setup.sh

#!/bin/bash

# Define InterProScan version
IPS_VERSION="5.75-106.0"
CONDA_ENV_NAME="bioanalysis" #or your own conda environment name

IPS_DIR="interproscan-${IPS_VERSION}"
IPS_TAR="interproscan-${IPS_VERSION}-64-bit.tar.gz"
IPS_URL="https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${IPS_VERSION}/${IPS_TAR}"


# Check if conda is available
if ! command -v conda &> /dev/null; then
    echo "Error: conda is not installed or not in PATH"
    echo "Please install Miniconda or Anaconda first"
    exit 1
fi

# Check if conda environment already exists
if conda env list | grep -q "^${CONDA_ENV_NAME} "; then
    echo "Found existing conda environment '${CONDA_ENV_NAME}', using it..."
else
    # Create conda environment with Java 11
    echo "Creating conda environment '${CONDA_ENV_NAME}' with OpenJDK 11..."
    conda create -y -n ${CONDA_ENV_NAME} openjdk=11 python=3.10
    if [ $? -ne 0 ]; then
        echo "Error: Failed to create conda environment"
        exit 1
    fi
fi

# Activate conda environment
echo "Activating conda environment..."
source $(conda info --base)/etc/profile.d/conda.sh
conda activate ${CONDA_ENV_NAME}

# Install Java 11 if not present in the existing environment
if ! java -version 2>&1 | grep -q "openjdk.*11"; then
    echo "Installing OpenJDK 11 in existing environment..."
    conda install -y openjdk=11
fi

# Create installation directory
echo "Setting up InterProScan ${IPS_VERSION}..."
mkdir -p interproscan
cd interproscan || exit 1

# Check if InterProScan archive already exists (from Hugging Face download)
if [ -f "${IPS_TAR}" ] && [ -f "${IPS_TAR}.md5" ]; then
    echo "✓ Found existing InterProScan archive in interproscan/ directory"
    echo "  Verifying MD5 checksum..."
    if md5sum -c "${IPS_TAR}.md5" 2>/dev/null; then
        echo "  ✓ MD5 checksum verified. Using existing archive."
    else
        echo "  ⚠ MD5 checksum verification failed. Re-downloading..."
        rm -f "${IPS_TAR}" "${IPS_TAR}.md5"
    fi
fi

# Download InterProScan and checksum if not present
if [ ! -f "${IPS_TAR}" ] || [ ! -f "${IPS_TAR}.md5" ]; then
    echo "Downloading InterProScan..."
    wget -nc "${IPS_URL}"
    wget -nc "${IPS_URL}.md5"
    
    # Verify MD5 checksum
    echo "Verifying download integrity..."
    if ! md5sum -c "${IPS_TAR}.md5"; then
        echo "ERROR: MD5 checksum verification failed!"
        echo "The downloaded file may be corrupted. Please try downloading again."
        echo "Alternatively, download from Hugging Face: https://huggingface.co/datasets/opendatalab-raiser/CoKE"
        exit 1
    fi
fi

# Extract package if not already extracted
if [ ! -d "${IPS_DIR}" ]; then
    echo "Extracting InterProScan..."
    tar -xzf "${IPS_TAR}"
else
    echo "✓ InterProScan already extracted. Skipping extraction."
fi

# Verify Java installation in conda env
echo "Checking Java environment in conda env..."
JAVA_VER=$(java -version 2>&1 | head -n 1 | awk -F '"' '{print $2}')

if [[ "$JAVA_VER" =~ ^11\. ]]; then
    echo "Found compatible Java version in conda env: $JAVA_VER"
else
    echo "Error: Java version in conda env is not 11.x (found: $JAVA_VER)"
    exit 1
fi

# Run setup
echo "Running InterProScan setup..."
cd "${IPS_DIR}" || exit 1
python setup.py -f interproscan.properties

echo ""
echo "InterProScan installation completed in conda environment '${CONDA_ENV_NAME}'!"
echo "To use InterProScan, first activate the conda environment:"
echo "conda activate ${CONDA_ENV_NAME}"
echo "Then add InterProScan to your PATH:"
echo "export PATH=\$PATH:$(pwd)"
echo "You may also need to set INTERPROSCAN_HOME=$(pwd)"

cd ../..

# install biopython for blast
echo "Installing Biopython for BLAST support..."
pip install biopython

echo "Biopython installation completed."

