vampirus_startup.sh

#!/usr/bin/env bash

usage () {
echo "

Run this script in the vAMPirus directory to set up Conda and the vAMPirus Conda environment

You can also use this script to download reference databases for taxonomy assignment by useing the -d option described below.

General execution:

vampirus_startup.sh -h [-d 1|2|3|4] [-s]

    Command line options:

        [ -h ]                       	Print help information

        [ -d 1|2|3|4 ]                Set this option to create a database directiory within the current working directory and download the following databases for taxonomy assignment:

                                                    1 - Download the proteic version of the Reference Viral DataBase (See the paper for more information on this database: https://f1000research.com/articles/8-530)
                                                    2 - Download only NCBIs Viral protein RefSeq database
                                                    3 - Download only the complete NCBI NR protein database
                                                    4 - Download all three databases

        [ -s ]                       Set this option to skip conda installation and environment set up (you can use if you plan to run with Singularity and the vAMPirus Docker container)

        [ -t ]                       Set this option to download NCBI taxonomy files needed for DIAMOND to assign taxonomic classification to sequences (works with NCBI type databases only, see manual for more information)

"

}

while getopts "hstd:" OPTION; do
     case $OPTION in
         h) usage; exit;;
         d) DATABASE=${OPTARG};;
         s) CONDA="no";;
         t) TAX="yes";;
     esac
done
shift $((OPTIND-1))      # required, to "eat" the options that have been processed

export mypwd="$(pwd)"

sed "s|VAMPDIR|${mypwd}|g" ${mypwd}/vampirus.config > tmp.config
cat tmp.config > vampirus.config
rm tmp.config

os_c() {
    if [ -f /etc/os-release ];then
        echo -e "\n\t -- Downloading Linux Miniconda3 installation for Linux OS-- \n"
        curl -o Miniconda3-latest-Linux-x86_64.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
    elif [ `which sw_vers | wc -l` -eq 1 ];then
        echo -e "\n\t -- Downloading Linux Miniconda3 installation for MacOS -- \n"
        curl -o Miniconda3-latest-MacOSX-x86_64.sh https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
    else
        echo "Error in Miniconda installation"
        exit 0
    fi
}
# get version of GNU tool
toolversion() {
    local prog="$1" operator="$2" value="$3" version

    version=$($prog --version | awk '{print $NF; exit}')

    awk -vv1="$version" -vv2="$value" 'BEGIN {
        split(v1, a, /\./); split(v2, b, /\./);
        if (a[1] == b[1]) {
            exit (a[2] '$operator' b[2]) ? 0 : 1
        }
        else {
            exit (a[1] '$operator' b[1]) ? 0 : 1
        }
    }'
}
source_c() {
    if [ -f ~/.bashrc ];then
        source ~/.bashrc
    else
        source ~/.bash_profile
    fi
}
conda_c() {
    source_c ~/.bashrc
    cd $mypwd
    #Check conda and environment
    check_conda=$( command -v conda )
    if [ "$check_conda" != "" ];then #&& [ "$ver" -gt "45" ];then
        echo -e "\n\t -- Conda seems to be installed in your system --\n"
        #ver=$( conda -V | awk '{print $2}' | cut -f 1,2 -d "." )
        vern=4.8
        if toolversion conda '>=' $vern;then
            echo -e "\n\t -- Conda is installed (v4.8 or higher)."
        fi
    else
        echo -e "\n\t -- Conda is not intalled."
        echo -e -n "\n\t    Do you want to install Miniconda3? (y,n,exit): "
        read ans
        case $ans in
            [yY] | [yY][eE][sS])
                os_c
                echo -e "\n\t -- Starting Anaconda installation -- \n"
                bash Miniconda3*.sh
                echo -e "\n\t -- Installation done -- \n"
                rm Miniconda3*.sh
                source_c
                if [ -f vampirus_env.yml ];then
                    echo -e "\n\t -- vAMPirus environment file found. Creating environments... --\n"
                    conda env create -f vampirus_env.yml
                    conda env create -f vampirus_deseq_env.yml
                else
                    echo -e "\n\t\e[31m -- ERROR: vAMPirus environment file not found (vAMPirus_env.yml). Please check requirements and rerun the pre-check --\e[39m\n"
                    exit 0
                fi
            ;;
            [nN] | [nN][oO])
                echo -e "\n\t\e[31m -- ERROR: Download and Install Miniconda or Anaconda. Then rerun the pre-check  --\e[39m\n"
                exit 0
            ;;
            exit)
	           echo -e "\n\t -- Exiting -- \n"
               exit 0
            ;;
            *)
                echo -e "\n\n\t\e[31m -- Yes or No answer not specified. Try again --\e[39m\n"
	            conda_c
            ;;
        esac
    fi
}

