Vini/AlphaFold_install at main · draskot/Vini · GitHub

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#!/bin/bash
# VINI AlphaFold installer (modules or custom installation)
# Assumes sourceme already defines INSTALL

#--------------------------------------
# Load VINI variables
#--------------------------------------
SOURCEME="$HOME/Vini/sourceme"
INSTALL=$(grep '^export INSTALL=' "$SOURCEME" | cut -d= -f2)

if [ -z "$INSTALL" ]; then
    echo "Error: INSTALL directory not found in sourceme."
    exit 1
fi

if grep -q "AlphaFold" "$SOURCEME"; then
    read -p "AlphaFold section exists in $SOURCEME. Overwrite? (y/N): " ans
    case "$ans" in
        [Yy]*)
            # remove old AlphaFold section
            sed -i '/AlphaFold/,+2d' "$SOURCEME"
            ;;
        *)
            echo "Keeping existing AlphaFold section. Exiting."
            exit 0
            ;;
    esac
fi

#--------------------------------------
# Check for available AlphaFold modules
#--------------------------------------
echo "Listing available AlphaFold modules..."
module_spider_output=$(mktemp)
module spider alphafold &> "$module_spider_output"

# Extract AlphaFold module names
mapfile -t module_list < <(grep -oE "AlphaFold/[^[:space:]]+" "$module_spider_output" | uniq)
rm -f "$module_spider_output"

if [ ${#module_list[@]} -gt 0 ]; then
    echo "Available AlphaFold modules:"
    for m in "${module_list[@]}"; do
        echo "  $m"
    done
    if  [ ${#module_list[@]} -eq 1 ]; then
        selected_module="${module_list[0]}"
        echo "Only one AlphaFold module found. Using: $selected_module"
    else
        read -p "Enter the module name to use (exactly as shown above): " selected_module
    fi
    echo "#*****AlphaFold section******" >> "$SOURCEME"
    echo "module load $selected_module" >> "$SOURCEME"
    echo "export selected_module=\"${selected_module}\"" >> "$SOURCEME"
    echo "export ALPHAFOLD_DATA_DIR=/ceph/hpc/software/alphafold" >> "$SOURCEME"
    echo "export ALPHAFOLD_START=$(module show $selected_module 2>&1 | grep -oE '/.*/alphafold')" >> "$SOURCEME"
    echo "AlphaFold environment configured via module."
    exit 0
fi

#--------------------------------------
# No module found → fallback to custom installation
#--------------------------------------
echo "No AlphaFold module found. Proceeding with custom installation..."

# Create conda environment if not exists
source "$INSTALL/miniconda3/bin/activate"

if ! conda env list | grep -q "^alphafold"; then
    conda create -y --name alphafold python=3.8

    conda run -n alphafold conda install -y -c conda-forge \
        openmm==7.5.1 cudatoolkit==11.2.2 pdbfixer

    conda run -n alphafold conda install -y -c bioconda \
        hmmer hhsuite==3.3.0 kalign2

    conda run -n alphafold pip install --no-cache-dir \
        absl-py==1.0.0 \
        biopython==1.79 \
        chex==0.0.7 \
        dm-haiku==0.0.9 \
        dm-tree==0.1.6 \
        immutabledict==2.0.0 \
        jax==0.3.25 \
        ml-collections==0.1.0 \
        numpy==1.21.6 \
        pandas==1.3.4 \
        protobuf==3.20.1 \
        scipy==1.7.0 \
        tensorflow-cpu==2.9.0

    conda run -n alphafold pip install --upgrade --no-cache-dir \
        jax==0.3.25 \
        jaxlib==0.3.25+cuda11.cudnn805 \
        -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
fi

ALPHAFOLD_VERSION="2.3.1"
ALPHAFOLD_DIR="$INSTALL/alphafold-$ALPHAFOLD_VERSION"
ALPHAFOLD_PATH="$ALPHAFOLD_DIR"


if [ ! -d "$ALPHAFOLD_DIR" ]; then
    echo "AlphaFold source not found. Downloading v$ALPHAFOLD_VERSION..."

    wget -O "$INSTALL/v$ALPHAFOLD_VERSION.tar.gz" \
        https://github.com/deepmind/alphafold/archive/refs/tags/v$ALPHAFOLD_VERSION.tar.gz

    tar -xzf "$INSTALL/v$ALPHAFOLD_VERSION.tar.gz" -C "$INSTALL"
    rm -f "$INSTALL/v$ALPHAFOLD_VERSION.tar.gz"
else
    echo "AlphaFold source already present."
fi


if [ ! -d "$INSTALL/alphafold_data" ]; then # Download databases if not present
    sh "$HOME/Vini/download_db.sh" -d "$INSTALL/alphafold_data"
fi

# Additional setup
wget -P "$ALPHAFOLD_PATH/alphafold/common" \
     https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt

PATCH_DIR="$INSTALL/miniconda3/envs/alphafold/lib/python3.8/site-packages"

if [ ! -f "$PATCH_DIR/.openmm_patch_done" ]; then
    patch -p0 -d "$PATCH_DIR" < "$ALPHAFOLD_PATH/docker/openmm.patch"
    touch "$PATCH_DIR/.openmm_patch_done"
fi

cp "$HOME/Vini/run_alphafold.sh" "$ALPHAFOLD_PATH"


# Write single section to sourceme
echo "#***** AlphaFold section ******" >> "$SOURCEME"
echo "export ALPHAFOLD_DATA_DIR=\"$INSTALL/alphafold_data\"" >> "$SOURCEME"
echo "export ALPHAFOLD_START=\"$ALPHAFOLD_PATH/run_alphafold.sh\"" >> "$SOURCEME"
./write_cuda_module