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Download files from Illumina's BaseSpace

References:

Steps:

  1. Follow steps 1-5 in the first link above to acquire access_token. This will take a while, but you only need to do this once. Never share this token!!
  2. Find the file you want to download. Copy the link, which looks something like: https://basespace.illumina.com/sample/9804795/files/tree/NA12878-L1_S1_L001_R1_001.fastq.gz?id=515013503. The "id" is the unique file identifier.
  3. Download the file with: wget -O filename 'https://api.basespace.illumina.com/v1pre3/files/{id}/content?access_token={token}', where {token} is from step 1 and {id} from step 2.

A final note on security. It seems that the token acquired at step 1 does not automatically expire (in that case, this really needs improvement), so it is VERY IMPORTANT NOT to share this token, or others will gain access to all your data. Step 3 is not secure as others may see your download link with ps -f.

@shaharbr

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commented Jan 25, 2018

Hi,
Thanks for putting up this tutorial!
However, when trying to follow it, I noticed that the first link is broken.
Bellow is the updated link:
https://help.basespace.illumina.com/articles/tutorials/using-the-python-run-downloader/
Also, its steps 2-6, not 1-5.


Copied from there:

  1. Go to https://developer.basespace.illumina.com/ and log in.
  2. From the toolbar, select My Apps.
  3. In the applications tab, select Create a New Application.
  4. Fill out the Applications Details and then select Create Application.
  5. On the application page, select the Credentials tab and copy the Access Token.
@Pickledzebra

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commented Apr 7, 2019

That python script is old and broken. It has hard-coded directory paths that are wrong.

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