# Install BLAST from bioconda
echo "Installing BLAST from bioconda..."
conda config --add channels bioconda
conda config --add channels conda-forge
conda install -c bioconda blast=2.16.0 -y

mkdir -p blast_db
cd blast_db || exit 1

echo "Downloading UniProt SwissProt database..."
wget --quiet --show-progress -N https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz

if [ -f "uniprot_sprot.fasta.gz" ]; then
    echo "Decompressing database..."
    # gunzip -k uniprot_sprot.fasta.gz
    gunzip -c uniprot_sprot.fasta.gz > uniprot_sprot.fasta
    
    if [ -f "uniprot_sprot.fasta" ]; then
        echo "Creating BLAST database..."
        makeblastdb -in uniprot_sprot.fasta -dbtype prot -out uniprot_swissprot -parse_seqids -title "UniProt SwissProt"
        
        # Verify database creation
        if [ -f "uniprot_swissprot.phr" ]; then
            echo "BLAST database created successfully."
            echo "You can now use it with: blastp -db uniprot_swissprot -query your_file.fasta"
        else
            echo "Error: BLAST database files not created!" >&2
            exit 1
        fi
    else
        echo "Error: Failed to decompress database!" >&2
        exit 1
    fi
else
    echo "Error: Failed to download database!" >&2
    exit 1
fi

# Get the absolute path for the BLAST database
BLASTDB_PATH=$(pwd)
export BLASTDB=$BLASTDB_PATH
echo "BLASTDB environment variable set for current session: $BLASTDB"

# Function to add BLASTDB to shell config file
setup_blastdb_env() {
    local shell_config_file=$1
    if [ -f "$shell_config_file" ]; then
        if grep -q "export BLASTDB=" "$shell_config_file"; then
            echo "BLASTDB variable is already set in $shell_config_file."
        else
            echo "Adding BLASTDB to $shell_config_file..."
            echo "" >> "$shell_config_file"
            echo "# Set BLASTDB for local BLAST searches" >> "$shell_config_file"
            echo "export BLASTDB=\"$BLASTDB_PATH\"" >> "$shell_config_file"
            echo "Successfully added BLASTDB to $shell_config_file."
            echo "Please run 'source $shell_config_file' or restart your terminal to apply changes."
        fi
    else
        echo "Could not find $shell_config_file. Please add the following line to your shell's startup file:"
        echo "export BLASTDB=\"$BLASTDB_PATH\""
    fi
}

# Detect shell and update config file
if [ -n "$BASH_VERSION" ]; then
    setup_blastdb_env "$HOME/.bashrc"
elif [ -n "$ZSH_VERSION" ]; then
    setup_blastdb_env "$HOME/.zshrc"
else
    echo "Could not automatically detect your shell's config file."
    echo "Please add the following line to your shell's startup file (e.g., .bash_profile, .profile):"
    echo "export BLASTDB=\"$BLASTDB_PATH\""
fi

# install python packages
echo "Installing required Python packages..."
pip install -i https://pypi.tuna.tsinghua.edu.cn/simple \
    fastmcp \
    biopython \
    numpy \
    pandas \
    jinja2 \
    openai \
    requests \
    gradio-client \
    jsonlines \
    tqdm \
    gradio \
    lmdb \
    multiprocess \
    matplotlib \
    flask \
    werkzeug 

# Install and configure Foldseek
echo "Installing Foldseek from bioconda..."
# First install updated libstdcxx-ng to avoid library version issues
conda install -c conda-forge libstdcxx-ng -y
conda install -c conda-forge -c bioconda foldseek -y

if [ $? -ne 0 ]; then
    echo "Error: Failed to install Foldseek"
    exit 1
fi

echo "Foldseek installation completed."

# Create Foldseek database directory
PROJECT_ROOT=$(pwd)
mkdir -p foldseek_db

# Check if foldseek_db directory exists and contains all required files
check_foldseek_db_complete() {
    local db_dir="$1"
    local required_files=(
        "sp"
        "sp.dbtype"
        "sp.index"
        "sp.lookup"
        "sp.version"
        "sp_ca"
        "sp_ca.dbtype"
        "sp_ca.index"
        "sp_h"
        "sp_h.dbtype"
        "sp_h.index"
        "sp_ss"
        "sp_ss.dbtype"
        "sp_ss.index"
        "sp_mapping"
        "sp_taxonomy"
    )
    
    for file in "${required_files[@]}"; do
        if [ ! -f "$db_dir/$file" ]; then
            return 1  # File missing
        fi
    done
    return 0  # All files present
}

# Check if foldseek_db directory exists and contains all required files
# Check two possible locations:
# 1. Files directly in foldseek_db/ (from Hugging Face download)
# 2. Files in foldseek_db/sp/ (from foldseek command)
FOLDSEEK_DB_EXISTS=false
if [ -d "foldseek_db/sp" ] && check_foldseek_db_complete "foldseek_db/sp"; then
    echo "✓ Found existing Foldseek database in foldseek_db/sp/"
    echo "  All required files are present. Skipping download."
    FOLDSEEK_DB_EXISTS=true
elif [ -d "foldseek_db" ] && check_foldseek_db_complete "foldseek_db"; then
    echo "✓ Found existing Foldseek database in foldseek_db/"
    echo "  All required files are present. Skipping download."
    FOLDSEEK_DB_EXISTS=true
fi

if [ "$FOLDSEEK_DB_EXISTS" = false ]; then
    cd foldseek_db || exit 1
    echo "Downloading AlphaFold Swiss-Prot database for Foldseek..."
    echo "This may take a while depending on your network connection..."