nextflow_c() {
    source_c
    cd $mypwd
    echo "Checking if Nextflow installed system-wide.."
    check_nextflow=$( command -v nextflow )
    if [ "$check_nextflow" = "" ];then #&& [ "$ver" -gt "45" ];then
        echo "Nextflow is not system-wide, checking if its in the current working directory.."
        check_nextflow=$( ls "$mypwd"| grep -wc "nextflow" )
    fi
    if [ "$check_nextflow" -eq 1 ];then #&& [ "$ver" -gt "45" ];then
        echo "Nextflow seems to be installed in your system and in your current \$PATH, great!"
    else
        echo "Nextflow does not to seem to be downloaded or specified in your \$PATH.."
        echo "If you know you have it downloaded, answer n/N to the following question, add nextflow to your \$PATH variable and re-run this script to test. "
        echo "Otherwise, would you like me to install Nextflow for you now? (y,n,exit): "
        read ans
        case $ans in
            [yY] | [yY][eE][sS])
            echo "Awesome,starting Nextflow installation now ..."
            curl -fsSL get.nextflow.io | bash
            echo "Nextflow installation finished, execultable in "$mypwd""
        ;;
        [nN] | [nN][oO])
            echo "ERROR: It seems like you answered with something other than y... Download and install Nextflow on your own and rerun re-run the script to make sure path is sepcified correctly."
            echo "If it was a mistake you regret your original answer, just re-run the script and all will be forgiven ^__^."
            exit 0
        ;;
        exit)
           echo "Alright, if you say so, exiting now."
           exit 0
        ;;
        *)
            echo "Yes or No answer not specified. Lets try this again..."
            nextflow_c
        ;;
        esac
    fi
}

if [[ "$CONDA" == "no" ]]
then  echo "Skipping Conda install and set up, if this was a mistake, you can always rerun the startup script."
      environment="/PATH/TO/"
else
      echo "Alright, lets check your system for Conda..."
      conda_c
      echo "Editing path to conda directory in vampirus.config"
      environment="$(conda info -e | awk '$1 == "vAMPirus" {print $2}')"
      sed "s|CONDADIR|${environment}|g" "$mypwd"/vampirus.config > tmp1.config
      cat tmp1.config > "$mypwd"/vampirus.config
      rm tmp1.config
fi

echo "-------------------------------------------------------------------------------- Conda check/install done"

echo "Now lets check the status of Nextflow on your system..."
nextflow_c

echo "-------------------------------------------------------------------------------- Nextflow check/install done"

