Command Line Interface Reference

crunch

crunch [OPTIONS] COMMAND [ARGS]...

Options

--install-completion: Install completion for the current shell.

--show-completion: Show completion for the current shell, to copy it or customize the installation.

add-boolean-attribute

Adds a new boolean attribute to an item.

crunch add-boolean-attribute [OPTIONS] ITEM KEY VALUE

Options

--verbose, --no-verbose

Default: True

--url <url>: Required The URL for the endpoint for the project on the crunch hosted site.

--token <token>: Required An access token for a user on the hosted site.

Arguments

ITEM: Required argument The slug for the item. STRING

KEY: Required argument The key for this attribute. STRING

VALUE: Required argument The value of this attribute. BOOL

Environment variables

CRUNCH_URL: Provide a default for --url

CRUNCH_TOKEN: Provide a default for --token

add-char-attribute

Adds a new char attribute to an item.

crunch add-char-attribute [OPTIONS] ITEM KEY VALUE

Options

--verbose, --no-verbose

Default: True

--url <url>: Required The URL for the endpoint for the project on the crunch hosted site.

--token <token>: Required An access token for a user on the hosted site.

Arguments

ITEM: Required argument The slug for the item. STRING

KEY: Required argument The key for this attribute. STRING

VALUE: Required argument The value of this attribute. STRING

Environment variables

CRUNCH_URL: Provide a default for --url

CRUNCH_TOKEN: Provide a default for --token

add-dataset

Adds a new dataset to a project on the hosted site.

crunch add-dataset [OPTIONS] PROJECT DATASET

Options

--description <description>

A brief description of this new dataset.

Default

--details <details>

A long description of this dataset in Markdown format.

Default

--verbose, --no-verbose

Default: True

--url <url>: Required The URL for the endpoint for the project on the crunch hosted site.

--token <token>: Required An access token for a user on the hosted site.

Arguments

PROJECT: Required argument The slug of the project that this dataset is to be added to. STRING

DATASET: Required argument The name of the new dataset STRING

Environment variables

CRUNCH_URL: Provide a default for --url

CRUNCH_TOKEN: Provide a default for --token

add-date-attribute

Adds a new date attribute to an item.

crunch add-date-attribute [OPTIONS] ITEM KEY VALUE

Options

--format <format>

Default

--verbose, --no-verbose

Default: True

--url <url>: Required The URL for the endpoint for the project on the crunch hosted site.

--token <token>: Required An access token for a user on the hosted site.

Arguments

ITEM: Required argument The slug for the item. STRING

KEY: Required argument The key for this attribute. STRING

VALUE: Required argument The value of this attribute. STRING

Environment variables

CRUNCH_URL: Provide a default for --url

CRUNCH_TOKEN: Provide a default for --token

add-datetime-attribute

Adds a new datetime attribute to an item.

crunch add-datetime-attribute [OPTIONS] ITEM KEY VALUE

Options

--format <format>

Default

--verbose, --no-verbose

Default: True

--url <url>: Required The URL for the endpoint for the project on the crunch hosted site.

--token <token>: Required An access token for a user on the hosted site.

Arguments

ITEM: Required argument The slug for the item. STRING

KEY: Required argument The key for this attribute. STRING

VALUE: Required argument The value of this attribute. STRING

Environment variables

CRUNCH_URL: Provide a default for --url

CRUNCH_TOKEN: Provide a default for --token

add-filesize-attribute

Adds a new filesize attribute to an item.

crunch add-filesize-attribute [OPTIONS] ITEM KEY VALUE

Options

--verbose, --no-verbose

Default: True

--url <url>: Required The URL for the endpoint for the project on the crunch hosted site.

--token <token>: Required An access token for a user on the hosted site.

Arguments

ITEM: Required argument The slug for the item. STRING

KEY: Required argument The key for this attribute. STRING

VALUE: Required argument The value of this attribute. INT

Environment variables

CRUNCH_URL: Provide a default for --url

CRUNCH_TOKEN: Provide a default for --token

add-float-attribute

Adds a new float attribute to an item.

crunch add-float-attribute [OPTIONS] ITEM KEY VALUE

Options

--verbose, --no-verbose

Default: True

--url <url>: Required The URL for the endpoint for the project on the crunch hosted site.

