sanogenetics/htslib-bcftools-samtools repository overview

⁠docker-htslib-bcftools-samtools

This is a Dockerfile that builds an image based on amazonlinux:2⁠ containing htslib⁠ as well as bcftools and samtools. This also contains the AWS CLI tool.

To read/write from S3 and htslib/bcftools/samtools see the official instructions⁠. In particular, note that it does not support role-based IAM access. A consequence of this is that using AWS Batch execution roles will not allow access to private S3 objects.

There is an issue⁠ on htslib for this. In there a comment describes using a shell script to set the role credentials before invoking the intended htslib/bcftools/samtools command. It could be used like:

docker run --rm htslib-bcftools-samtools:1.15.1 s3role bcftools view --header-only s3://bucket/key.vcf.gz

Note: long running tasks may have problems, since the credentials are automatically rotated periodically by AWS but the container does not refresh them.