ${COLABFOLDDIR} | ||
| wget https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt --no-check-certificate | ||
| wget -q -P . https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh | ||
| bash ./Miniconda3-latest-Linux-x86_64.sh -b -p ${COLABFOLDDIR}/conda | ||
| rm Miniconda3-latest-Linux-x86_64.sh | ||
| . "${COLABFOLDDIR}/conda/etc/profile.d/conda.sh" | ||
| export PATH="${COLABFOLDDIR}/conda/condabin:${PATH}" | ||
| conda create -p $COLABFOLDDIR/colabfold-conda python=3.7 -y | ||
| conda activate $COLABFOLDDIR/colabfold-conda | ||
| conda update -n base conda -y | ||
| conda install -c conda-forge python=3.7 cudnn==8.2.1.32 cudatoolkit==11.1.1 openmm==7.5.1 pdbfixer -y | ||
| # patch to openmm | ||
| wget -qnc https://raw.githubusercontent.com/deepmind/alphafold/main/docker/openmm.patch --no-check-certificate | ||
| (cd ${COLABFOLDDIR}/colabfold-conda/lib/python3.7/site-packages; patch -s -p0 < ${COLABFOLDDIR}/openmm.patch) | ||
| rm openmm.patch | ||
| # install alignment tools | ||
| conda install -c conda-forge -c bioconda kalign3=3.2.2 hhsuite=3.3.0 -y | ||
| # install ColabFold and Jaxlib | ||
| colabfold-conda/bin/python3.7 -m pip install "colabfold[alphafold] @ git+https://github.com/sokrypton/ColabFold" | ||
| colabfold-conda/bin/python3.7 -m pip install https://storage.googleapis.com/jax-releases/cuda111/jaxlib-0.1.72+cuda111-cp37-none-manylinux2010_x86_64.whl | ||
|
|
||
| # bin directory to run | ||
| mkdir -p $COLABFOLDDIR/bin | ||
| cd $COLABFOLDDIR/bin | ||
| cat << EOF > colabfold_batch | ||
| #!/bin/sh | ||
| export TF_FORCE_UNIFIED_MEMORY="1" | ||
| export XLA_PYTHON_CLIENT_MEM_FRACTION="4.0" | ||
| $COLABFOLDDIR/colabfold-conda/bin/colabfold_batch \$@ | ||
| EOF | ||
| chmod +x colabfold_batch | ||
|
|
||
| # hack to share the parameter files in a workstation. | ||
| cd ${COLABFOLDDIR}/colabfold-conda/lib/python3.7/site-packages/colabfold | ||
| sed -i -e "s#props_path = \"stereo_chemical_props.txt\"#props_path = \"${COLABFOLDDIR}/stereo_chemical_props.txt\"#" batch.py | ||
| sed -i -e "s#kalign_binary_path=\"kalign\"#kalign_binary_path=\"${COLABFOLDDIR}/colabfold-conda/bin/kalign\"#g" ${COLABFOLDDIR}/colabfold-conda/lib/python3.7/site-packages/colabfold/batch.py | ||
| sed -i -e "s#binary_path=\"hhsearch\"#binary_path=\"${COLABFOLDDIR}/colabfold-conda/bin/hhsearch\"#g" ${COLABFOLDDIR}/colabfold-conda/lib/python3.7/site-packages/colabfold/batch.py | ||
| sed -i -e "s#Path(appdirs.user_cache_dir(__package__ or \"colabfold\"))#\"${COLABFOLDDIR}\"#g" download.py | ||
| cd ${COLABFOLDDIR}/colabfold-conda/lib/python3.7/site-packages/alphafold/relax | ||
| sed -i -e 's/CPU/CUDA/g' amber_minimize.py | ||
|
|
||
| echo "Installation of colabFold_batch finished." | ||
| echo "Note: AlphaFold2 weight parameters will be donwloaded at ${COLABFOLDDIR}/params directory in the first run." | ||
| echo "Please set your PATH to ${COLABFOLDDIR}/bin to run 'colabfold_batch'." | ||
| echo "i.e. For Bash, export PATH=\"${COLABFOLDDIR}/bin:\$PATH\"" | ||
| echo "For more details, please type 'colabfold_batch --help'." |
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