--token <token>: Required An access token for a user on the hosted site.

Arguments

ITEM: Required argument The slug for the item. STRING

KEY: Required argument The key for this attribute. STRING

VALUE: Required argument The value of this attribute. FLOAT

Environment variables

CRUNCH_URL: Provide a default for --url

CRUNCH_TOKEN: Provide a default for --token

add-integer-attribute

Adds a new integer attribute to an item.

crunch add-integer-attribute [OPTIONS] ITEM KEY VALUE

Options

--verbose, --no-verbose

Default: True

--url <url>: Required The URL for the endpoint for the project on the crunch hosted site.

--token <token>: Required An access token for a user on the hosted site.

Arguments

ITEM: Required argument The slug for the item. STRING

KEY: Required argument The key for this attribute. STRING

VALUE: Required argument The value of this attribute. INT

Environment variables

CRUNCH_URL: Provide a default for --url

CRUNCH_TOKEN: Provide a default for --token

add-item

Adds a new item to an item on the hosted site.

crunch add-item [OPTIONS] PARENT ITEM

Options

--description <description>

A brief description of this new item.

Default

--details <details>

A long description of this item in Markdown format.

Default

--verbose, --no-verbose

Default: True

--url <url>: Required The URL for the endpoint for the project on the crunch hosted site.

--token <token>: Required An access token for a user on the hosted site.

Arguments

PARENT: Required argument The slug of the item that this item is to be added to. STRING

ITEM: Required argument The name of the new item STRING

Environment variables

CRUNCH_URL: Provide a default for --url

CRUNCH_TOKEN: Provide a default for --token

add-lat-long-attribute

Adds a new lat-long coorinate as an attribute to an item.

crunch add-lat-long-attribute [OPTIONS] ITEM KEY LATITUDE LONGITUDE

Options

--verbose, --no-verbose

Default: True

--url <url>: Required The URL for the endpoint for the project on the crunch hosted site.

--token <token>: Required An access token for a user on the hosted site.

Arguments

ITEM: Required argument The slug for the item. STRING

KEY: Required argument The key for this attribute. STRING

LATITUDE: Required argument The latitude of the coordinate in decimal degrees. STRING

LONGITUDE: Required argument The longitude of the coordinate in decimal degrees. STRING

Environment variables

CRUNCH_URL: Provide a default for --url

CRUNCH_TOKEN: Provide a default for --token

add-project

Adds a new project on the hosted site.

crunch add-project [OPTIONS] PROJECT

Options

--description <description>

A brief description of this new project.

Default

--details <details>

A long description of this project in Markdown format.

Default

--verbose, --no-verbose

Default: True

--url <url>: Required The URL for the endpoint for the project on the crunch hosted site.

--token <token>: Required An access token for a user on the hosted site.

Arguments

PROJECT: Required argument The name of the new crunch project. STRING

Environment variables

CRUNCH_URL: Provide a default for --url

CRUNCH_TOKEN: Provide a default for --token

add-url-attribute

Adds a new URL attribute to an item.

crunch add-url-attribute [OPTIONS] ITEM KEY VALUE

Options

--verbose, --no-verbose

Default: True

--url <url>: Required The URL for the endpoint for the project on the crunch hosted site.

--token <token>: Required An access token for a user on the hosted site.

Arguments

ITEM: Required argument The slug for the item. STRING

KEY: Required argument The key for this attribute. STRING

VALUE: Required argument The value of this attribute. STRING

Environment variables

CRUNCH_URL: Provide a default for --url

CRUNCH_TOKEN: Provide a default for --token

diagnostics

Display system diagnostics.

crunch diagnostics [OPTIONS]

files

Displays the files for a dataset.

crunch files [OPTIONS] DATASET

Options

--storage-settings <storage_settings>: Required The path to a JSON or TOML file with the Django settings for the storage.

