Retrieve data from Illumina BaseSpace

Description

This tool retrieves data from the Illumina BaseSpace service. It allows you to:

List the data sets you have in Illumina BaseSpace.
Download content of a data set as a gzipped tar archive file.
Display content of a specific data set as a table.
Display detailed information of a data set

In order to use this tool you need

Illumina BaseSpace user account
Access token for the Illumina BaseSpace client bs (please find instructions below)

Parameters

You must define the Illumina BaseSpace API server and your personal access token for every task. The data sets are identified by their names (id code is not accepted). In the case of data set listing, the name parameter can be left blank.

Obtaining server name and access token for Illumina BaseSpace

In order to create the access token you must use a computer that has the bs client installed. You can easily install the bs client on your local computer, or if you have CSC account you can use the bs client installed in taito.csc.fi. The access token is created with the following bs setup command:

bs auth

The command prints out a link that you should paste to a web browser to verify your authentication. After the authentication, Illumina BaseSpace configuration file is created in your home directory on the computer where you executed the command. This configuration file contains information about the server name and access token you should use in Chipster. If you do this in Taito, you can print out the content of the configuration file with command:

cat $HOME/.basespace/default.cfg

Note that you need to set the access token for BaseSpace only once. However, you must include the access token to every BaseSpace command in Chipster, as Chipster does not store the access token information.