download_superseded

Synopsis

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

Description

Download data from the Illumina BaseSpace Sequence Hub.

Warning

This app has been superseded by the download app, which uses the BaseSpace CLI for downloading data.

Options

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

# Optional
-h    Print the help page.

Download Destination

Data will be downloaded to /opt/analysis. A directory may be mounted to this path to customize the download destination.

Authentication Credential File

Note

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

An authentication token must be generated in order to download data from the BaseSpace Sequence Hub. In order to do so, you consult the authentication credential file section of the download app. Once generated authentication token must be copied to base_resources/access-token.txt.

Note

The authentication credential file section of the download app will generate a configuration file that indicates an API server to contact and an access token to authenticate against BaseSpace Sequence Hub. Only the access token value must be copied to base_resources/access-token.txt.

Examples

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