A fastq downloader from basespace that actually works.
If using walk up service, the sequencing data won't go through Sanger pipeline. The files are located in Illumina BaseSpace.
Illumina has a python script for downloading data, but it won't give you fastq files. You can download fastq files following this instruction https://gist.github.com/lh3/54f535b11a9ee5d3be8e but you have to do it one by one.
This script download all fastq files associated with a project. I found out that when you have many files in a project, the download often stops randomly, and gives you an error message like this:
ssl.SSLError: ('The read operation timed out',)
This script handles that situation by ignoring already downloaded fastq files, so if donwload terminates prematurally, simply run it again.
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Go to this link and follow the instructions to get you access credentials including Client Id, Client Secret, and Access Token (Illumina's python script is also there): https://help.basespace.illumina.com/articles/tutorials/using-the-python-run-downloader/
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Create a file called
.basespacepy.cfgin your home directory with the following content:
[DEFAULT]
clientKey = your_Client_Id
clientSecret = your_Client_Secret
accessToken = your_Access_Token
apiServer = https://api.basespace.illumina.com/
apiVersion = v1pre3
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Protect that file by
chmod 600 ~/.basespacepy.cfg -
Install BaseSpacePy (seems to be python 2 only): https://github.com/basespace/basespace-python-sdk
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Create a directory where you want to put your fastq files, and run:
python download_fq_from_basespace.py your_project_name