BaseSpace Sequence Hub CLI

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.

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 download the latest CLI release using your web browser, the latest release version is: version badge

Alternatively you can install from the command-line. These install instructions assume installation into the $HOME/bin directory. You can create this directory with mkdir $HOME/bin.

# Linux
$ wget "https://launch.basespace.illumina.com/CLI/latest/amd64-linux/bs" -O $HOME/bin/bs
# Mac
$ wget "https://launch.basespace.illumina.com/CLI/latest/amd64-osx/bs" -O $HOME/bin/bs
# Windows
$ wget "https://launch.basespace.illumina.com/CLI/latest/amd64-windows/bs.exe" -O bs.exe

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

$ wget "https://launch.basespace.illumina.com/CLI/latest/amd64-linux/bs" -O $HOME/bin/bs

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

$ chmod u+x $HOME/bin/bs

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

$ brew tap basespace/basespace && brew install bs-cli

Binaries for other platforms are also available, see complete file listings via launch.basespace.illumina.com.

Authenticate

$ bs auth

Note this command will authenticate to a default server located in AWS Virginia (https://api.basespace.illumina.com/) for localised authentication and tips for authenticating against Professional and Enterprise workgroups, please see the Authenticate section.

Command Structure

The BaseSpace Sequence Hub CLI is based on a pattern of 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

$ bs auth --help                                                   
Usage:                                                              
    bs [OPTIONS] authenticate [authenticate-OPTIONS]               

Application Options:                                                  
    -V, --version   Display version                                         

Help Options:                                                         
    -h, --help      Show this help message                                     

[authenticate command options]                                      
-c, --config= Output to this BaseSpaceCLI configuration               
--force Overwrite existing configuration file, if it already exists   
--api-server= BaseSpace API hostname (default:                         
https://api.basespace.illumina.com) [$BASESPACE_API_SERVER]      
--scopes= List of scopes to authenticate with (default: READ GLOBAL, CREATE GLOBAL)                                                        
--timeout= Time in seconds before giving up (default: 120)  

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 set project 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:

$ bs list appsession --help                                          
...                                                                   
[list command options]                                              
--exec-status= Filter by execution status                             
--input-biosamples= Filter by Input BioSample                         
...                                                                    

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:

$ bs --help
...
Available actions:
  add           Add lane or workflow settings
  authenticate  Make an authentication request to BaseSpace (aliases: auth)
  clear         Clear lane or workflow settings
  content       Show all files in an entity (aliases: contents, dir)
  create        Create an entity
  delete        Move entities to your trash (aliases: rm, move-to-trash)
  download      Download files from an entity
  export        Export lane or workflow settings
  get           Get detailed information about an entity (aliases: info, inspect)
  import        Import lane or workflow settings
  kill          Abort entities
  list          List and filter entities (aliases: filter, list-all)
  set           Set properties in an entity
  upload        Upload files to an entity
  whoami        Get information about selected user/configuration

Available entities:
  application  View and manage applications (aliases: applications)
  appresult    View and manage appresults (aliases: appresults)
  appsession   View and manage appsessions (aliases: appsessions)
  biosample    View and manage biosamples (aliases: biosamples)
  config       View and manage installed confgurations (aliases: configs, configuration)
  dataset      View and manage datasets (aliases: datasets)
  lane         View and manage automated lane QC thresholds (aliases: lanes)
  project      View and manage projects (aliases: projects)
  run          View and manage runs (aliases: runs)
  workflow     View and manage workflow applications (aliases: workflows)

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

$ bs list
Please specify one command of: application, appresult, appsession, attribute, biosample, config, dataset, project, property or run
$ bs import
Please specify one command of: lane or workflow

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

$ bs application
Please specify one command of: get, header, launch or list
$ bs workflow
Please specify one command of: create, dependency or threshold

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:

$ bs appsession --help
...
Available commands:
  delete    Move an appsession to your trash (aliases: rm, move-to-trash)
  get       Get detailed information about an appsession (aliases: info, inspect)
  header    List all available fields for an appsession (aliases: headers)
  kill      Abort an appsession
  list      List and filter all appsessions (aliases: filter, list-all)
  property  Manage properties on an appsession (aliases: properties)

$ bs appsession kill --help
...
[kill command arguments]
  ID:                 IDs of the appsession to kill (multiple positional arguments)

bs set property --help
Available commands:
  appresult   set properties of an appresult (aliases: appresults)
  appsession  set properties of an appsession (aliases: appsessions)
  biosample   set properties of a biosample (aliases: biosamples)
  dataset     set properties of a dataset (aliases: datasets)
  project     set properties of a project (aliases: projects)
  run         set properties of a run (aliases: runs)

Command Reference

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 some examples.
  • The Sub-Entities table lists the owning entity.
  • The Actions table lists the entities and sub-entities the action applies to, with some examples.

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.

# -n refers to the name of the project
$ bs project property all -n "MyProject"
# -n refers to the name of the project and --property-name refers to the name of the property within that project
$ bs project property get -n "My Project" --property-name="MyProperty"

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

$ bs project property
Please specify one command of: all, delete, get or set

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:

$ bs auth
$ bs authenticate

Note: auth is an alias for authenticate. Either example below runs the same command):

This command will generate a URL which must be pasted into a browser where the user can log into their BaseSpace account and accept the authentication request.

