FastConformation/install_cli.sh at main · GMdSilva/FastConformation · GitHub

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#!/bin/bash -e

type wget 2>/dev/null || { echo "wget is not installed. Please install it using apt or yum." ; exit 1 ; }

CURRENTPATH=`pwd`
PACKAGEDIR="${CURRENTPATH}/fast_conf"

mkdir -p "${PACKAGEDIR}"
cd "${PACKAGEDIR}"
wget -q -P . https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
bash ./Mambaforge-Linux-x86_64.sh -b -p "${PACKAGEDIR}/conda"
rm Mambaforge-Linux-x86_64.sh

source "${PACKAGEDIR}/conda/etc/profile.d/conda.sh"
export PATH="${PACKAGEDIR}/conda/condabin:${PATH}"
conda update -n base conda -y
conda create -p "$PACKAGEDIR/fast_conf-conda" -c conda-forge -c bioconda -c biocore \
    git python=3.10 openmm==7.7.0 pdbfixer \
    kalign2=2.04 hhsuite=3.3.0 mmseqs2=15.6f452 hmmer scikit-learn mdanalysis seaborn scipy -y
conda activate "$PACKAGEDIR/fast_conf-conda"

# Install ColabFold and Jaxlib
"$PACKAGEDIR/fast_conf-conda/bin/pip" install --no-warn-conflicts \
    "colabfold[alphafold-minus-jax] @ git+https://github.com/GMdSilva/ColabFold"
"$PACKAGEDIR/fast_conf-conda/bin/pip" install "colabfold[alphafold]"
"$PACKAGEDIR/fast_conf-conda/bin/pip" install --upgrade "jax[cuda12]"==0.4.28
"$PACKAGEDIR/fast_conf-conda/bin/pip" install --upgrade tensorflow
"$PACKAGEDIR/fast_conf-conda/bin/pip" install silence_tensorflow
"$PACKAGEDIR/fast_conf-conda/bin/pip" install pdb-tools

"$PACKAGEDIR/fast_conf-conda/bin/pip" install --no-warn-conflicts \
    "fast_conformation @ git+https://github.com/GMdSilva/FastConformation"

# use 'agg' for non-GUI backend
cd "${PACKAGEDIR}/fast_conf-conda/lib/python3.10/site-packages/colabfold"
sed -i -e "s#from matplotlib import pyplot as plt#import matplotlib\nmatplotlib.use('Agg')\nimport matplotlib.pyplot as plt#g" plot.py
# modify the default params directory
sed -i -e "s#appdirs.user_cache_dir(__package__ or \"colabfold\")#\"${PACKAGEDIR}/colabfold\"#g" download.py
# suppress warnings related to tensorflow
sed -i -e "s#from io import StringIO#from io import StringIO\nfrom silence_tensorflow import silence_tensorflow\nsilence_tensorflow()#g" batch.py
# remove cache directory
rm -rf __pycache__

# install tm-score
sudo apt install tm-align

# Download weights
"$PACKAGEDIR/fast_conf-conda/bin/python3" -m colabfold.download
echo "Download of alphafold2 weights finished."
echo "-----------------------------------------"
echo "Installation of fast_conformation CLI version finished."
echo "Add ${PACKAGEDIR}/fast_conf-conda/bin to your PATH environment variable to run 'fast_conformation'."
echo -e "i.e. for Bash:\n\texport PATH=\"${PACKAGEDIR}/fast_conf-conda/bin:\$PATH\""
echo "For more details, please run 'fast_conformation --help'."

cd $PACKAGEDIR

# Add environment to PATH in the user's .bashrc
echo "Adding ${PACKAGEDIR}/fast_conf-conda/bin to PATH in ~/.bashrc"
echo -e "\n# Added by fast_conformation installation script\nexport PATH=\"${PACKAGEDIR}/fast_conf-conda/bin:\$PATH\"" >> ~/.bashrc

echo "Open a new terminal window."
echo "To initialize a sample config file run 'fast_conf_init'."
echo "Next, run any command of your choosing listed in our ReadTheDocs page and on the README."