Illumina BaseSpace

Illumina BaseSpace command line client, bs, can be used to retrieve data from the Illumina BaseSpace environment to Puhti.

• Illumina BaseSpace
  • License
  • Available
  • Usage
  • More information

License

Software is free to use.

Available

• Puhti: 1.0.0

Usage

First load the biokit module:

module load biokit

When biokit is loaded, the Illumina BaseSpace command line client starts with the command:

bs

To be able to use this service, you must have an account in the Illumina BaseSpace service.

As the first step, you must set up your authentication so that you can access your data in Illumina BaseSpace. This is done by running the command:

bs auth

The authentication information is stored to your home directory on Puhti ($HOME/.basespace/default.cfg). Thus, the authentication needs to be done only once.

After that you can start working with your Illumina data. For example, available datasets can be listed with the command:

bs list datasets

Single dataset can be downloaded to Puhti with the command:

bs download dataset -i dataset_id -o local_download_dir

More information

More detailed information about using Illumne BaseSpace client can be found form the links below:

• bs examples
• bs overview

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