Download files from Illumina's BaseSpace

BSdownload.md

References:

• https://support.basespace.illumina.com/knowledgebase/articles/403618-python-run-downloader
• https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference

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.

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

Yes. Is there a working version?

@shaharbr is there a new solution? links are broken :(