EasyLink Command-Line Interface
easylink
The command line entrypoint to the EasyLink utility.
Usage
easylink [OPTIONS] COMMAND [ARGS]...
run
Runs a pipeline from the command line.
In addition to running the pipeline, this command will also generate the directed
acyclic graph (DAG) image. If you only want to generate the image without actually
running the pipeline, use the easylink generate-dag command.
Usage
easylink run [OPTIONS]
Options
- --no-timestamp
Do not save the results in a timestamped sub-directory of
--output-dir.
- -o, --output-dir <output_dir>
The directory to write results and incidental files (logs, etc.) to. If no value is passed, results will be written to a ‘results/’ directory in the current working directory.
- -i, --input-data <input_data>
Required The path to the input data specification YAML file (not the paths to the input data themselves).
- -p, --pipeline-specification <pipeline_specification>
Required The path to the pipeline specification YAML file.
- -e, --computing-environment <computing_environment>
Path to the computing environment specification YAML file. If no value is passed, the pipeline will be run locally.
generate-dag
Generates an image of the proposed pipeline directed acyclic graph (DAG).
This command only generates the DAG image of the pipeline; it does not actually
run it. To run the pipeline, use the easylink run command.
Usage
easylink generate-dag [OPTIONS]
Options
- --no-timestamp
Do not save the results in a timestamped sub-directory of
--output-dir.
- -o, --output-dir <output_dir>
The directory to write results and incidental files (logs, etc.) to. If no value is passed, results will be written to a ‘results/’ directory in the current working directory.
- -i, --input-data <input_data>
Required The path to the input data specification YAML file (not the paths to the input data themselves).
- -p, --pipeline-specification <pipeline_specification>
Required The path to the pipeline specification YAML file.
easylink.cli module
This module is responsible for defining the command line interface (CLI) for running
the EasyLink utility. We use the click
library to define the commands and their respective options. All commands are accessible
via the easylink group.
Once installed, you can run a pipeline by typing easylink run into the command
line and passing in the paths to both a pipeline specification and an input data
specification:
$ easylink run -p <PIPELINE-SPECIFICATION> -i <INPUT-DATA-SPECIFICATION>
There are several other optional arguments to easylink run as well;
for help, use easylink run --help. Notably, there is an optional argument to
change where the results are saved (-o) as well as one to configure the computing
environment (-e).
Note that a schematic of the pipeline’s directed acyclic graph (DAG) is automatically
generated and saved to the output directory as an SVG file which can be rendered
by most internet browsers. If this schematic is desired _without_ actually running
the pipeline, use easylink generate-dag:
$ easylink generate-dag -p <PIPELINE-SPECIFICATION> -i <INPUT-DATA-SPECIFICATION
As before, refer to easylink generate-dag --help for information on other options.
For usage documentation, see EasyLink Command-Line Interface.