AcetoScan_software_check.sh

#!/bin/bash

#   File: AcetoScan_software_check.sh
#   Last modified: Apr 1, 2020 10:00
#   Sign: Abhi

### User

    user="${SUDO_USER:-${USER}}"

### Checking if cutadapt is installed

    if ! command -v "cutadapt" > /dev/null ; then
        echo -ne "\n#\tError: cutadapt not found, Aborting !!!"
        exit 1
    fi

### Checking if vsearch is installed

    if ! command -v "vsearch" > /dev/null ; then
        echo -ne "\n#\tError: vsearch not found, Aborting !!!"
        exit 1
    fi

### Checking if Blast is installed

    if ! command -v "blastx" > /dev/null ; then
        echo -ne "\n#\tError: NCBI Blast+ (blastx) not found, Aborting !!!"
        exit 1
    fi

### Checking if Mafft is installed

    if ! command -v "mafft" > /dev/null ; then
        echo -ne "\n#\tError: Mafft not found, Aborting !!!"
        exit 1
    fi

### Checking if FastTree is installed

    if ! command -v "fasttree" > /dev/null ; then
        echo -ne "\n#\tError: Fasttree (2.1.9+) not found, Aborting !!!"
        exit 1
    fi

### Checking if Bioperl is installed

    if ! command -v perl -MBio::SeqIO -e 'printf "%vd\n", $Bio::SeqIO::VERSION, "\n"' > /dev/null ; then
    echo -ne "\n#\tError: Bioperl not found, Aborting !!!"
    exit 1
    fi

### Checking if R and Rscript are installed

    #   R program

    if ! command -v "R" > /dev/null ; then
        echo -ne "\n#\tError: R not found, Aborting !!!"
        exit 1
    fi

    #   Rscript

        if ! command -v "Rscript" > /dev/null ; then
            echo -ne "\n#\tError: Rscript not found, Aborting !!!"
            exit 1
        fi

### Checking if acetobase is formatted and accessible

    if [ ! -f "/Users/${user}/acetoscan/db/AcetoBase.phr" ];then
        echo -ne "\n#\tError: Cannot access acetobase"
        echo -ne "\n#\tTrying to Download AcetoBase"

    #   Downloading

        echo -e "#\tDownloading AcetoBase\n"
        wget --no-check-certificate -O "/Users/${user}/acetoscan/db/AcetoBase_ref.tar.gz" \
                https://acetobase.molbio.slu.se/download/ref/1
    #   Extracting

        echo -e "\n#\tExtracting AcetoBase\n"
        tar xvzf "/Users/${user}/acetoscan/db/"AcetoBase_ref.tar.gz -C "/Users/${user}/acetoscan/db/" --strip-components 1
        rm "/Users/${user}/acetoscan/db/"AcetoBase_ref.tar.gz

    #   Formatting blast database

        echo -e "\n#\tBuilding AcetoBase database"
        cd "/Users/${user}/acetoscan/db/" && makeblastdb -in AcetoBase.fasta -dbtype prot -title AcetoBase -out AcetoBase
        find "/Users/${user}/acetoscan/db/" -type f -name "AcetoBase*" -exec chmod +x {} \;

    fi

### Check complete

    echo -e "\n#\tEverything looks good\n"

### End of script