if [[ $DATABASE -eq 1 ]]
then    mkdir "$mypwd"/Databases
        cd "$mypwd"/Databases
        dir="$(pwd)"
        echo "Database installation: RVDB version 24.1 (latest as of 2022-08)"
        curl -o U-RVDBv24.1-prot.fasta.xz https://rvdb-prot.pasteur.fr/files/U-RVDBv24.1-prot.fasta.xz
        xz -d U-RVDBv24.1-prot.fasta.xz
        curl -o U-RVDBv24.1-prot-hmm-txt.tar.xz https://rvdb-prot.pasteur.fr/files/U-RVDBv24.1-prot-hmm-txt.tar.xz
        tar -xJf U-RVDBv24.1-prot-hmm-txt.tar.xz
        mv annot ./RVDBannot/
        echo "Editing confiration file for you now..."
        sed 's/DATABASENAME/U-RVDBv24.1-prot.fasta/g' "$mypwd"/vampirus.config > tmp1.config
        sed "s|DATABASEDIR|${dir}|g" tmp1.config > tmp2.config
        sed "s|DATABASEANNOT|${dir}/RVDBannot|g" tmp2.config | sed 's/TYPE/RVDB/g' > tmp3.config
        rm tmp1.config
        rm tmp2.config
        cat tmp3.config > "$mypwd"/vampirus.config
        rm tmp3.config
        echo "Database downloaded and configuration file edited, you should confirm the path and database name was set correctly in the config file."
elif [[ $DATABASE -eq 2 ]]
then    mkdir "$mypwd"/Databases
        cd "$mypwd"/Databases
        dir="$(pwd)"
        echo "Database installation: Viral RefSeq database (latest as of 2022-11)"
        curl -o viral.1.protein.faa.gz https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.1.protein.faa.gz
        gunzip viral.1.protein.faa.gz
        curl -o U-RVDBv24.1-prot-hmm-txt.tar.xz https://rvdb-prot.pasteur.fr/files/U-RVDBv24.1-prot-hmm-txt.tar.xz
        tar -xJf U-RVDBv24.1-prot-hmm-txt.tar.xz
        mv annot ./RVDBannot
        echo "Editing confiration file for you now..."
        sed 's/DATABASENAME/complete_virus_refseq_prot.fasta/g' "$mypwd"/vampirus.config > tmp1.config
        sed "s|DATABASEDIR|${dir}|g" tmp1.config | sed "s|DATABASEANNOT|${dir}/RVDBannot|g" | sed 's/TYPE/NCBI/g' > tmp2.config
        rm tmp1.config
        cat tmp2.config > "$mypwd"/vampirus.config
        rm tmp2.config
        echo "Database downloaded and configuration file edited, you should confirm the path and database name was set correctly in the config file."
elif [[ $DATABASE -eq 3 ]]
then    mkdir "$mypwd"/Databases
        cd "$mypwd"/Databases
        dir="$(pwd)"
        echo "Database installation: NCBI NR protein database (should be the most up to date at time of running this script)"
        curl -o NCBI_nr_proteindb.faa.gz https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz
        gunzip NCBI_nr_proteindb.faa.gz
        curl -o U-RVDBv24.1-prot-hmm-txt.tar.xz https://rvdb-prot.pasteur.fr/files/U-RVDBv24.1-prot-hmm-txt.tar.xz
        tar -xJf U-RVDBv24.1-prot-hmm-txt.tar.xz
        mv annot ./RVDBannot
        echo "Editing confiration file for you now..."
        sed 's/DATABASENAME/NCBI_nr_proteindb.faa/g' "$mypwd"/vampirus.config > tmp1.config
        sed "s|DATABASEDIR|${dir}|g" tmp1.config | sed "s|DATABASEANNOT|${dir}/RVDBannot|g" | sed 's/TYPE/NCBI/g' > tmp2.config
        rm tmp1.config
        cat tmp2.config > "$mypwd"/vampirus.config
        rm tmp2.config
        echo "Database downloaded and configuration file edited, you should confirm the path and database name was set correctly in the config file."
elif [[ $DATABASE -eq 4 ]]
then    mkdir "$mypwd"/Databases
        cd "$mypwd"/Databases
        dir="$(pwd)"
        echo "Database installation: We want 'em all! Might take a little while....'"
        curl -o NCBI_nr_proteindb.faa.gz https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz
        curl -o viral.1.protein.faa.gz https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.1.protein.faa.gz
        curl -o U-RVDBv24.1-prot.fasta.xz https://rvdb-prot.pasteur.fr/files/U-RVDBv24.1-prot.fasta.xz
        sed "s|DATABASEDIR|${dir}|g" "$mypwd"/vampirus.config > tmp1.config
        cat tmp1.config > "$mypwd"/vampirus.config
        rm tmp1.config
        curl -o U-RVDBv24.1-prot-hmm-txt.tar.xz https://rvdb-prot.pasteur.fr/files/U-RVDBv24.1-prot-hmm-txt.tar.xz
        tar -xJf U-RVDBv24.1-prot-hmm-txt.tar.xz
        echo "Databases downloaded, make sure you update the config file with the one you would like to use and decompress the database before running."
elif [[ $DATABASE != "" ]]
then    echo "Error: Database download signaled but not given a value between 1-4"
        exit 1
fi

if [[ "$TAX" == "yes"  ]]
then  mkdir "$mypwd"/Databases/NCBItaxonomy
      cd "$mypwd"/Databases/NCBItaxonomy
      curl -o prot.accession2taxid.FULL.gz ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.FULL.gz
      echo "Gunzipping accession2tax map, might take a moment.."
      gunzip prot.accession2taxid.FULL.gz
      curl -o taxdmp.zip ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdmp.zip
      unzip taxdmp.zip
fi

echo "-------------------------------------------------------------------------------- Database loop done"

cd "$mypwd"
echo "Ok, everything downloaded. To test installation, check out the EXAMPLE_COMMANDS.txt file within "$mypwd" for instructions for testing the installation and running vAMPirus with your own data."


