execute¶

Command-line tool¶

Boutiques local executor

usage: bosh execute [--help] {launch,simulate,prepare}

Positional Arguments¶

mode

Possible choices: launch, simulate, prepare

Mode of operation to use. Launch: takes a set of inputs compliant with invocation schema and launches the tool. Simulate: shows sample command-lines based on the provided descriptor based on provided or randomly generated inputs. Prepare: pulls the Docker or Singularity container image for a given descriptor.

Named Arguments¶

--help, -h

show this help message and exit

Default: False

execute launch¶

Launches an invocation.

usage: bosh execute launch [-h] [-v VOLUMES] [-x] [-u] [-s]
                           [--imagepath IMAGEPATH] [--skip-data-collection]
                           [--provenance PROVENANCE] [--no-container]
                           [--sandbox] [--force-docker | --force-singularity]
                           descriptor invocation

Positional Arguments¶

descriptor: The Boutiques descriptor as a JSON file, JSON string or Zenodo ID (prefixed by ‘zenodo.’).
invocation: Input JSON complying to invocation.

Named Arguments¶

-v, --volumes

Volumes to mount when launching the container. Format consistently the following: /a:/b will mount local directory /a to container directory /b.

-x, --debug

Keeps temporary scripts used during execution, and prints additional debug messages.

Default: False

-u, --user

Runs the container as local user (glatard) instead of root.

Default: False

-s, --stream

Streams stdout and stderr in real time during execution.

Default: False

--imagepath

Path to Singularity image. If not specified, will use current directory.

--skip-data-collection

Skips execution data collection and savingto cache.

Default: False

--provenance

Append JSON object to the generated record.

--no-container

Launch invocation on the host computer, with no container. If ‘container-image’ appears in the descriptor, it is ignored.

Default: False

--sandbox

Get descriptor from Zenodo’s sandbox instead of production server.

Default: False

--force-docker

Tries to run Singularity images with Docker. This only works if the image is onDocker Hub, i.e. has index docker://

Default: False

--force-singularity

Tries to run Docker images with Singularity.

Default: False

execute prepare¶

Pulls the container image for a given descriptor

usage: bosh execute prepare [-h] [-x] [-s] [--imagepath IMAGEPATH] [--sandbox]
                            descriptor

Positional Arguments¶

descriptor: The Boutiques descriptor as a JSON file, JSON string or Zenodo ID (prefixed by ‘zenodo.’).

Named Arguments¶

-x, --debug

Keeps temporary scripts used during execution, and prints additional debug messages.

Default: False

-s, --stream

Streams stdout and stderr in real time during execution.

Default: False

--imagepath

Path to Singularity image. If not specified, will use current directory.

--sandbox

Get descriptor from Zenodo’s sandbox instead of production server.

Default: False

execute simulate¶

Simulates an invocation.

usage: bosh execute simulate [-h] [-i INPUT] [-j] [-c] [--sandbox] descriptor

Positional Arguments¶

descriptor: The Boutiques descriptor as a JSON file, JSON string or Zenodo ID (prefixed by ‘zenodo.’).

Named Arguments¶

-i, --input

Input JSON complying to invocation.

-j, --json

Flag to generate invocation in JSON format.

Default: False

-c, --complete

Include optional parameters.

Default: False

--sandbox

Get descriptor from Zenodo’s sandbox instead of production server.

Default: False

Python API¶

boutiques.execute(*params): Refer to the Command-line tool section above