use python3.9 (Google Colab compatibility)

README.md

@@ -20,6 +20,7 @@ See also Change log: https://github.com/sokrypton/ColabFold/wiki/v1.5.0
 
 ## New Updates
 
+- 09Mar2023, version 1.5.2 released. The base directory has been changed to `localcolabfold` from `colabfold_batch` to distinguish it from the execution command.
 - 05Feb2023, version 1.5.0-pre released.
 - 16Jun2022, version 1.4.0 released. See [Release v1.4.0](https://github.com/YoshitakaMo/localcolabfold/releases/tag/v1.4.0)
 - 07May2022, **Updated `update_linux.sh`.** See also [How to update](#how-to-update). Please use a new option `--use-gpu-relax` if GPU relaxation is required (recommended).

beta_install_colabbatch_linux.sh

@@ -4,7 +4,7 @@ type wget || { echo "wget command is not installed. Please install it at first u
 type curl || { echo "curl command is not installed. Please install it at first using apt or yum. " ; exit 1 ; }
 
 CURRENTPATH=`pwd`
-COLABFOLDDIR="${CURRENTPATH}/colabfold_batch"
+COLABFOLDDIR="${CURRENTPATH}/localcolabfold"
 
 mkdir -p ${COLABFOLDDIR}
 cd ${COLABFOLDDIR}
@@ -13,30 +13,30 @@ 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=3.8 -y
+conda create -p $COLABFOLDDIR/colabfold-conda python=3.9 -y
 conda activate $COLABFOLDDIR/colabfold-conda
 conda update -n base conda -y
-conda install -c conda-forge python=3.8 cudnn==8.2.1.32 cudatoolkit==11.1.1 openmm==7.5.1 pdbfixer -y
+conda install -c conda-forge python=3.9 cudnn==8.2.1.32 cudatoolkit==11.1.1 openmm==7.5.1 pdbfixer -y
 # Download the updater
 wget -qnc https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/main/update_linux.sh --no-check-certificate
 chmod +x update_linux.sh
 # install alignment tools
 conda install -c conda-forge -c bioconda kalign2=2.04 hhsuite=3.3.0 mmseqs2=14.7e284 -y
 # install ColabFold and Jaxlib
-# colabfold-conda/bin/python3.8 -m pip install "colabfold[alphafold] @ git+https://github.com/sokrypton/ColabFold"
-colabfold-conda/bin/python3.8 -m pip install -q --no-warn-conflicts "colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold@beta"
-colabfold-conda/bin/python3.8 -m pip install https://storage.googleapis.com/jax-releases/cuda11/jaxlib-0.3.25+cuda11.cudnn82-cp38-cp38-manylinux2014_x86_64.whl
-colabfold-conda/bin/python3.8 -m pip install jax==0.3.25 biopython==1.79
+# colabfold-conda/bin/python3.9 -m pip install "colabfold[alphafold] @ git+https://github.com/sokrypton/ColabFold"
+colabfold-conda/bin/python3.9 -m pip install -q --no-warn-conflicts "colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold@beta"
+colabfold-conda/bin/python3.9 -m pip install https://storage.googleapis.com/jax-releases/cuda11/jaxlib-0.3.25+cuda11.cudnn82-cp39-cp39-manylinux2014_x86_64.whl
+colabfold-conda/bin/python3.9 -m pip install jax==0.3.25 biopython==1.79
 
 # Use 'Agg' for non-GUI backend
-cd ${COLABFOLDDIR}/colabfold-conda/lib/python3.8/site-packages/colabfold
+cd ${COLABFOLDDIR}/colabfold-conda/lib/python3.9/site-packages/colabfold
 sed -i -e "s#from matplotlib import pyplot as plt#import matplotlib\nmatplotlib.use('Agg')\nimport matplotlib.pyplot as plt#g" plot.py
 # modify the default params directory
 sed -i -e "s#appdirs.user_cache_dir(__package__ or \"colabfold\")#\"${COLABFOLDDIR}/colabfold\"#g" download.py
 
 # start downloading weights
 cd ${COLABFOLDDIR}
-colabfold-conda/bin/python3.8 -m colabfold.download
+colabfold-conda/bin/python3.9 -m colabfold.download
 cd ${CURRENTPATH}
 
 echo "Download of alphafold2 weights finished."

beta_update_linux.sh

@@ -21,7 +21,7 @@ python3.8 -m pip uninstall alphafold-colabfold -y
 python3.8 -m pip install --no-warn-conflicts "colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold@beta"
 
