Probably one of the first hurdles you'll come across when first looking to start an online store is whether to go for an "off the shelf" package or for a bespoke, custom solution. Both options have their merits and pitfalls...
Off The Shelf Package
With an off the shelf solution the hard work is done for you. They come with many features and have usually been tested by all the users who have used them before. Installation is usually straight-forward and quick, giving you a working online store within minutes. This will save you a lot of time and usually money too.
Before getting too excited however, there can be complexities. Firstly, you will no doubt want to change the default template to your own custom design to suit your needs. Some packages can be extremely complex when it comes to editing templates, some will be limited a great deal as to what you can change, and some will come with template coding languages built in giving you an extra learning curve to deal with. It's essential you have a good look at the templating abilities of a package before comitting to it. See what you can do, what you can't do, and what's going to be difficult.
Secondly, packages will be limited somewhat in what features they offer you. If there is a feature you really want to include, but is not available with your chosen package, you may run into difficulties editing the package's code and extending it to suit your needs - or it may not even be possible! Equally they may offer a lot more than you want to have. Be sure to check that a package has all the features you need, the ability to disable features you don't want, and see how easy it is to add your own features or "extensions" if you want or need to.
Bespoke Solution
Your other option is a fully bespoke solution just for you. Whether you develop it yourself or commission development company, you can be sure it will fill your needs, look how you want it to look and operate just how you want it to.
There are disadvantages though. Custom solutions take time to develop, and therefore money too. If you commission the work you will find the cost a great deal higher than an off the shelf package. There may also be some security issues if it is not thoroughly and vigorously tested - as at the end of the day you will be dealing with people's personal information and taking payments (either on your own server or via a payment gateway), you do not want to have to deal with missing orders and angry customers!
What Should I Go For?
Your best bet is to ask yourself if you have the budget for a custom solution? (Or indeed the ability and time). If you do not then an off the shelf package is the only option really. Even if you think you do need a custom solution, I would take a look at the software available anyway to see what it offers. A quick search on google and a poke around hotscripts.com should provide you with plenty to whet your appetite.
Personally I think the majority of store owners are better off working with an off the shelf package. Even though I am yet to find one that I can say is a great product, I don't think it's worth re-inventing the wheel with your own solution if you can pick up a package that already does it immediately.
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