CLE@R (Curricular Linux Environment at Rice) (Rice login required) is a Linux cluster available for the Linux-based needs of classes. For research needs, the Research Computing Clusters are more suitable.
Subversion is a version control system that can store documents of all varieties.
Turnin can be enabled on a subversion repository. This will automatically configure your repository to give each student in your course access to a protected folder within the repository and will manage the permissions so that Instructors and TAs have access to these student folders.