 # use 'agg' for non-GUI backend
-pushd ${COLABFOLDDIR}/colabfold-conda/lib/python3.8/site-packages/colabfold
+pushd ${COLABFOLDDIR}/colabfold-conda/lib/python3.9/site-packages/colabfold
 sed -i -e "s#from matplotlib import pyplot as plt#import matplotlib\nmatplotlib.use('Agg')\nimport matplotlib.pyplot as plt#g" plot.py
 sed -i -e "s#appdirs.user_cache_dir(__package__ or \"colabfold\")#\"${COLABFOLDDIR}/colabfold\"#g" download.py
 popd

install_colabbatch_M1mac.sh

@@ -28,33 +28,33 @@ else
 fi
 
 CURRENTPATH=`pwd`
-COLABFOLDDIR="${CURRENTPATH}/colabfold_batch"
+COLABFOLDDIR="${CURRENTPATH}/localcolabfold"
 
 mkdir -p ${COLABFOLDDIR}
 cd ${COLABFOLDDIR}
 . "/opt/homebrew/Caskroom/miniforge/base/etc/profile.d/conda.sh"
-conda create -p $COLABFOLDDIR/colabfold-conda python=3.8 -y
+conda create -p $COLABFOLDDIR/colabfold-conda python=3.9 -y
 conda activate $COLABFOLDDIR/colabfold-conda
 conda update -n base conda -y
 
-conda install -y -c conda-forge python=3.8 openmm==7.5.1 pdbfixer jupyter matplotlib py3Dmol tqdm biopython==1.79 immutabledict==2.0.0
+conda install -y -c conda-forge python=3.9 openmm==7.5.1 pdbfixer jupyter matplotlib py3Dmol tqdm biopython==1.79 immutabledict==2.0.0
 conda install -y -c apple tensorflow-deps
 # Download the updater
 wget -qnc https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/main/update_M1mac.sh --no-check-certificate
 chmod +x update_M1mac.sh
 # install ColabFold and Jaxlib
-colabfold-conda/bin/python3.8 -m pip install https://files.pythonhosted.org/packages/bd/57/88cea9e14dacaea82ca86fac2bf6ecb8b7fd99622d776e4131786ce5b65e/tensorflow_macos-2.7.0-cp38-cp38-macosx_11_0_arm64.whl
-colabfold-conda/bin/python3.8 -m pip install git+https://github.com/deepmind/tree.git
-colabfold-conda/bin/python3.8 -m pip install git+https://github.com/google/ml_collections.git
-colabfold-conda/bin/python3.8 -m pip install dm-haiku appdirs pandas absl-py docker
-colabfold-conda/bin/python3.8 -m pip install alphafold-colabfold --no-deps --no-color
-colabfold-conda/bin/python3.8 -m pip install "colabfold[alphafold] @ git+https://github.com/sokrypton/ColabFold" --no-deps --no-color
-colabfold-conda/bin/python3.8 -m pip install jaxlib==0.3.25 --no-deps --no-color
-colabfold-conda/bin/python3.8 -m pip install jax==0.3.25 chex scipy toolz --no-deps --no-color
+colabfold-conda/bin/python3.9 -m pip install https://files.pythonhosted.org/packages/bd/57/88cea9e14dacaea82ca86fac2bf6ecb8b7fd99622d776e4131786ce5b65e/tensorflow_macos-2.7.0-cp38-cp38-macosx_11_0_arm64.whl
+colabfold-conda/bin/python3.9 -m pip install git+https://github.com/deepmind/tree.git
+colabfold-conda/bin/python3.9 -m pip install git+https://github.com/google/ml_collections.git
+colabfold-conda/bin/python3.9 -m pip install dm-haiku appdirs pandas absl-py docker
+colabfold-conda/bin/python3.9 -m pip install alphafold-colabfold --no-deps --no-color
+colabfold-conda/bin/python3.9 -m pip install "colabfold[alphafold] @ git+https://github.com/sokrypton/ColabFold" --no-deps --no-color
+colabfold-conda/bin/python3.9 -m pip install jaxlib==0.3.25 --no-deps --no-color
+colabfold-conda/bin/python3.9 -m pip install jax==0.3.25 chex scipy toolz --no-deps --no-color
 
 # start downloading weights
 cd ${COLABFOLDDIR}
-colabfold-conda/bin/python3.8 -m colabfold.download
+colabfold-conda/bin/python3.9 -m colabfold.download
 cd ${CURRENTPATH}
 
 echo "Download of alphafold2 weights finished."

install_colabbatch_intelmac.sh

@@ -25,7 +25,7 @@ else
 fi
 
 CURRENTPATH=`pwd`
-COLABFOLDDIR="${CURRENTPATH}/colabfold_batch"
+COLABFOLDDIR="${CURRENTPATH}/localcolabfold"
 
