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Published 20 hours ago • verified publisher icon arq5x

remote file support

Open geertvandeweyer opened this issue 1 year ago • 0 comments

It was mentioned in other issues that since v 2.28.0 , htslib was supported/included in bedtools. Does this mean that streaming data from s3 should be possible?

I tried this command using bedtools 2.30.0 installed from conda.

bedtools coverage -a local_file.bed -b s3://myBucket/myObject.bam

The S3 object is reachable. I got this error:

Error: Unable to open file s3://myBucket/myObject.bam. Exiting

It's unclear to me if I misconfigured, or if this is not (yet) supported.

Best, Geert

geertvandeweyer avatar Jan 12 '24 12:01 geertvandeweyer