Command-line interface

The main Pimlico command-line interface (usually accessed via pimlico.sh in your project root) provides subcommands to perform different operations. Call it like so, using one of the subcommands documented below to access particular functionality:

./pimlico.sh <config-file> [general options...] <subcommand> [subcommand args/options]

The commands you are likely to use most often are: status, run, reset and maybe browse.

For a reference for each command’s options, see the command-line documentation: ./pimlico.sh --help, for a general reference and ./pimlico.sh <config_file> <command> --help for a specific subcommand’s reference.

Below is a more detailed guide for each subcommand, including all of the documentation available via the command line.

browse View the data output by a module
clean Remove all module output directories that do not correspond to a module in the pipeline
deps List information about software dependencies: whether they’re available, versions, etc
dump Dump the entire available output data from a given pipeline module to a tarball
email Test email settings and try sending an email using them
inputs Show the (expected) locations of the inputs of a given module
install Install missing module library dependencies
load Load a module’s output data from a tarball previously created by the dump command
movestores Move data between stores
newmodule Create a new module type
output Show the location where the given module’s output data will be (or has been) stored
python Load the pipeline config and enter a Python interpreter with access to it in the environment
recover Examine and fix a partially executed map module’s output state after forcible termination
reset Delete any output from the given module and restore it to unexecuted state
run Execute an individual pipeline module, or a sequence
shell Open a shell to give access to the data output by a module
status Output a module execution schedule for the pipeline and execution status for every module
stores List named Pimlico stores
unlock Forcibly remove an execution lock from a module
variants List the available variants of a pipeline config
visualize Comming soon…visualize the pipeline in a pretty way