install

#!/usr/bin/env bash
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"

echo "[+] Checking dependencies..."
wget=$(which wget)
if [ -x "$wget" ] ; then
    echo "    [+] [wget] $wget"; else
    echo "    [X] [wget] ... please install wget";
fi
gunzip=$(which gunzip)
if [ -x "$gunzip" ] ; then
    echo "    [+] [gunzip] $gunzip"; else
    echo "    [X] [gunzip] ... please install gunzip";
fi

# Download files
echo "[+] Checking data files..."
pfam_dest=$DIR/data/Pfam-A.clans.tsv.gz
ipr_dest=$DIR/data/entry.list
go_dest=$DIR/data/interpro2go
nodesdbgz=$DIR/data/nodesdb.gz
nodesdb=$DIR/data/nodesdb.txt
if [ -f "$nodesdb" ]; then
    echo "    [+] $nodesdb"
else
    if [ -f "$nodesdbgz" ]; then
        echo -n "    [+] Extracting $nodesdbgz ..."
        $gunzip -c $nodesdbgz > $nodesdb
        if [ $? -eq 0 ]; then
            echo "done."
        else
            echo "FAIL... Please download kinfin again."
            exit 1
        fi
    else
        echo "[-] $nodesdbgz not found... Please download kinfin again."
            exit 1
    fi
fi

if [ -f "$pfam_dest" ]; then
    echo "    [+] $pfam_dest"
else
    echo -n "    [-] $pfam_dest. Downloading ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.clans.tsv.gz ..."
    $wget -qN ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.clans.tsv.gz -P $DIR/data/
    if [ $? -eq 0 ]; then
        echo "done."
    else
        echo "FAIL."
    fi
fi

if [ -f "$ipr_dest" ]; then
    echo "    [+] $ipr_dest"
else
    echo -n "    [-] $ipr_dest. Downloading ftp://ftp.ebi.ac.uk/pub/databases/interpro/current_release/entry.list ..."
    $wget -qN ftp://ftp.ebi.ac.uk/pub/databases/interpro/current_release/entry.list -P $DIR/data/
    if [ $? -eq 0 ]; then
        echo "done."
    else
        echo "FAIL."
    fi
fi

if [ -f "$go_dest" ]; then
    echo "    [+] $go_dest"
else
    echo -n "    [-] $go_dest. Downloading ftp://ftp.ebi.ac.uk/pub/databases/interpro/current_release/interpro2go ... "
    $wget -qN ftp://ftp.ebi.ac.uk/pub/databases/interpro/current_release/interpro2go -P $DIR/data/
    if [ $? -eq 0 ]; then
        echo "done."
    else
        echo "FAIL."
    fi
fi

# Create executable
echo "[+] Creating executable..."
echo '#!/usr/bin/env bash
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
$DIR/src/kinfin.py "$@"' > $DIR/kinfin && chmod +x $DIR/kinfin

# Done
echo "[+] Kinfin was installed. Please run ./kinfin"