Malware Repository Framework (MRF) is a malware repository website, useful to manage your own malware zoo (for malware researchers mostly)
If you are feeling difficulties handling large amount of malware samples, MRF would be one of good solution. It supports virustotal api and even cuckoo sandbox auto analysis. Even though there are some issues like storing all samples in one directory, non-ascii character file name missing, MRF has its own support forum and in my case, developer replied on my thread in less than one day.
You can install MRF open source version (free) or premium version (49.5$/m). MRF also offers video install instruction. You can download MRF here