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From Command-line Agent v3.0.1 onwards, operation of the software is based around the syntax of commands. Each command encapsulates a specific behaviour and accepts a different set of options. Each of the commands also includes its own help text explaining what it does, what options it accepts and what they are used for.
Commands are composed in the format
<epi2me-binary-name> CATEGORY ACTION
. For example (assuming the binary has been renamed toepi2me
):epi2me workflows list
will display a list of workflows, and
epi2me workflows run
will execute a specified workflow.
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Accessing help
Help is available at every level of the application and is accessed by adding the keyword help at the end of any command. Help has the general form:
<epi2me-binary-name> help
<epi2me-binary-name> CATEGORY help
<epi2me-binary-name> CATEGORY ACTION help
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Example of ACTION help:
> ./epi2me-3.0.0-6800812 workflows detail help
Get the details of a workflow
USAGE: epi2me workflows detail [options] [arg1]
EXAMPLES:
epi2me workflows detail
epi2me workflows detail $WORKFLOW_ID
epi2me workflows detail $WORKFLOW_ID --docs
COMMANDS:
help Display help
version Display version
OPTIONS:
--apikey An apikey to use for authentication instead of a profile. Must be used with a apisecret.
--apisecret An apisecret to use for authentication instead of a profile. Must be used with a apikey.
--docs Print the documentation for the workflow, if it exists.
--h, --help Output usage information
--product ID of the product to use.
--profile The name of a local user profile to use for authentication.
--proxy Address of a network proxy to use.
--quiet Disable interactive prompts and omit supplementary output.
--region The region to run the given command in.
--v, --version Output the version number
--workflow ID of the workflow to use.
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Example of CATEGORY help:
> ./epi2me-3.0.0-6800812 workflows help
View workflows and start new instances
USAGE: epi2me workflows [options] [command]
EXAMPLES:
epi2me workflows
epi2me workflows list
epi2me workflows run $INPUT_1 $INPUT_2 ... $INPUT_N
epi2me workflows detail
epi2me workflows detail $WORKFLOW_ID
epi2me workflows detail $WORKFLOW_ID --docs
epi2me workflows favourite
epi2me workflows favourite $WORKFLOW_ID
epi2me workflows unfavourite
epi2me workflows unfavourite $WORKFLOW_ID
COMMANDS:
detail Get the details of a workflow
favourite Favourite a workflow
help Display help
list List all the available workflows
run Start a new analysis
unfavourite Unfavourite a workflow
version Display version
OPTIONS:
-h, --help Output usage information
-v, --version Output the version number
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Example of APPLICATION help:
> ./epi2me-3.0.0-6800812 help
USAGE: epi2me [options] [command]
EXAMPLES:
epi2me accounts
epi2me accounts list
epi2me datasets
epi2me datasets list
epi2me datasets detail
epi2me datasets detail $DATASET_ID
epi2me datasets download
epi2me datasets download $DATASET_ID
epi2me datasets download $DATASET_ID $DESTINATION_FOLDER
epi2me profiles
epi2me profiles list
epi2me profiles register
epi2me profiles register $REGISTRATION_CODE
epi2me profiles register $REGISTRATION_CODE --name $PROFILE_NAME
epi2me profiles delete
epi2me profiles delete $PROFILE_NAME
epi2me profiles rename
epi2me profiles rename $OLD_PROFILE_NAME
epi2me profiles rename $OLD_PROFILE_NAME $NEW_PROFILE_NAME
epi2me instances
epi2me instances list
epi2me instances detail
epi2me instances detail $INSTANCE_ID
epi2me products
epi2me products list
epi2me products workflows
epi2me products workflows $PRODUCT_ID
epi2me settings
epi2me settings get region
epi2me settings get disablePrompts
epi2me settings get profile
epi2me settings get admin
epi2me settings get proxy
epi2me settings get analytics
epi2me settings change region
epi2me settings change region $REGION_NAME
epi2me settings change disablePrompts $DISABLE_PROMPTS
epi2me settings change profile
epi2me settings change profile $PROFILE_NAME
epi2me settings change admin $IS_ADMIN
epi2me settings change proxy $PROXY
epi2me settings change analytics $ENABLE_ANALYTICS
epi2me settings list
epi2me workflows
epi2me workflows list
epi2me workflows run $INPUT_1 $INPUT_2 ... $INPUT_N
epi2me workflows detail
epi2me workflows detail $WORKFLOW_ID
epi2me workflows detail $WORKFLOW_ID --docs
epi2me workflows favourite
epi2me workflows favourite $WORKFLOW_ID
epi2me workflows unfavourite
epi2me workflows unfavourite $WORKFLOW_ID
COMMANDS:
accounts View the accounts associated with the current user
datasets View and download datasets
help Display help
instances Get the telemetry for a workflow instance
products View products, create new products and add workflows to products
profiles View, edit and create epi2me profiles
settings View and modify the configuration of the local application and your user account
version Display version
workflows View workflows and start new instances
OPTIONS:
-h, --help Output usage information
-v, --version Output the version number