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.
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.bamThe S3 object is reachable. I got this error:
Error: Unable to open file s3://myBucket/myObject.bam. ExitingIt's unclear to me if I misconfigured, or if this is not (yet) supported.
Best, Geert