    # Use LD_PRELOAD to ensure foldseek uses the updated libstdc++ from conda
    # This fixes the GLIBCXX_3.4.29 and CXXABI_1.3.13 version issues
    export LD_PRELOAD="$CONDA_PREFIX/lib/libstdc++.so.6.0.34"
    echo "Using preloaded library: $LD_PRELOAD"

    foldseek databases Alphafold/Swiss-Prot sp tmp
    unset LD_PRELOAD

    if [ $? -ne 0 ]; then
        echo "Error: Failed to download Foldseek database!"
        echo "You can try downloading manually later by running:"
        echo "foldseek databases Alphafold/Swiss-Prot foldseek_db/sp tmp"
        echo ""
        echo "Alternatively, you can download the database from Hugging Face:"
        echo "https://huggingface.co/datasets/opendatalab-raiser/CoKE"
        cd ..
    else
        echo "Foldseek database downloaded successfully."
        cd ..
    fi
fi

# Continue with environment variable setup if database exists
# Determine the correct path based on where files are located
if [ -d "foldseek_db/sp" ] && [ -f "foldseek_db/sp/sp" ]; then
    # Files are in foldseek_db/sp/ subdirectory (from foldseek command)
    FOLDSEEK_DB_PATH=$(pwd)/foldseek_db/sp
elif [ -d "foldseek_db" ] && [ -f "foldseek_db/sp" ]; then
    # Files are directly in foldseek_db/ directory (from Hugging Face)
    FOLDSEEK_DB_PATH=$(pwd)/foldseek_db
else
    FOLDSEEK_DB_PATH=""
fi

if [ -n "$FOLDSEEK_DB_PATH" ]; then
    # Get the absolute path for the Foldseek database
    export FOLDSEEK_DB=$FOLDSEEK_DB_PATH
    echo "FOLDSEEK_DB environment variable set for current session: $FOLDSEEK_DB"
    
    # Function to add FOLDSEEK_DB to shell config file
    setup_foldseek_env() {
        local shell_config_file=$1
        if [ -f "$shell_config_file" ]; then
            if grep -q "export FOLDSEEK_DB=" "$shell_config_file"; then
                echo "FOLDSEEK_DB variable is already set in $shell_config_file."
            else
                echo "Adding FOLDSEEK_DB to $shell_config_file..."
                echo "" >> "$shell_config_file"
                echo "# Set FOLDSEEK_DB for Foldseek searches" >> "$shell_config_file"
                echo "export FOLDSEEK_DB=\"$FOLDSEEK_DB_PATH\"" >> "$shell_config_file"
                echo "Successfully added FOLDSEEK_DB to $shell_config_file."
                echo "Please run 'source $shell_config_file' or restart your terminal to apply changes."
            fi
        else
            echo "Could not find $shell_config_file. Please add the following line to your shell's startup file:"
            echo "export FOLDSEEK_DB=\"$FOLDSEEK_DB_PATH\""
        fi
    }
    
    # Detect shell and update config file
    if [ -n "$BASH_VERSION" ]; then
        setup_foldseek_env "$HOME/.bashrc"
    elif [ -n "$ZSH_VERSION" ]; then
        setup_foldseek_env "$HOME/.zshrc"
    else
        echo "Could not automatically detect your shell's config file."
        echo "Please add the following line to your shell's startup file (e.g., .bash_profile, .profile):"
        echo "export FOLDSEEK_DB=\"$FOLDSEEK_DB_PATH\""
    fi
fi

echo ""
echo "===================================="
echo "Setup Complete!"
echo "===================================="
echo "Summary:"
echo "- InterProScan installed in conda environment '${CONDA_ENV_NAME}'"
echo "- BLAST database: $(pwd)/blast_db"
if [ -n "$FOLDSEEK_DB_PATH" ]; then
    echo "- Foldseek database: $FOLDSEEK_DB_PATH"
else
    echo "- Foldseek database: Not found (download manually or from Hugging Face)"
fi
echo ""
echo "To activate the environment:"
echo "conda activate ${CONDA_ENV_NAME}"
echo ""
echo "Environment variables set:"
echo "export BLASTDB=\"$(pwd)/blast_db\""
if [ -n "$FOLDSEEK_DB_PATH" ]; then
    echo "export FOLDSEEK_DB=\"$FOLDSEEK_DB_PATH\""
fi