What do you need?
-
Apache (mod_rewrite + allowoverride)
-
PHP 5.4 (cURL + mcrypt + memcache)
-
MySQL (optional for blacklist).
-
CloudFlare (optional but highly recommended)
Instructions:
Step 1: upload megacrypter to your server.
Step 2: prepare virtual host (set document root point to megacrypter public dir)
Step 3: install composer dependencies -> php composer.phar install
Step 4: remove ALL /config .sample extension and edit miscellaneous.php and any other file you need.
Step 5 (optional): ask developers of your favourite download manager to recognize your new megacrypter links.
You're alone from here. Good luck!

