download

Synopsis

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

Description

Download data from the Illumina BaseSpace Sequence Hub.

Options

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

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. The steps to do so are outlined below:

1. Go to https://developer.basespace.illumina.com/ and log in.

2. From the toolbar, select My Apps.

3. In the applications tab, select Create a New Application.

4. Fill out the Applications Details and then select Create Application.

5. On the application page, select the Credentials tab and copy the Access Token.

Once generated, the authentication token must be copied to base_resources/access-token.txt.

Examples

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