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You can work with your BaseSpace Sequence Hub data using the command line interface (CLI). The BaseSpace Sequence Hub CLI supports scripting and programmatic access to BaseSpace Sequence Hub for automation, bulk operations, and other routine functions. It can be used independently or in conjunction with BaseMount.

Command Line Interface
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The file format used here is shared with other BSSH command line tools such as BaseMount, so if you have a BaseMount config file you do not need to derive another one. Command Line —Use -api-server / -access-token to specify the API server and access token on the command line.
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The BaseSpace Sequence Hub CLI has been updated to support automation features in the latest BaseSpace Sequence Hub.

To see the overall capabilities of the CLI and to help you get started post-installation, we recommend you use the Worked Examples.

Install BaseSpace Sequence Hub CLI

The BaseSpace Sequence Hub CLI is supported on Linux, Mac, and Windows (32 and 64 bit). It carries a small memory footprint, but for safety it should be installed on a machine with at least 1GB RAM.

For information on the most recent version of BaseSpace Sequence Hub CLI see Release Notes.

Install:

You can install from your web browser directly: or install from the command line, as described below.

These install instructions assume installation into the $HOME/bin directory. You can create this directory with mkdir $HOME/bin.

You can change the installation location (for example, to preserve a previous installation) by changing the option after -O, e.g.

Note that your operating system might require that you change the file permissions to make the downloaded binary executable:

If you are using a Mac, you can also install and update BaseSpace Sequence Hub CLI using Homebrew:

Binaries for other platforms are also available, see complete file listings via bintray.

Installing bscp

BaseSpace Copy (bscp) is an optional plugin to the Sequence Hub CLI, however it is no longer maintained as bscp upload and download functionality has now been integrated into native CLI upload and download commands.If you still need to install this tool, download the binary into a location in your $PATH with a bs- prefix to make it available via the bs cp command:

Authenticate

Note this command will authenticate to a default server located in AWS Virginia (https://api.basespace.illumina.com/)for localised authentication, please see Authenticate section.

Command Structure

The BaseSpace Sequence Hub CLI is based on a patternof a command prefix and a tree of subcommands. Just as in docker there is docker run, docker build, docker exec and in git there is git pull, git push,git commit, the the BaseSpace Sequence Hub CLI has bs list, bs create and bs authenticate. Some commands have subcommands, such as bs list appsession and bs create project.

Each subcommand has its own set of options which can be accessed with--help or -h, as in the following example

Command Summary

CLI commands can use the following patterns:

Standalone commands—Single commands, e.g. auth. See Standalone Commands.
Actions on entities—Actions on entities, e.g. list appsession,import dataset, get biosample. These can be used in reverse, for example create project is equivalent to project create. See Entity Reference.
Actions on sub-entities—Actions on sub-entities, e.g. export workflow threshold or setproject property. See Sub-Entity Reference.

The following table summarizes the CLI functions and commands. For detailed descriptions of commands, see Command Reference.

Function	Available Commands
List and explore entities	`bs list`, `bs get`, `bs headers`
List and download files within entities	`bs contents`, `bs download`
Kill running apps	`bs kill appsession`
Delete entities	`bs delete`
Create biosamples and upload fastq files for them	`bs create biosample`, `bs upload dataset`
Create analysis and configure analysis workflows from apps	`bs create workflow`, `bs workflow threshold` ..., `bs workflow dependency` ...

Some command combinations have specific options. Review the usage message for more information. For example:

Specify API server and Access Token

Most BaseSpace Sequence Hub CLI commands require that you specify an API server to contact and an access token to authenticate against BaseSpace Sequence Hub. These can be specified in the following ways.

Config—Use -c / --config to specify the config name to use e.g. bs -c virginia to use the virginia.cfg configuration file. Configuration files are generated by bs auth and stored in $HOME/.basespace. The file format used here is shared with other BSSH command line tools such as BaseMount, so if you have a BaseMount config file you do not need to derive another one.
Command Line—Use --api-server / --access-token to specify the API server and access token on the command line.Warning: This method can store details in your command history and threaten the security of your token.
Environment variables—Provide access credentials by specifying the environment variables $BASESPACE_ACCESS_TOKEN and $BASESPACE_API_SERVER. These can also be loaded from a config using bs config load. This is useful for injecting access credentials into Docker containers.

For example:

API Servers:

USA: https://api.basespace.illumina.com (default if no api-server is specified)
Germany: https://api.euc1.sh.basespace.illumina.com
Australia: https://api.aps2.sh.basespace.illumina.com
China: https://api.cnn1.sh.basespace.illumina.com.cn

Command Discovery

The CLI has been designed to help you discover commands. By typing the main bs command with --help you can see all the entities that are supported and all the actions that can be performed:

You can type the action by itself to see the entities to which that action can be applied:

Similarly, you can specify an entity and see which actions are available:

For each command combination, you can always run --help to see which sub-options are available and to get more details on the sub-commands:

The following sections list the standalone commands and action commands grouped by entity, sub-entity, and action. For more information about how the commands work in practice, see the Worked Examples.

