Basespace-cli-Sapelo2

Category

Bioinformatics

Program On

Sapelo2

Version

1.2.1

Author / Distributor

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

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

 
[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)

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Installation

Installed pre-compiled RPM for CentOS7.

System

64-bit Linux