Root vs. Directory. A root generally implies some sort of inheritance throughout a tree of directories. A directory identifies just one spot in the file system.

LabKey installation directory. The default directory in the file system for LabKey Server that contains folders for files, modules, the webapp, etc. Sometimes referred to as [LABKEY_HOME]. (Example: /data/labkey or C:labkey)

Site-level file root. The directory in the LabKey Server's file system that contains your server's file directory structure (Example: /data/labkey/files). It can be set, typically at install time. This location is called a root, not just a directory, because it determines where the tree of file directories lives, not just the location of a single directory. The structure reflects your server's tree of projects and folders. See: Set File Roots.

File directory. The specific location on the file system where files associated with a particular project or folder are placed. (Example: /data/labkey/files/project1/folder1/@files, where the folder of interest is folder1, a child of project1.) See: Set File Roots.

File root. The directory in LabKey Server's file system that contains your project's file directory structure. (Example: /data/labkey/otherdata/project1/) This structure contains file directories in subfolders that match the structure of your project. See: Set File Roots.

File root override. A custom destination for files for a given project. Can be set at the project level only. (Example: /data/labkey/otherdata/project1/myfiles). If a file root override is set, this root determines the the location of the tree of file directories for that project's subfolders. See: Set File Roots.

Data processing pipeline. Provides a set of actions that can be performed against a given file. See: Data Processing Pipeline.

Pipeline override. An explicitly set location for files that are subject to actions. Also determines the location where files are uploaded when uploaded via the pipeline UI. Allows security to be set separately vs. the default, folder-specific permissions. See Set a Pipeline Override.

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