/basespace_project_downloader

Download project fastq files from BaseSpace

Primary LanguagePython

Basespace Project Downloader

Download fastq.gz files en-masse from a Project in Basespace

Step 1

Follow steps 1-5 from here to get a access token (you only need to do this once):

https://support.basespace.illumina.com/knowledgebase/articles/403618-python-run-downloader

Your access token should look something like "ab637cf829938dedcc672798f382cd21".

Step 2

Go to Basespace, click Projects, and click the project you wish to download the FASTQ files from.

Your address bar should look like this: https://basespace.illumina.com/projects/18274645

The final number (18274645) is your project id, take note of this.

Step 3

Run this script:

`basespace_project_downloader.py -p <project_id> -a <access_token> -o <output_dir>`

For example (using the example parameters in the previous steps)

`basespace_project_downloader.py -p 18274645 -a ab637cf829938dedcc672798f382cd21 -o .`