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#!/bin/bash
# This script sets up a comprehensive histopathology environment
# Set up colors for output
GREEN='\033[0;32m'
RED='\033[0;31m'
YELLOW='\033[1;33m'
BLUE='\033[0;34m'
NC='\033[0m' # No Color
# Default tools directory is the current directory
DEFAULT_TOOLS_DIR="$(pwd)/histopath_tools"
TOOLS_DIR=""
echo -e "${YELLOW}=== HistoPath Environment Setup ===${NC}"
echo -e "${BLUE}This script will set up a comprehensive histopathology environment with various tools and packages.${NC}"
# Check if conda is installed
if ! command -v conda &> /dev/null && ! command -v micromamba &> /dev/null; then
echo -e "${RED}Error: Conda is not installed or not in PATH.${NC}"
echo "Please install Miniconda or Anaconda first."
echo "Visit: https://docs.conda.io/en/latest/miniconda.html"
exit 1
fi
# Function to handle errors
handle_error() {
local exit_code=$1
local error_message=$2
local optional=${3:-false}
if [ $exit_code -ne 0 ]; then
echo -e "${RED}Error: $error_message${NC}"
if [ "$optional" = true ]; then
echo -e "${YELLOW}Continuing with setup as this component is optional.${NC}"
return 0
else
if [ -z "$NON_INTERACTIVE" ]; then
read -p "Continue with setup? (y/n) " -n 1 -r
echo
if [[ ! $REPLY =~ ^[Yy]$ ]]; then
echo -e "${RED}Setup aborted.${NC}"
exit 1
fi
else
echo -e "${YELLOW}Non-interactive mode: continuing despite error.${NC}"
fi
fi
fi
return $exit_code
}
# Function to install a specific environment file
install_env_file() {
local env_file=$1
local description=$2
local optional=${3:-false}
echo -e "\n${BLUE}=== Installing $description ===${NC}"
if [ "$optional" = true ]; then
if [ -z "$NON_INTERACTIVE" ]; then
read -p "Do you want to install $description? (y/n) " -n 1 -r
echo
if [[ ! $REPLY =~ ^[Yy]$ ]]; then
echo -e "${YELLOW}Skipping $description installation.${NC}"
return 0
fi
else
echo -e "${YELLOW}Non-interactive mode: automatically installing $description.${NC}"
fi
fi
echo -e "${YELLOW}Installing $description from $env_file...${NC}"
conda env update -f $env_file
handle_error $? "Failed to install $description." $optional
if [ $? -eq 0 ]; then
echo -e "${GREEN}Successfully installed $description!${NC}"
fi
}
# Main installation process
main() {
# Step 1: Create base conda environment
echo -e "\n${YELLOW}Step 1: Creating base environment from environment.yml...${NC}"
conda env create -n histopath -f environment.yml
handle_error $? "Failed to create base conda environment."
# Step 2: Activate the environment
echo -e "\n${YELLOW}Step 2: Activating conda environment...${NC}"
if command -v micromamba &> /dev/null; then
eval "$("$MAMBA_EXE" shell hook --shell bash)"
micromamba activate histopath
else
eval "$(conda shell.bash hook)"
conda activate histopath
fi
handle_error $? "Failed to activate histopath environment."
# Step 3: Install core histopathology tools
echo -e "\n${YELLOW}Step 3: Installing core histopathology tools...${NC}"
install_env_file "histo_env.yml" "core bioinformatics tools"
}
# Run the main installation process
main |