INSTALL

#!/bin/sh

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##                                                        ##
## install pySeqRNA                                       ##
## Author: Naveen Duhan                                   ##
##                                                        ##
############################################################

# Check if script is executed using Bash
if [ -n "$BASH_VERSION" ]; then
    SHELL_TYPE="bash"
elif [ -n "$ZSH_VERSION" ]; then
    SHELL_TYPE="zsh"
else
    SHELL_TYPE="sh"
fi

# Function to check if a command is available
command_exists() {
  command -v "$1" >/dev/null 2>&1
}

echo "\nPlease wait, checking development environment..."
# Check operating system
OS=$(uname -s)

if [ "$OS" = "Linux" ]; then
    echo "\nLinux development environment found\nProceeding with Linux-based installation\n"
elif [ "$OS" = "Darwin" ]; then
    ARCH=$(uname -m)
    if [ "$ARCH" = "arm64" ]; then
        echo "\nARM64 Darwin development environment found\nProceeding with ARM64-based macOS installation\n"
    else
        echo "\nIntel Darwin development environment found\nProceeding with Intel-based macOS installation\n"
    fi
else
    echo "\nUnsupported operating system: $OS\nPlease install using dockerfile\n"
    exit 1
fi

# Check if Miniconda is already installed
if [ ! -d "$HOME/miniconda3" ]; then
    echo "Miniconda3 is not installed. Installing..."

    # Download Miniconda installer based on OS and architecture
    if [ "$OS" = "Linux" ]; then
        echo "\nDownloading Miniconda3 for Linux\n"
        wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh || { echo "Error: Failed to download Miniconda for Linux."; exit 1; }
    elif [ "$OS" = "Darwin" ]; then
        ARCH=$(uname -m)
        if [ "$ARCH" = "arm64" ]; then
            echo "\nDownloading Miniconda3 for ARM-based macOS\n"
            wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh -O miniconda.sh || { echo "Error: Failed to download Miniconda for ARM-based macOS."; exit 1; }
            echo "\nNot all software compiles on ARM-based macOS; adding osx-x64 subdir\n"
            conda config --env --set subdir osx-x64
        else
            echo "\nDownloading Miniconda3 for Intel-based macOS\n"
            wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh || { echo "Error: Failed to download Miniconda for Intel-based macOS."; exit 1; }
        fi
    else
        echo "\nUnsupported operating system: $OS\nPlease install using dockerfile\n"
        exit 1
    fi

    echo "\nInstalling Miniconda3 environment...\n"
    sh miniconda.sh -b -p ~/miniconda3 || { echo "Error: Miniconda installation failed."; exit 1; }
fi

# Activate Miniconda
. ~/miniconda3/bin/activate || { echo "Error: Failed to activate Miniconda."; exit 1; }

# Check if the conda environment already exists
if conda env list | grep -q "pyseqrna-0.2"; then
    echo "pySeqRNA environment already exists. Deleting and recreating..."
    conda env remove -n pyseqrna-0.2 --yes || { echo "Error: Failed to remove existing pySeqRNA environment."; exit 1; }
fi

echo "Creating pySeqRNA conda environment...\n"
# Install dependencies via conda
if [ "$OS" = "Linux" ]; then
    conda env create -f pyseqrna_environment.yml || { echo "Error: Failed to create pySeqRNA conda environment."; exit 1; }
elif [ "$OS" = "Darwin" ]; then
    ARCH=$(uname -m)
    if [ "$ARCH" = "arm64" ]; then
        # Activate the environment
        CONDA_SUBDIR=osx-64 conda env create -f pyseqrna_environment.yml || { echo "Error: Failed to create pySeqRNA conda environment."; exit 1; }
    else
        conda env create -f pyseqrna_environment.yml || { echo "Error: Failed to create pySeqRNA conda environment."; exit 1; }
    fi
else
    echo "\nUnsupported operating system: $OS\nPlease install using dockerfile\n"
    exit 1
fi

conda activate pyseqrna-0.2 || { echo "Error: Failed to activate pySeqRNA environment."; exit 1; }

# Install pySeqRNA
echo "\nInstalling pySeqRNA package\n"
pip install . || { echo "Error: Failed to install pySeqRNA package."; exit 1; }

# Set up initialization for shell
if [ "$SHELL_TYPE" = "bash" ]; then
    conda init "$SHELL_TYPE" >/dev/null 2>&1
    echo "source ~/miniconda3/bin/activate pyseqrna-0.2" >>~/.bashrc
    source ~/.bashrc
elif [ "$SHELL_TYPE" = "zsh" ]; then
    conda init "$SHELL_TYPE" >/dev/null 2>&1
    echo "source ~/miniconda3/bin/activate pyseqrna-0.2" >>~/.zshrc
    source ~/.zshrc
fi

echo "\n\npySeqRNA installation successfully completed\nThank you for using pySeqRNA\n\nTo execute pyseqrna, run:\n\nsource ~/miniconda3/bin/activate pyseqrna-0.2\n\npyseqrna -h\n\n"

##################################################################
##                                                              ##
##  Written by Naveen Duhan (naveen.duhan@outlook.com)          ##
##  Kaundal Bioinformatics Lab, Utah State University           ##
##  Released under the terms of GNU General Public Licence v3   ##
##                                                              ##
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