On 26 Sep 2016, at 19:49, Xing Xu <[email protected]> wrote:
>
> I am trying to access bam files that are stored on aws S3 storage of my own
> bucket.
>
> I read the release note of samtools and htslib 1.3 support the access to aws
> s3.
>
> Could you provide a detailed instruction that how I can access the bam file
> on aws s3 with samtools directly without downloading the file?
First build samtools with libcurl enabled as described in
samtools-1.3.1/README. Then you should be able to access your files directly
on S3 by referring to them as s3://bucket/filename.bam etc.
Samtools/htslib will read the usual environment variables (AWS_ACCESS_KEY_ID,
etc) and configuration files (~/.aws/credentials, ~/.s3cfg, ~/.awssecret) to
find your credentials to use in authenticating to AWS S3.
John
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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