roadies_env.sh

#!/bin/bash

# Required installations: (uncomment next 2 lines if you have sudo access, otherwise make sure following tools are installed before proceeding)
sudo apt-get update
sudo apt-get install -y wget unzip make g++ python3 python3-pip python3-setuptools git vim screen default-jre libgomp1 libboost-all-dev cmake

# Define installation paths and check for directory
CONDA_PATH="${HOME}/conda"
ROADIES_ENV_SETUP="roadies_env.sh"

# Download and install Mambaforge if not already installed
if [ ! -d "${CONDA_PATH}" ]; then
    wget -q https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh -O Mambaforge-Linux-x86_64.sh
    bash Mambaforge-Linux-x86_64.sh -b -p "${CONDA_PATH}"
fi

# Create and setup the Conda environment if it doesn't exist
source "${CONDA_PATH}/etc/profile.d/conda.sh"  # Temporarily source conda for this script
source "${CONDA_PATH}/etc/profile.d/mamba.sh"  # Temporarily source mamba for this script
if ! conda env list | grep -q "roadies_env"; then
    mamba create -y -c conda-forge -c bioconda --name roadies_env snakemake alive-progress biopython iqtree=2.2.0.3 numpy lastz mashtree matplotlib seaborn treeswift=1.1.28 fasttree=2.1.11 python=3.11 raxml-ng ete3
fi
conda activate roadies_env

# Download and setup ASTER repository if not already done
if [ ! -d "ASTER-Linux" ]; then
    wget -q https://github.com/chaoszhang/ASTER/archive/refs/heads/Linux.zip -O Linux.zip
    unzip -q Linux.zip
    cd ASTER-Linux
    make
    g++ -D CASTLES -std=gnu++11 -march=native -Ofast -pthread src/astral-pro.cpp -o bin/astral-pro2
    cd ..
fi

# Clone PASTA if not already done
if [ ! -d "pasta" ]; then
    git clone https://github.com/smirarab/pasta.git
fi

# Clone Sate-Tools if not already done
if [ ! -d "sate-tools-linux" ]; then
    git clone https://github.com/smirarab/sate-tools-linux.git
fi

# Setup PASTA if not already done
if [ -d "pasta" ]; then
    mafft_file="pasta/bin/mafft"
    if [ ! -f "$mafft_file" ]; then
        cd pasta
        python3 setup.py develop --user
        cd ..
    fi
fi

# Build sampling code
if [ ! -d "workflow/scripts/sampling/build" ]; then
    cd workflow/scripts/sampling
    mkdir build
    cd build
    cmake ..
    make
    cd ../../../..
fi

# Install ete3 for the user, only if it is not already installed
python3 -m pip show ete3 &>/dev/null || python3 -m pip install --user ete3

echo "Setup complete. Remember to source '${ROADIES_ENV_SETUP}' before running your projects."