download

Synopsis

singularity run [run options...] --app download <container> [app options...]

Description

Download data from the Illumina BaseSpace Sequence Hub.

Options

# Required
-i    The run ID of the data to download.

# Optional
-o    The path to the output directory.
-c    The path to the authentication credentials file.
-h    Print the help page.

Defaults

-o    Default: '/opt/analysis'
-c    Default: '/opt/resources/basespace.cfg'

Authentication Credential File

Note

Users must first authenticate their account in order to download data from the BaseSpace Sequence Hub.

The authentication credential file can be generated via the BaseSpace CLI. The bs auth command generates a configuration file that indicates an API server to contact and an access token to authenticate against BaseSpace Sequence Hub. The default API server defaults to Virginia, USA. Other options include Europe and the UK, among others. To override the default API server, use the --api-server option.

singularity exec [options] <container> bs auth --force

# Specify UK API server
singularity exec [options] <container> bs auth --force --api-server https://api.euw2.sh.basespace.illumina.com

These commands will generate a configuration file: basespace.cfg in ${HOME}/.basespace. In order for the download app to access the configuration file, you must copy the file into base_resources.

cp ${HOME}/.basespace/basespace.cfg base_resources

Examples

singularity run \
  -B base_resources:/opt/resources \
  -B downloaded:/opt/analysis \
  --app download miptools.sif -i 12345