--url <url>: Required The URL for the endpoint for the project on the crunch hosted site.

--token <token>: Required An access token for a user on the hosted site.

Arguments

DATASET: Required argument The slug for the dataset. STRING

Environment variables

CRUNCH_STORAGE_SETTINGS: Provide a default for --storage-settings

CRUNCH_URL: Provide a default for --url

CRUNCH_TOKEN: Provide a default for --token

loop

Loops through all the datasets in a project and stops when complete.

crunch loop [OPTIONS]

Options

--storage-settings <storage_settings>: Required The path to a JSON or TOML file with the Django settings for the storage.

--directory <directory>

The path to a directory to store the temporary files.

Default: ./tmp

--cores <cores>

The maximum number of cores/jobs to use to run the workflow. If ‘all’ then it uses all available cores.

Default: 1

--url <url>: Required The URL for the endpoint for the project on the crunch hosted site.

--token <token>: Required An access token for a user on the hosted site.

--project <project>

The slug for a project the dataset is in. If not given, then it chooses any project.

Default

--workflow <workflow>

Workflow type (snakemake/script).

Default: snakemake
Options: snakemake | script

--path <path>: The path to the workflow file.

--download, --no-download

Whether or not to download the data from storage in the setup of a run.

Default: True

--upload, --no-upload

Whether or not to upload the data to storage after a run.

Default: True

--cleanup, --no-cleanup

Whether or not to delete the local data after a run.

Default: False

Environment variables

CRUNCH_STORAGE_SETTINGS: Provide a default for --storage-settings

CRUNCH_URL: Provide a default for --url

CRUNCH_TOKEN: Provide a default for --token

next

Processes the next dataset in a project.

crunch next [OPTIONS]

Options

--storage-settings <storage_settings>: Required The path to a JSON or TOML file with the Django settings for the storage.

--directory <directory>

The path to a directory to store the temporary files.

Default: ./tmp

--cores <cores>

The maximum number of cores/jobs to use to run the workflow. If ‘all’ then it uses all available cores.

Default: 1

--url <url>: Required The URL for the endpoint for the project on the crunch hosted site.

--token <token>: Required An access token for a user on the hosted site.

--project <project>

The slug for a project the dataset is in. If not given, then it chooses any project.

Default

--workflow <workflow>

Workflow type (snakemake/script).

Default: snakemake
Options: snakemake | script

--path <path>: The path to the workflow file.

--download, --no-download

Whether or not to download the data from storage in the setup of a run.

Default: True

--upload, --no-upload

Whether or not to upload the data to storage after a run.

Default: True

--cleanup, --no-cleanup

Whether or not to delete the local data after a run.

Default: False

Environment variables

CRUNCH_STORAGE_SETTINGS: Provide a default for --storage-settings

CRUNCH_URL: Provide a default for --url

CRUNCH_TOKEN: Provide a default for --token

run

Processes a dataset.

crunch run [OPTIONS] DATASET

Options

--storage-settings <storage_settings>: Required The path to a JSON or TOML file with the Django settings for the storage.

--directory <directory>

The path to a directory to store the temporary files.

Default: ./tmp

--cores <cores>

The maximum number of cores/jobs to use to run the workflow. If ‘all’ then it uses all available cores.

Default: 1

--url <url>: Required The URL for the endpoint for the project on the crunch hosted site.

--token <token>: Required An access token for a user on the hosted site.

--workflow <workflow>

Workflow type (snakemake/script).

Default: snakemake
Options: snakemake | script

--path <path>: The path to the workflow file.

--download, --no-download

Whether or not to download the data from storage in the setup of a run.

Default: True

--upload, --no-upload

Whether or not to upload the data to storage after a run.

Default: True

--cleanup, --no-cleanup

Whether or not to delete the local data after a run.

Default: False

Arguments

DATASET: Required argument The slug for the dataset. STRING

Environment variables

CRUNCH_STORAGE_SETTINGS: Provide a default for --storage-settings

CRUNCH_URL: Provide a default for --url

CRUNCH_TOKEN: Provide a default for --token