To install pyxy-gallery, simply unzip the .php file and move it into a directory on your web server with lots of images in it.
Pyxy-gallery will automatically download the file prototype.js and place it in the directory where you installed pyxy. If you do not want this to happen, set $pref['autoinstall'] = 0;, as described below. If the automatic installation fails, you will need to download this file yourself and install it as prototype.js. (You don't need to turn off the autoinstaller if you do this.)
— lightbox.js support —
lightbox.js cannot be automatically installed. There are several files involved, and some of them are images- and chances are you don't want these images showing up in your gallery.
If you would like to install lightbox.js, you should download it from the official lightbox.js site and place it a directory somewhere in your web server. Then, set $pref['lightbox_path'] to that directory (be sure to use a trailing slash!). For example, on fennecfoxen.org I installed lightbox.js into /shiny/js/lightbox, so I would set $pref['lightbox_path'] = '/shiny/js/lightbox/'. Finally, set $pref['lightbox_ver'] to either 1 or 2, depending on which version of Lightbox you use.
You may also need to edit the lightbox.js file to reference the images that lightbox.js uses. Update the lines that set var loadingImage and var closeButton so that they point to an actual image file. This is necessary for the animated progress bar and Close button to appear.