if [[ $(ls "$mypwd"| grep -wc "EXAMPLE_COMMANDS.txt") -eq 0 ]]
then
      touch EXAMPLE_COMMANDS.txt
      echo "-------------------------------------------------------------------------------------------------------------------------------- TESTING YOUR INSTALLATION; be sure to run from inside the vAMPirus program directory" >> EXAMPLE_COMMANDS.txt
      echo "   " >> EXAMPLE_COMMANDS.txt
      echo "Ok, everything downloaded. To test installation, run the following commands and check for errors (be sure to run from inside the vAMPirus program directory):" >> EXAMPLE_COMMANDS.txt
      echo "   " >> EXAMPLE_COMMANDS.txt
      echo "Checking DataCheck mode:" >> EXAMPLE_COMMANDS.txt
      echo "   " >> EXAMPLE_COMMANDS.txt
      echo ""$mypwd"/nextflow run  "$mypwd"/vAMPirus.nf -c  "$mypwd"/vampirus.config -profile conda,test --DataCheck -resume" >> EXAMPLE_COMMANDS.txt
      echo "   " >> EXAMPLE_COMMANDS.txt
      echo "Or if you plan to run vAMPirus using Singularity, use this test command:" >> EXAMPLE_COMMANDS.txt
      echo "   " >> EXAMPLE_COMMANDS.txt
      echo ""$mypwd"/nextflow run  "$mypwd"/vAMPirus.nf -c  "$mypwd"/vampirus.config -profile singularity,test --DataCheck -resume" >> EXAMPLE_COMMANDS.txt
      echo "    " >> EXAMPLE_COMMANDS.txt
      echo "Next, test the analysis pipeline:" >> EXAMPLE_COMMANDS.txt
      echo ""$mypwd"/nextflow run  "$mypwd"/vAMPirus.nf -c  "$mypwd"/vampirus.config -profile conda,test --Analyze -resume" >> EXAMPLE_COMMANDS.txt
      echo "   " >> EXAMPLE_COMMANDS.txt
      echo "Or if you plan to run vAMPirus using Singularity, use this test command:" >> EXAMPLE_COMMANDS.txt
      echo "   " >> EXAMPLE_COMMANDS.txt
      echo ""$mypwd"/nextflow run  "$mypwd"/vAMPirus.nf -c  "$mypwd"/vampirus.config -profile singularity,test --Analyze -resume" >> EXAMPLE_COMMANDS.txt
      echo "--------------------------------------------------------------------------------------------------------------------------------" >> EXAMPLE_COMMANDS.txt
      echo "   " >> EXAMPLE_COMMANDS.txt
      echo "Ok, if everything went well (green text was spit out by Nextflow), now you can move on to the fun. First, you should review the help docs and the vampirus.config in the vAMPirus directory." >> EXAMPLE_COMMANDS.txt
      echo "   " >> EXAMPLE_COMMANDS.txt
      echo "-------------------------------------------------------------------------------------------------------------------------------- RUNNING DataCheck PIPELINE WITH YOUR DATA" >> EXAMPLE_COMMANDS.txt
      echo "If everything looks good, here are a example lanch commands to submit after testing installation and editing the paths to your data and other parameters for the run in the vampirus.config file:"
      echo "   " >> EXAMPLE_COMMANDS.txt
      echo "First, run the DataCheck part of the pipeline using the -with-conda Nextflow option:" >> EXAMPLE_COMMANDS.txt
      echo "   " >> EXAMPLE_COMMANDS.txt
      echo ""$mypwd"/nextflow run  "$mypwd"/vAMPirus.nf -c  "$mypwd"/vampirus.config -with-conda "$environment" --DataCheck" >> EXAMPLE_COMMANDS.txt
      echo "   " >> EXAMPLE_COMMANDS.txt
      echo "OR using -profile option of Nextflow ..." >> EXAMPLE_COMMANDS.txt
      echo ""$mypwd"/nextflow run  "$mypwd"/vAMPirus.nf -c  "$mypwd"/vampirus.config -profile [conda|singularity] --DataCheck" >> EXAMPLE_COMMANDS.txt
      echo "   " >> EXAMPLE_COMMANDS.txt
      echo "--------------------------------------------------------------------------------------------------------------------------------" >> EXAMPLE_COMMANDS.txt
      echo "   " >> EXAMPLE_COMMANDS.txt
      echo "-------------------------------------------------------------------------------------------------------------------------------- RUNNING Analyze PIPELINE WITH YOUR DATA" >> EXAMPLE_COMMANDS.txt
      echo "Then you can run the analysis using the -with-conda Nextflow option, here is a launch command to run the complete analysis and statistical tests:" >> EXAMPLE_COMMANDS.txt
      echo "   " >> EXAMPLE_COMMANDS.txt
      echo ""$mypwd"/nextflow run  "$mypwd"/vAMPirus.nf -c  "$mypwd"/vampirus.config -with-conda "$environment" --Analyze --ncASV --pcASV --stats" >> EXAMPLE_COMMANDS.txt
      echo "   " >> EXAMPLE_COMMANDS.txt
      echo "OR same command using -profile option of Nextflow ..." >> EXAMPLE_COMMANDS.txt
      echo "   " >> EXAMPLE_COMMANDS.txt
      echo ""$mypwd"/nextflow run  "$mypwd"/vAMPirus.nf -c  "$mypwd"/vampirus.config -profile [conda|singularity] --Analyze --ncASV --pcASV --stats" >> EXAMPLE_COMMANDS.txt
      echo "   " >> EXAMPLE_COMMANDS.txt
      echo "--------------------------------------------------------------------------------------------------------------------------------" >> EXAMPLE_COMMANDS.txt
fi
echo "    "
echo "Setup script is complete!"
echo "Check out the EXAMPLE_COMMANDS.txt file for more information on how to move forward with the analysis."