Container bind mounts

Default bind paths

By default, only a few files are writable from the container (listed here).

Configuring SMRT Link directories

SMRT Link directories

The SL installation process includes the designation of several directories which SL will use for storage, etc. By default, these directories are created within the installation directory (pointed to by $SMRT_ROOT). However, this is not sufficient for the production instance of SL.

Container configuration

To allow SL to write to an arbitrary directory, this directory must be made accessible to the container using bind mounts (unless it is one of the default bind mounts or below a default bind mount).