Runnig javascript files located on my server via node js command prompt

I want to configure an app that requires that I run node generate.js and node generate_texts_index.js on node's command prompt. These files are to build the data required for the app to work. When i run these files locally the app works in my browser. Now I have the same set of files located on my server, how can I run node generate.js when the files are on my server at www.example.com. I am new to node js. Thanks!

Here's what generate.js looks like

// MODULES
var fs = require('fs'),
    path = require('path'),
    bibleData = require('bible_data');


//console.log( bibleData.getBookInfoByUnboundCode('40N') );
//return;


// VARS
var
    baseOutput = '../../app/content/texts/',
    baseInput = 'input',
    createIndex = true;

console.log('\r\r\r');

function convertFolder(inputPath) {

    var infoFilePath = path.join(inputPath, 'info.json'),
        startDate = new Date();

    if (fs.existsSync(infoFilePath)) {

        var info = JSON.parse( fs.readFileSync(infoFilePath, 'utf8') ),
            generatorName = info.generator,
            generator = require('generate_' + generatorName),
            outputPath = path.join(baseOutput, info['id']),
            indexOutputPath = path.join(outputPath, 'index');

        console.log('-----');
        console.log(info['name'],  outputPath);

        // remove existing data
        if (fs.existsSync(outputPath)) {
            var files = fs.readdirSync(outputPath);

            // DELETE all files
            files.forEach(function(data) {
                var filePath = path.join(outputPath, data);
                if (fs.statSync(filePath).isFile()) {
                    fs.unlinkSync(filePath);                
                }
            });
        } else {
            fs.mkdirSync(outputPath);
        }

        // index data
        if (createIndex) {      
            if (fs.existsSync(indexOutputPath)) {
                var files = fs.readdirSync(indexOutputPath);

                // DELETE all files
                files.forEach(function(data) {
                    var filePath = path.join(indexOutputPath, data);
                    if (fs.statSync(filePath).isFile()) {
                        fs.unlinkSync(filePath);                
                    }
                });         
            } else {
                fs.mkdirSync(indexOutputPath);
            }           
        }

        generator.generate(inputPath, outputPath, indexOutputPath, info, createIndex);

        var endDate = new Date();       
        console.log('time: ' + MillisecondsToDuration(endDate - startDate));            
    }   
}

function convertFolders() {
    var files = fs.readdirSync(baseInput),
        startDate = new Date();

    // DO ALL
    for (var f in files) {
        var folder = files[f],
            inputPath = path.join(baseInput, folder);

        convertFolder(inputPath);
    }   

    var endDate = new Date();

    console.log('TOTAL: ' + MillisecondsToDuration(endDate - startDate));
}


function MillisecondsToDuration(n) {
    var hms = "";
    var dtm = new Date();
    dtm.setTime(n);

    var h = "000" + Math.floor(n / 3600000);
    var m = "0" + dtm.getMinutes();
    var s = "0" + dtm.getSeconds();
    var cs = "0" + Math.round(dtm.getMilliseconds() / 10);

    hms = h.substr(h.length-4) + ":" + m.substr(m.length-2) + ":";
    hms += s.substr(s.length-2) + "." + cs.substr(cs.length-2);

    return hms;
}


// START


// make /texts/ folder
if (!fs.existsSync(baseInput)) {
    fs.mkdirSync(baseInput);
}


// process 1 or more folders
if (process.argv.length > 2) {

    var folders = process.argv[2].split(',');

    folders.forEach(function(folder) {
        convertFolder(baseInput + '/' + folder);    
    });


} else {
    convertFolders();       
}