TCGA bam path
Hi,
I am authorized to access TCGA data but there seems to be something wrong with the new exome bam paths. For e.g., this is a bam path in the broad-firecloud-tcga/TCGA_SKCM_ControlledAccess_V1-0_DATA workspace:
$gsutil ls drs://dataguids.org/10c5e468-e5dd-4922-801a-e6b7746986e6
InvalidUrlError: Unrecognized scheme "drs".
Can you please help?
Comments
6 comments
Hi Sachet Shukla,
gsutil does not currently support DRS URIs (drs://). A member of our team is currently working on putting together a CLI you can use instead. I will update you as soon as I get word for how long it will take to set this up. In the meantime, please let us know if you have any questions!
Kind regards,
Jason
Hi Sachet Shukla,
We have developed a script you can use to run these types of commands. I will be sending you a message with the script attached shortly.
Kind regards,
Jason
Hi Jason,
Can this script be shared publicly, and linked to in this thread, so that other users who have this question can interface with these samples via gsutil? Thanks,
Hi Brendan,
Let me check with the product managers on the current status of development efforts for a more robust version of this script. I'll get back to you as soon as I can.
Kind regards,
Jason
Hi,
Can this script be shared?
I don't need it for production, just to check something in one file, so if the more robust script is not ready yet, it should still be fine.
Thanks!
Binyamin
Hi Binyamin,
I will follow up with you to provide the script we have!
Kind regards,
Jason
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