$ bs auth
Please go to this URL to authenticate:  https://basespace.illumina.com/oauth/device?code=6Cesj

Enterprise Domains & Workgroups

If accessing a Professional or Enterprise workgroup, be sure to log into the desired domain and/or workgroup prior to running the authenticate command with BaseSpace CLI. Running the command below will set the default configuration and access token for whatever account and domain/workgroup the user is logged into. If needed, additional authentication configurations may be generated and stored using the -c <config-name> option. See below for more details.

Note: for Enterprise domains, the API URL used for authentication does not include the domain name. Only authentication with non-USE1 instances requires addition of the --api-server option (see below for details).

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.

API Servers:

Region Name Country City/State API URL
USE1 (default)USAVirgina, USAhttps://api.basespace.illumina.com
CAC1CanadaMontréal, Québechttps://api.cac1.sh.basespace.illumina.com
EUC1EuropeFrankfurt, Germanyhttps://api.euc1.sh.basespace.illumina.com
EUW2UKLondon, UKhttps://api.euw2.sh.basespace.illumina.com
CNN1ChinaBeijing, Chinahttps://api.cnn1.sh.basespace.illumina.com.cn
APS2AustraliaSydney, Australiahttps://api.aps2.sh.basespace.illumina.com

To authenticate on a BaseSpace instance for a region other than USE1 the --api-server option must be used in conjunction with the appropriate API URL:

$ bs auth --api-server https://api.euc1.sh.basespace.illumina.com # Authenticate on EUC1

Similar to the auth command above, this will generate an authentication URL with appropriate API URL:

$ bs auth --api-server https://api.euc1.sh.basespace.illumina.com
Please go to this URL to authenticate: https://euc1.sh.basespace.illumina.com/oauth/device?code=ElVQx

Configs:

The command above will write the token to the default config file ($HOME/.basespace/default.cfg). If this is not desired, a new config file can be created using the -c / --config option:

$ bs auth -c eu --api-server https://api.euc1.sh.basespace.illumina.com # Authenticate on EUC1 and save to a config file called "eu"

Any number of uniquely names config files may be generated in order to interact with different accounts, regions, and workgroups. Use the command below to list all saved config file names:

$ bs list config

If saving the access token in a non-default config file, the -c <config-name> option must be used for every invocation of bs in order to send the proper access token. To avoid needing to use the -c <config-name> for every command, the eval command can be used in conjunction with the bs load config command to load the proper API URL and access tokens into the variables BASESPACE_API_SERVER and BASESPACE_ACCESS_TOKEN, respectively.

$ eval $(bs load config eu)

This command is specific to Linux and Mac OS and the setting will last for the duration of the terminal session, or until changed by the user. In order to set these variables in Windows, there is a two-step process and it depends on whether PowerShell or the CMD terminal is used:

First, print the API server URL and access token for the desired config file:

$ bs load config eu
BASESPACE_API_SERVER=https://api.euc1.sh.basespace.illumina.com
BASESPACE_ACCESS_TOKEN=<private-access-token>

Second, for each of the lines printed from the command above, copy the line, and run the $env command within Windows PowerShell:

$env:BASESPACE_API_SERVER="https://api.basespace.illumina.com"
$env:BASESPACE_ACCESS_TOKEN="<private-access-token>"

Note: Both the URL and access token values must be enclosed in double quotes in order to successfully set the environment variables

If using Windows CMD rather than PowerShell, the set command can accomplish the same goal, but the quotation marks must be omitted:

$ set BASESPACE_API_SERVER=https://api.basespace.illumina.com
$ set BASESPACE_ACCESS_TOKEN=<private-access-token>

To verify the settings, run bs whoami and verify the "Host" URL is now set to the desired instance/region API URL.

It is also possible to pass the API URL and access token values on the command line, but this is not recommended.

Example:

$ bs list projects --api-server=https://api.euc1.sh.basespace.illumina.com/ --access-token=XXXXX

Additional options for the auth command:

  • --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:

Actions

Scopes

Accessing data

READ GLOBAL
BROWSE GLOBAL

Creating data

CREATE GLOBAL

Deleting data

MOVETOTRASH GLOBAL
EMPTY TRASH

Working with apps

MANAGE APPLICATIONS
START APPLICATIONS

Uploading sequencing run folders

CREATE RUNS

More information about scopes is available in the API documentation

For example:

# get a powerful token with lots of capabilities
$ bs auth --scopes "BROWSE GLOBAL,READ GLOBAL,CREATE GLOBAL,MOVETOTRASH GLOBAL,START APPLICATIONS,MANAGE APPLICATIONS"

Whoami

Returns information about the current user and token.

