BaseSpace Invaders

This contains a collection of scripts (one for now!) that I found useful to retrieve files from Illumina's BaseSpace. Please run a script with --help to see its usage.

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Pre-requisites

Python BaseSpace SDK

Please download and install the python basespace sdk. It is recommended to use a virtual environment for this (e.g. via conda).

Illumina's BaseSpace Developer Credentials

You will need proper credentials in order to communicate with Illumina's BaseSpace with these tools. Here are the steps to get one for your current BaseSpace account:

1. Go to https://developer.basespace.illumina.com/ and login.
2. Click on the "My Apps" link in the tool bar.
3. In the applications tab, click on the "Create New Application" button.
4. Fill out the Applications Details and then click the "Create Application" button. Put dummy values if you encounter problems.
5. In the Credentials tab, you will need "Client Key", "Client Secret", and " Access Token".

You will need to provide the credentials for your app either via the command line (security risk) or with a master config file (preferred). To create a master config file, create a file named ~/.basespacepy.cfg with the following content, filling in the clientKey, clientSecret, and accessToken (optionally appSessionId):

[DEFAULT]
name = my new app
clientKey =
clientSecret = 
accessToken = 
appSessionId =
apiServer = https://api.basespace.illumina.com/
apiVersion = v1pre3

You can put in '' for appSessionId if you do not have one.

Get sample files

The download_files.py script downloads the sample-level files from BaseSpace. The user can specify project Id, project name, sample Id, and sample Name. Project Id and project name should not be specified together; similarly sample Id and sample name should not be specified together.

1. If only a project Id or only a project name is given, all files for all samples will be downloaded within that project. If additionally a sample Id or sample name is given, then only the first matching sample within the project will be downloaded.
2. If only a sample Id is given, then all files for that sample will be downloaded.
3. If only a sample name is given, then all files within the first project containing a sample with matching name will be downloaded.