Usage:
bs [OPTIONS] <command>
The BaseSpace Sequence Hub CLI tool suite is a set of command-line tools available for interacting with BaseSpace, Illumina's cloud-based sequencing informatics platform.
There are two types of internal commands, actions and entity-related, as well as the possibility to plug-in a number of external commands.
Application Options:
-V, --version Display version
Logging Options:
-v, --verbose Increase verbosity (additive)
-q, --quiet Only print errors (overrides verbosity)
--log= Path to standard logging destination (if given, captures both STDOUT and STDERR with timestamps)
Output Options:
--stdout= Standard Output destination, "path/to/file" or "-" for system's <STDOUT> (default: -)
--stderr= Standard Error destination, "path/to/file" or "-" for system's <STDERR> (default: -)
BaseSpace Connection Options:
-c, --config= Use this BaseSpaceCLI configuration
--api-server= BaseSpace API hostname [$BASESPACE_API_SERVER]
--access-token= Manual BaseSpace API access token [$BASESPACE_ACCESS_TOKEN]
--retry retry failed calls 5 times (with backoff)
Help Options:
-h, --help Show this help message
Available actions:
add Add lane or workflow settings
authenticate Make an authentication request to BaseSpace (aliases: auth)
await Await completion or status change
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
empty Empty a store
export Export lane or workflow settings
get Get detailed information about an entity (aliases: info, inspect)
header List headers for an entity (aliases: headers)
history Retrieve account activity records for a user or workgroup
import Import lane or workflow settings
kill Abort entities
launch Execute a task
link Get a direct link for an entity
list List and filter entities (aliases: filter, list-all)
load Load into your environment
rename Rename entities
restore Restore items
set Set properties in an entity
translate Translate v1 <-> v2 entity IDs
unlock Unlock a locked 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)
file View and manage files (aliases: files)
lane View and manage automated lane QC thresholds (aliases: lanes)
project View and manage projects (aliases: projects)
run View and manage runs (aliases: runs)
trash View and manage trashs (aliases: trashs)
workflow View and manage workflow applications (aliases: workflows)
Available external commands:
cp Provided by $PATH
mount Provided by $PATH