Download data from Illumina BaseSpace

Question

I want to be able to download data from BaseSpace in fastq-format. I know that you can download data through the browser, but I would like to do this using the Linux-command line.

I'm already looking into creating an API, but I don't have any experience with that whatsoever...

Is there a simple way to achieve this?

Answer 1

There is basemount --a tool developed by Illumina-- that streamline what you want to do. With basemount I can mount my BaseSpace Sequence Hub within my linux machine.

For instance, when I run:

mkdir BaseSpace    
basemount BaseSpace

I get a folder (BaseSpace) with the same directory structure of the one shown in the website of my BaseSpace account. Then, to copy files from BaseSpace to my local machine, I just do:

cp BaseSpace/path/to/file/fileName /path/in/local/machine/

Please, look at the documentation for how to install basemount and log-in into your BaseSpace account.