Tool Registry Service (TRS) subcommands

Table 7 Tools subcommands

Subcommand

Description

Argument

delete-version

Delete a TRS tool version based on the tool ID and tool version ID.

--tool-id STR
Specify a TRS ID (required).
--version-id STR
Specify a TRS version.

execs

Create a SeqsLab exec.json file.

--working-dir STR
Specify the absolute working directory path hosting all WDL files (required). For example, /home/ubuntu/wdl/.
--inputs STR
Specify the folder path of inputs.json in relation to the working directory (required). For example, inputs.json.
--main-wdl STR
Specify the folder path of the main WDL file in relation to the working directory (required). For example, main.wdl.
--output STR
Specify the output filename of execs.json in relation to the working directory (optional, default = execs.json).

file

Register TRS file object.

--tool-id STR
Specify the ID of a tool that you have already registered, where you plan to register the file in (required).
--version-id STR
Specify the ID of a version that you have already registered, where you plan to register the file in (required).
--descriptor-type {WDL,CWL,NFL}
Specify the descriptor type of a tool that you have already registered, where you plan to register the file in (required).
--working-dir STR
Specify the path of the working directory (required).
--file-info STR
Specify the file description used to register TRS. The default value is extracted from the workflow section of the execs.json file (optional).

get

Get tool files using the SeqsLab API request /trs/v2/tools/{id}/versions/ {version_id}/{type}/files/.

--tool-id STR
Specify a TRS ID.
--version-id STR
Specify a TRS version.
--download-path STR
Specify the file path for the tool ZIP file download (required).
--descriptor-type {WDL,CWL}
Specify the TRS descriptor type (optional, default = WDL).

images

List Docker images in the workspace.container_registry.container_registry.

--workspace STR
Specify the workspace based on the signed in account.

list

Display a list of existing tools.

--output {json,table}
Specify the output format of the stdout file (optional, default = json).

tool

Register a TRS tool object.

--name STR
Specify the name of the tool that you want to register (required).
--has-checker
Specify whether or not this tool has a checker tool associated with it (optional).
--checker-url CHECKER_URL
Specify the URL of the checker tool that you want to register (optional).
--aliases ALIASES
Specify the aliases of the tool that you want to register (optional).
--description STR
Specify the description of the tool that you want to register (optional).
--toolclass-description STR
Specify the type of tool that you want to register (optional).
--toolclass-name STR
Specify the type of tool that you want to register (optional).
--id STR
Specify a custom identifier for the tool (optional). The identifier must only contain alphanumeric characters, hyphen, and underline.

version

Register the TRS object version.

--workspace STR
Specify the workspace based on the signed in account (required).
--tool-id STR
Specify the ID of a tool that you have already registered where you plan to register the file in (required).
--id STR
Specify the version of the tool that you want to register (required). For example, 0.1, 0.1.2, 1.0, 1.1, etc.
--descriptor-type {WDL,CWL,NFL}
Specify the descriptor type of the tool that you want to register in this version (required).
--images STR
Specify a JSON string describing a list of images you want to register in this version (required).
--name STR
Specify the name of the version that you want to register (optional).
--is-production
Specify whether or not this version of the tool that you want to register is for production use (optional, default = false).
--signed
Specify whether or not this version of the tool that you want to register is signed (optional, default = false).
--included-apps INCLUDED_APPS
Specify the apps that you want to include with the tool that you want to register in this version (optional).
--verified-source VERIFIED_SOURCE
Specify the verified source of the tool that you want to register in this version (optional).
--verified
Specify whether or not this version of the tool that you want to register is verified (optional, default = false).
--author AUTHOR
Specify the name of the author of the tool that you want to register in this version (optional).