env_setup.sh

#!/bin/bash

  echo '
=================================================================================================================================
Developed by: Francisco Zorrilla, Kiran R. Patil, and Aleksej Zelezniak___________________________________________________________
Publication: doi.org/10.1101/2020.12.31.424982___________________________/\\\\\\\\\\\\___/\\\\\\\\\\\\\\\___/\\\\____________/\\\\_        
________________________________________________________________________/\\\//////////___\/\\\///////////___\/\\\\\\________/\\\\\\_       
____________________________________________/\\\________________________/\\\______________\/\\\______________\/\\\//\\\____/\\\//\\\_      
_______/\\\\\__/\\\\\________/\\\\\\\\____/\\\\\\\\\\\___/\\\\\\\\\_____\/\\\____/\\\\\\\__\/\\\\\\\\\\\______\/\\\\///\\\/\\\/_\/\\\_     
______/\\\///\\\\\///\\\____/\\\/////\\\__\////\\\////___\////////\\\____\/\\\___\/////\\\__\/\\\///////_______\/\\\__\///\\\/___\/\\\_    
______\/\\\_\//\\\__\/\\\___/\\\\\\\\\\\______\/\\\_________/\\\\\\\\\\___\/\\\_______\/\\\__\/\\\______________\/\\\____\///_____\/\\\_   
_______\/\\\__\/\\\__\/\\\__\//\\///////_______\/\\\_/\\____/\\\/////\\\___\/\\\_______\/\\\__\/\\\______________\/\\\_____________\/\\\_  
________\/\\\__\/\\\__\/\\\___\//\\\\\\\\\\_____\//\\\\\____\//\\\\\\\\/\\__\//\\\\\\\\\\\\/___\/\\\\\\\\\\\\\\\__\/\\\_____________\/\\\_ 
_________\///___\///___\///_____\//////////_______\/////______\////////\//____\////////////_____\///////////////___\///______________\///__
=============================================================================================================================================
A Snakemake-based pipeline desinged to predict metabolic interactions directly from metagenomics data using high performance computer clusters
===============================================================================================================================================
'

#check if conda is installed/available
echo -ne "Checking if conda is available ... "
condatest=$(conda list|wc -l)

if [[ "$condatest" -eq 0 ]]; then
    echo -e "\nWARNING: Conda is not available! Please load your cluster's conda module or install locally and re-run the env_setup.sh script using:\n\nbash env_setup.sh\n" && exit
elif [[ "$condatest" -gt 0 ]]; then
    condav=$(conda --version|cut -d ' ' -f2)
    echo -e "detected version $condav!"
fi

#check if mamba or mamba env are available
echo -ne "Checking if mamba environment is available ... "
mambatest=$(mamba --version|wc -l)
mambaenv=$(conda info --envs|grep mamba|wc -l)

if [[ "$mambaenv" -ge 1 ]]; then
    if [[ "$mambatest" -ge 1 ]]; then
        #mamba env installed and activated
        mambav=$(mamba --version|head -n1|cut -d ' ' -f2) && echo -e "detected version $mambav!\n"
    else
        #mamba env installed but not activated
        source activate mamba && echo "activated mamba environment!"
    fi
else
    while true; do
        read -p "Do you wish to create an environment for mamba installation? This is recommended for faster setup (y/n)" yn
        case $yn in
            [Yy]* ) echo "conda deactivate && conda create -n mamba mamba -c conda-forge"|bash; break;;
            [Nn]* ) echo -e "\nPlease set up mamba before proceeding.\n"; exit;;
            * ) echo "Please answer yes or no.";;
        esac
    done
fi

while true; do
    read -p "Do you wish to download and set up metaGEM conda environment? (y/n)" yn
    case $yn in
        [Yy]* ) echo "mamba env create --prefix ./envs/metagem -f envs/metaGEM_env.yml && source activate envs/metagem && pip install --user memote carveme smetana &&  echo "|bash; break;;
        [Nn]* ) echo -e "\nSkipping metaGEM env setup, note that you will need this for refinement & reassembly of MAGs.\n"; break;;
        * ) echo "Please answer yes or no.";;
    esac
done

while true; do
    read -p "Do you wish to download the GTDB-tk database (~25 Gb)? (y/n)" yn
    case $yn in
        [Yy]* ) echo "download-db.sh && source deactivate && source activate mamba"|bash; break;;
        [Nn]* ) echo -e "\nSkipping GTDB-tk database download, note that you will need this for taxonomic classification of MAGs.\n"; break;;
        * ) echo "Please answer yes or no.";;
    esac
done

while true; do
    read -p "Do you wish to download and set up metaWRAP conda environment? (y/n)" yn
    case $yn in
        [Yy]* ) echo "mamba env create --prefix ./envs/metawrap -f envs/metaWRAP_env.yml"|bash; break;;
        [Nn]* ) echo -e "\nSkipping metaWRAP env setup, note that you will need this for refinement & reassembly of MAGs.\n"; break;;
        * ) echo "Please answer yes or no.";;
    esac
done

while true; do
    read -p "Do you wish to download the CheckM database (~275 Mb)? (y/n)" yn
    case $yn in
        [Yy]* ) echo "wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz"|bash; break;;
        [Nn]* ) echo -e "\nSkipping CheckM database download, note that you will need this for bin refinement & reassembly.\n"; break;;
        * ) echo "Please answer yes or no.";;
    esac
done

while true; do
    read -p "Do you wish to download and set up prokka + roary conda environment? (y/n)" yn
    case $yn in
        [Yy]* ) echo "mamba env create --prefix ./envs/prokkaroary -f envs/prokkaroary_env.yml"|bash; break;;
        [Nn]* ) echo -e "\nSkipping prokka-roary env setup, note that you will need this for pangenome analysis of MAGs.\n"; break;;
        * ) echo "Please answer yes or no.";;
    esac
done

echo 'Please ensure that the installation directory is present in your $PATH variable if installation issues arise with any tools.'
echo ""