Command Line Interface

The biobricks cli has global and local commands.


Commands like configure, version, install that are not specific to a directory.

When using a command like install, uninstall and assets, you can use a brickref to refer to the asset you want to install.

Run biobricks with no commands for a help message.

$ biobricks
Usage: biobricks [OPTIONS] COMMAND [ARGS]...

  --help  Show this message and exit.

GLOBAL: modify global config and installed bricks:
  configure  configure brick path and token
  install    Install a data dependency
  uninstall  Uninstall a data dependency
  assets     List assets in a data dependency
  version    Get version and check for updates

LOCAL: build new bricks and manage their dependencies:
  init       Initialize a .bb directory for data dependencies
  add        Import a data dependency
  pull       install local dependencies
  status     Show the status of the local brick


Commands for building a new brick with dependencies on other bricks.


Initializes a new brick repository by creating a .bb directory in the current directory and adding .bb/dependencies.txt

$ biobricks init


Adds a brickref to the dependencies.txt file.

$ biobricks add <brickref>


Installs all the bricks references in the dependencies.txt.

$ biobricks pull