Basespace-cli-Sapelo2 - Revision history

Shtsai at 00:01, 5 April 2026

2026-04-05T00:01:03Z

← Older revision		Revision as of 20:01, 4 April 2026
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	[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==

	Sapelo2		Sapelo2

	=== Version ===		== Version ==

	1.2.1		1.2.1

	=== Author / Distributor ===		== Author / Distributor ==

	Please see https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-overview		Please see https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-overview

	=== Description ===		== Description ==

	From https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-overview: "The main mechanism to interact with your BaseSpace Sequence Hub data is via the website at www.basespace.illumina.com. However, for some use-cases, it can be useful to work with the same data using the Linux command line interface (CLI).		From https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-overview: "The main mechanism to interact with your BaseSpace Sequence Hub data is via the website at www.basespace.illumina.com. However, for some use-cases, it can be useful to work with the same data using the Linux command line interface (CLI).
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	With BaseMount, we introduced a way to mount your BaseSpace Sequence Hub files and explore them on the command line as if they were a file system. Now, we are taking this a step further by introducing a suite of tools, BaseSpace Sequence Hub Command Line Interface (BaseSpaceCLI) to both read data from your BaseSpace Hub account and create new data, by uploading samples and launching apps. These tools integrate with BaseMount and provide a way to carry out many routine BaseSpace Sequence Hub tasks efficiently at the command line."		With BaseMount, we introduced a way to mount your BaseSpace Sequence Hub files and explore them on the command line as if they were a file system. Now, we are taking this a step further by introducing a suite of tools, BaseSpace Sequence Hub Command Line Interface (BaseSpaceCLI) to both read data from your BaseSpace Hub account and create new data, by uploading samples and launching apps. These tools integrate with BaseMount and provide a way to carry out many routine BaseSpace Sequence Hub tasks efficiently at the command line."

	=== Running Program ===		== Running Program ==

	* Version 1.2.1 is installed in the xfer nodes (not on the Sapelo2 login, qlogin, or compute nodes) in /usr/local/bin, a directory that is on user's default path. To use this program, first ssh into xfer.gacrc.uga.edu and you can access the command there.		* Version 1.2.1 is installed in the xfer nodes (not on the Sapelo2 login, qlogin, or compute nodes) in /usr/local/bin, a directory that is on user's default path. To use this program, first ssh into xfer.gacrc.uga.edu and you can access the command there.

	=== Documentation ===		== Documentation ==

	<pre class="gcommand">		<pre class="gcommand">
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	=== Installation ===		== Installation ==

	Installed pre-compiled RPM for CentOS7.		Installed pre-compiled RPM for CentOS7.

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Moses at 19:36, 5 May 2021

2021-05-05T19:36:18Z

← Older revision		Revision as of 15:36, 5 May 2021
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	=== Version ===		=== Version ===

	1.2.1		1.2.1

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	* Version 1.2.1 is installed in the xfer nodes (not on the Sapelo2 login, qlogin, or compute nodes) in /usr/local/bin, a directory that is on user's default path. To use this program, first ssh into xfer.gacrc.uga.edu and you can access the command there.		* Version 1.2.1 is installed in the xfer nodes (not on the Sapelo2 login, qlogin, or compute nodes) in /usr/local/bin, a directory that is on user's default path. To use this program, first ssh into xfer.gacrc.uga.edu and you can access the command there.


	=== Documentation ===		=== Documentation ===

Moses: /* Description */

2021-05-05T19:35:10Z

Description

← Older revision		Revision as of 15:35, 5 May 2021
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	=== Description ===		=== Description ===

	From https://~~help~~.basespace.illumina.com/~~articles~~/~~descriptive~~/~~basespace~~-~~cli#Overview~~: "The main mechanism to interact with your BaseSpace Sequence Hub data is via the website at www.basespace.illumina.com. However, for some use-cases, it can be useful to work with the same data using the Linux command line interface (CLI).		From https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-overview: "The main mechanism to interact with your BaseSpace Sequence Hub data is via the website at www.basespace.illumina.com. However, for some use-cases, it can be useful to work with the same data using the Linux command line interface (CLI).

	With BaseMount, we introduced a way to mount your BaseSpace Sequence Hub files and explore them on the command line as if they were a file system. Now, we are taking this a step further by introducing a suite of tools, BaseSpace Sequence Hub Command Line Interface (BaseSpaceCLI) to both read data from your BaseSpace Hub account and create new data, by uploading samples and launching apps. These tools integrate with BaseMount and provide a way to carry out many routine BaseSpace Sequence Hub tasks efficiently at the command line."		With BaseMount, we introduced a way to mount your BaseSpace Sequence Hub files and explore them on the command line as if they were a file system. Now, we are taking this a step further by introducing a suite of tools, BaseSpace Sequence Hub Command Line Interface (BaseSpaceCLI) to both read data from your BaseSpace Hub account and create new data, by uploading samples and launching apps. These tools integrate with BaseMount and provide a way to carry out many routine BaseSpace Sequence Hub tasks efficiently at the command line."


	=== Running Program ===		=== Running Program ===

Moses: /* Author / Distributor */

2021-05-05T19:34:32Z

Author / Distributor

← Older revision		Revision as of 15:34, 5 May 2021
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	=== Author / Distributor ===		=== Author / Distributor ===

	Please see https://~~help~~.basespace.illumina.com/~~articles~~/~~descriptive~~/~~basespace~~-~~cli~~		Please see https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-overview

	=== Description ===		=== Description ===

Moses: Created page with "Category:Sapelo2Category:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 1.2.1 === Author / Di..."

2021-05-05T19:33:57Z

Created page with "Category:Sapelo2 Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 1.2.1 === Author / Di..."

New page

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===

Bioinformatics

=== Program On ===

Sapelo2

=== Version ===

1.2.1

=== Author / Distributor ===

Please see https://help.basespace.illumina.com/articles/descriptive/basespace-cli

=== Description ===

From https://help.basespace.illumina.com/articles/descriptive/basespace-cli#Overview: "The main mechanism to interact with your BaseSpace Sequence Hub data is via the website at www.basespace.illumina.com. However, for some use-cases, it can be useful to work with the same data using the Linux command line interface (CLI).

With BaseMount, we introduced a way to mount your BaseSpace Sequence Hub files and explore them on the command line as if they were a file system. Now, we are taking this a step further by introducing a suite of tools, BaseSpace Sequence Hub Command Line Interface (BaseSpaceCLI) to both read data from your BaseSpace Hub account and create new data, by uploading samples and launching apps. These tools integrate with BaseMount and provide a way to carry out many routine BaseSpace Sequence Hub tasks efficiently at the command line."

=== Running Program ===

* Version 1.2.1 is installed in the xfer nodes (not on the Sapelo2 login, qlogin, or compute nodes) in /usr/local/bin, a directory that is on user's default path. To use this program, first ssh into xfer.gacrc.uga.edu and you can access the command there.

=== Documentation ===

<pre class="gcommand">
[shtsai@xfer3 ~]$ bs --help
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:
accession Register a new item
add Add lane or workflow settings
archive Archive entities
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
revoke Invalidate a resource (aliases: expire)
seqstats Sequencing stats
set Set properties in an entity
translate Translate v1 <-> v2 entity IDs
unarchive Restore entities from archival storage
unlock Unlock a locked entity
update Update entities
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 configurations (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)
manifest Biosample manifest actions (aliases: manifests)
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)
</pre>

[[#top|Back to Top]]

=== Installation ===

Installed pre-compiled RPM for CentOS7.

=== System ===
64-bit Linux