Example:

$bs -c configname whoami
+----------------+-------------------------------------------------+
| Name           | BaseSpace User                                  |
| Id             | 1234567                                         |
| Email          | basespaceuser@illumina.com                      |
| DateCreated    | 2015-01-16 15:31:22 +0000 UTC                   |
| DateLastActive | 2017-06-01 12:59:24 +0000 UTC                   |
| Host           | https://api.basespace.illumina.com              |
| Scopes         | ["READ GLOBAL" "CREATE GLOBAL" "BROWSE GLOBAL"] |
+----------------+-------------------------------------------------+

Entity Reference

Entity

Description

Available Actions

Sub-entities

Other notes

Example

Application

BaseSpace app

Get
Header
List
Rename

A token with MANAGE APPLICATIONS scope is needed for some operations

$ bs list applications --category=workflow

AppResult

Output from app

Content
Delete
Get
Header
List
Translate
Property

# get metadata about appresult with ID 123
$ bs get appresult -i 123
# show files in appresult with ID 123
$ bs contents appresults -i 123

AppSession

Representing an app during or after it has executed

Await
Delete
Get
Header
Kill
List
Rename
Property

# get all the appsessions for a particular biosample
$ bs list appsessions --input-biosample=LP1000123

Biosample

Data and metadata for a biological sample

Get
Header
Import
List
Rename
Property

See Worked Examples

Config

Configuration files stored in $HOME/.basespace

List Load

Not a BSSH entity, but used purely by BSSHCLI

# Show all configs
$ bs config list ... # print config in form to be imported # as environment variables $ bs config load default

Dataset

Output from app that captures typed output

Delete
Get
Header
Import
List
Translate
Property
$ bs dataset get --id=ds.123
...
$ bs dataset list --input-biosample=LP123
...
$ bs dataset delete --preserve-metadata -n "DatasetName"
...

Project

Collection of other BSSH entities

Create
Delete
Get
Header
List
Rename
Property

# create a project by name and with a description
$ bs create project -n MyProject -d "This is a new project"
# list all project in csv format
$ bs list projects -f csv

Run

Sequencing run, sometimes called a flow cell

Content
Delete
Get
Header
List
Property

# get metadata about a specific run
$ bs run get -i 123
# get all the files in a run
$ bs run contents -i 123

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

Entity

Description

Owning Entity

Example

Dependency Workflow
# export in json format the dependencies for workflow with ID 123
$ bs workflow dependency export -i 123
See Worked Examples for more details.
Lab Requeues The lab requeues that have been requested for a biosample Biosample
$ bs biosample requeue --requeue-type=NewLibrary -i 32853857
Property Key/value properties on entities AppResult AppSession Biosample Dataset Project
# show all properties for project with ID 123
$ bs project properties all -i 123
# get property with name PName from dataset with ID ds.123
$ bs dataset properties get -i ds.123 --property-name "Pname"

Threshold Workflow
# export in csv format the QC thresholds for workflow with ID 123
$ bs workflow threshold export -i 123

Action Reference

Action

Description

Available Entities

Notes

Example

All Get all properties for an entity Property
# get all properties for run with ID 123
$ bs run property all -i 123

Await Await the completion of appsessions Appsession
# wait for appsession 123 to finish and return just the output dataset
$ bs await appsession 123 --terse

Clear Used to remove workflow settings Workflow dependency
Workflow threshold
# remove all the workflow dependencies set for workflow 123
$ bs workflow dependency clear -i 123

Content Show the contents of a BSSH entity AppResult
Dataset
Run
# show all bam files from appresult with ID 123
$ bs appresult contents -i 123 --extension=bam

Delete Move an entity to trash AppResult
AppSession
Dataset
Project
Run
Items are not deleted until the trash is emptied
# delete project with name MyProject
$ bs delete project --name MyProject
# delete dataset with ID ds.123
$ bs delete dataset --id ds.123

Download Download BSSH data AppResult
Biosample
Dataset
File
Project
Run
# download files from appresult 123
$ bs appresult download --id 123 -o download/directory

Get Application
AppResult
Biosample
Dataset
Project
Property
Run
# get metadata about project with ID 123
$ bs get project --id 123

Headers Show available headers for an entity Application
AppResult
Biosample
Dataset
Project
Run
Useful to choose outputs for `bs list`
# Show available fields for an appsession
$ bs appsession headers

Kill Kill a running appsession Appsession
$ bs kill appsession 123

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
  • # list projects in yaml format
    $ bs list projects -f yaml
    # list appsessions with custom headers selected
    $ bs list appsessions -F Id -F ExecutionStatus
    # get the number of appresults $ bs list appresults --count
    # get data sets with just their IDs $ bs list data sets --terse

    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
    # get the appresult ID for dataset ds.123
    bs translate dataset -i ds.123
    

    CLI for the new data model

    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 be launched automatically and have an automated QC step, called analysis workflows. The new CLI includes commands to create, list and modify 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 list and filter datasets.

    • Biosamples—The biosample is an entity that groups together metadata and FASTQ data for a biological sample, including attaching analysis workflows to a biosample. The V2 CLI allows the listing and creation of biosamples and their metadata, including the creation of analysis workflows and inspecting lab requeues.

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

    • 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, projects and runs.

    • Ability to inspect files within BaseSpace Sequence Hub entities using the contents command

    • 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?

    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.