Use symbolic links

A brief introduction to best practices in data management using symbolic links.

We describe symbolic links in the section Link to files and directories.

Briefly, a symbolic link is a shortcuts to target file or directory.

The link itself is materialised as a very small file that only indicates the location of the target file.

As such:

  • The size of the target file does not impact in any way the size of the symbolic link.
  • A symbolic link will always be smaller than the target data file, or a copy of that file (unless the target file is empty).

A symbolic links make the target file accessible from a different location (i.e., directory) without the need to make a copy of the file, greatly reducing disk usage.

We describe the creation of symbolic links in the section Creating soft links.

Briefly:

ln -s target_file.txt link_file.txt

Symbolic links can be used in place of the original target file.

Often, symbolic links stored in the working directory offer a shorter alternative to longer file paths to target files located elsewhere in the filesystem.

For instance:

ln -s /path/to/target/file.txt link.txt
cat /path/to/target/file.txt
cat link.txt

In particular:

  • The ln -s command is used to create a symbolic link.
  • The two cat commands are entirely equivalent; the first command directly accesses the original file, while the second command follows the symbolic link ultimately accessing the same target file.

Best practices

Relative links should be used to create links within the project directory. In that way, links will remain valid even in the event that the project directory is moved.

Absolute links should be used only to link to files outside the project directory. Most commonly, absolute links are used to link to shared resources in stable locations (e.g., genome sequence, gene annotations).

Usage of absolute and relative links in projects.

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