 mkdir -p ${COLABFOLDDIR}
 cd ${COLABFOLDDIR}
@@ -34,22 +34,22 @@ 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=3.8 -y
+conda create -p $COLABFOLDDIR/colabfold-conda python=3.9 -y
 conda activate $COLABFOLDDIR/colabfold-conda
 conda update -n base conda -y
-conda install -c conda-forge python=3.8 openmm==7.5.1 pdbfixer -y
+conda install -c conda-forge python=3.9 openmm==7.5.1 pdbfixer -y
 # Download the updater
 wget -qnc https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/main/update_intelmac.sh --no-check-certificate
 chmod +x update_intelmac.sh
 # install ColabFold and Jaxlib
-colabfold-conda/bin/python3.8 -m pip install "colabfold[alphafold] @ git+https://github.com/sokrypton/ColabFold"
-colabfold-conda/bin/python3.8 -m pip install jaxlib==0.3.25
-colabfold-conda/bin/python3.8 -m pip install jax==0.3.25
-colabfold-conda/bin/python3.8 -m pip install biopython==1.79
+colabfold-conda/bin/python3.9 -m pip install "colabfold[alphafold] @ git+https://github.com/sokrypton/ColabFold"
+colabfold-conda/bin/python3.9 -m pip install jaxlib==0.3.25
+colabfold-conda/bin/python3.9 -m pip install jax==0.3.25
+colabfold-conda/bin/python3.9 -m pip install biopython==1.79
 
 # start downloading weights
 cd ${COLABFOLDDIR}
-colabfold-conda/bin/python3.8 -m colabfold.download
+colabfold-conda/bin/python3.9 -m colabfold.download
 cd ${CURRENTPATH}
 
 echo "Download of alphafold2 weights finished."

install_colabbatch_linux.sh

@@ -4,7 +4,7 @@ type wget || { echo "wget command is not installed. Please install it at first u
 type curl || { echo "curl command is not installed. Please install it at first using apt or yum. " ; exit 1 ; }
 
 CURRENTPATH=`pwd`
-COLABFOLDDIR="${CURRENTPATH}/colabfold_batch"
+COLABFOLDDIR="${CURRENTPATH}/localcolabfold"
 
 mkdir -p ${COLABFOLDDIR}
 cd ${COLABFOLDDIR}
@@ -13,23 +13,24 @@ 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=3.8 -y
+conda create -p $COLABFOLDDIR/colabfold-conda python=3.9 -y
 conda activate $COLABFOLDDIR/colabfold-conda
 conda update -n base conda -y
-conda install -c conda-forge python=3.8 cudnn==8.2.1.32 cudatoolkit==11.1.1 openmm==7.5.1 pdbfixer -y
+conda install -c conda-forge python=3.9 cudnn==8.2.1.32 cudatoolkit==11.1.1 openmm==7.5.1 pdbfixer -y
 # Download the updater
 wget -qnc https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/main/update_linux.sh --no-check-certificate
 chmod +x update_linux.sh
 # install alignment tools
 conda install -c conda-forge -c bioconda kalign2=2.04 hhsuite=3.3.0 mmseqs2=14.7e284 -y
 # install ColabFold and Jaxlib
-# colabfold-conda/bin/python3.8 -m pip install "colabfold[alphafold] @ git+https://github.com/sokrypton/ColabFold"
-colabfold-conda/bin/python3.8 -m pip install -q --no-warn-conflicts "colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold"
-colabfold-conda/bin/python3.8 -m pip install https://storage.googleapis.com/jax-releases/cuda11/jaxlib-0.3.25+cuda11.cudnn82-cp38-cp38-manylinux2014_x86_64.whl
-colabfold-conda/bin/python3.8 -m pip install jax==0.3.25 biopython==1.79
+# colabfold-conda/bin/python3.9 -m pip install "colabfold[alphafold] @ git+https://github.com/sokrypton/ColabFold"
+colabfold-conda/bin/python3.9 -m pip install --upgrade pip
+colabfold-conda/bin/python3.9 -m pip install --no-warn-conflicts "colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold"
+colabfold-conda/bin/python3.9 -m pip install https://storage.googleapis.com/jax-releases/cuda11/jaxlib-0.3.25+cuda11.cudnn82-cp39-cp39-manylinux2014_x86_64.whl
+colabfold-conda/bin/python3.9 -m pip install jax==0.3.25 biopython==1.79
 
 # Use 'Agg' for non-GUI backend
-cd ${COLABFOLDDIR}/colabfold-conda/lib/python3.8/site-packages/colabfold
+cd ${COLABFOLDDIR}/colabfold-conda/lib/python3.9/site-packages/colabfold
 sed -i -e "s#from matplotlib import pyplot as plt#import matplotlib\nmatplotlib.use('Agg')\nimport matplotlib.pyplot as plt#g" plot.py
 # modify the default params directory
 sed -i -e "s#appdirs.user_cache_dir(__package__ or \"colabfold\")#\"${COLABFOLDDIR}/colabfold\"#g" download.py
@@ -38,7 +39,7 @@ rm -rf __pycache__
 
 # start downloading weights
 cd ${COLABFOLDDIR}
-colabfold-conda/bin/python3.8 -m colabfold.download
+colabfold-conda/bin/python3.9 -m colabfold.download
 cd ${CURRENTPATH}
 
 echo "Download of alphafold2 weights finished."