The Entities table lists the actions that can be applied to the entity, with someexamples.
The Sub-Entities table lists the owning entity.
The Actions table lists the entities and sub-entities the action applies to, with some examples.

Command Line Interface

Entities and sub-entities

Some entities have sub-entities that have separate operations you can perform. These include:

Core Entities like projects, appsessions, datasets and runs which support properties on those entities.
The workflow entity has thresholds and dependencies with their own operations.
The biosample entity has requeue sub-entity used in communication with LIMS for high-throughput lab operations use-cases.

To use sub-entities, you need to provide switches to select the main entity (e.g. the project) as well as the sub-entity (e.g. the property name).

We recommend that you access sub-entities noun-first in this pattern bs <entity> <sub-entity> <verb> e.g.

You can also use this pattern to help explore the available commands, e.g.

For more information on using sub-entities, refer to the worked examples:

Standalone Commands

Authenticate

Authenticates against an instance of BaseSpace Sequence Hub, storing the API server used and the derived access token for use in future commands.

Example:

Additional options:

--scopes, to specify the scopes you obtain for your token.
--timeout, the amount of time to wait before giving up

Scopes

The following scopes are commonly used:

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For example:

Whoami

Returns information about the current user and token.

Example:

Entity Reference

Entity	Description	Available Actions	Sub-entities	Other notes
Application	BaseSpace app	Get Header List Rename	A token with MANAGE APPLICATIONS scope is needed for some operations
AppResult	Output from app	Content Delete Get Header List Translate	Property
AppSession	Representing an app during or after it has executed	Await Delete Get Header Kill List Rename	Property
Biosample	Data and metadata for a biological sample	Get Header Import List Rename	Property	See Worked Examples
Config	Configuration files stored in $HOME/.basespace	ListLoad	Not a BSSH entity, but used purely by BSSHCLI
Dataset	Output from app that captures typed output	Delete Get Header Import List Translate	Property
Project	Collection of other BSSH entities	Create Delete Get Header List Rename	Property
Run	Sequencing run, sometimes called a flow cell	Content Delete Get Header List	Property
Workflow	A type of BSSH app that can be configured with auto-launch dependencies and QC thresholds	Create Threshold Dependency	See Worked Examples for more details

Sub-Entity Reference

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Entity	Description	Owning Entity
Dependency	Workflow	See Worked Examples for more details.
Lab Requeues	The lab requeues that have been requested for a biosample	Biosample
Property	Key/value properties on entities	AppResultAppSessionBiosampleDatasetProject
Threshold	Workflow

Action Reference

Action	Description	Available Entities	Notes
All	Get all properties for an entity	Property
Await	Await the completion of appsessions	Appsession
Clear	Used to remove workflow settings	Workflow dependency Workflow threshold
Content	Show the contents of a BSSH entity	AppResult Dataset Run
Delete	Move an entity to trash	AppResult AppSession Dataset Project Run	Items are not deleted until the trash is emptied
Download	Download BSSH data	AppResult Biosample Dataset File Project Run
Get	Application AppResult Biosample Dataset Project Property Run
Headers	Show available headers for an entity	Application AppResult Biosample Dataset Project Run	Useful to choose outputs for `bs list`
Kill	Kill a running appsession	Appsession
List	List all entities	Application AppResult Biosample Dataset Project Property Run	Has options to customize output: Format (-f) which can be csv, yaml, json Ability to specify headers with -F Count items with --count Richer templated output with --template
Load	Allow config variables to be loaded into environment	Config
Rename	Rename an entity	Application Appsession Biosample Project
Set	Set a property or other setting	Property
Translate	Translate between V1 and V2 entity IDs	AppResult Dataset

What's New

The V2 CLI features has been designed to be fast, portable, and reflect as much of the API as possible. We have included commands to support features released in BaseSpace 5.0. These features include:

Workflows—BaseSpace Sequence Hub includes support for apps that can belaunched automatically and have an automated QC step, calledanalysis workflows. The new CLI includes commands to create, list andmodify these workflows.
Datasets—BaseSpace Sequence Hub apps have the ability to create datasets, an entity that stores data and metadata separately. The new CLI includes features to listand filter datasets.
Biosamples—The biosample is an entity that groupstogether metadata and FASTQ data for a biological sample, includingattaching analysis workflows to a biosample. The V2 CLI allows thelisting and creation of biosamples and their metadata, including thecreation of analysis workflows and inspecting lab requeues.

The V2 CLI includes the following enhancements on the previous V1 CLI:

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Rich options for listing entities and customising output
Additional get command to provide more details on a specific entity
Support for deleting appresults, appsessions, datasets, projectsand runs.
Ability to inspect files within BaseSpace Sequence Hub entities using the contentscommand
Support for downloading data using the download command
More flexible install process. The CLI can be installed by downloading a single binary, which enables you to install the CLI in an environment where you do not have sudo privileges. Using a single binary file also allows simpler distribution of updated versions.
Support for all Linux platforms in addition to Mac and Windows.

How Can I Get Support for CLI?

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The BaseSpace CLI v1.0 and higher is supported by the illumina support team: support@illumina.com. The BaseSpace Sequence Hub Google Group is a public forum for any BaseSpace developer information.