Bowtie 2 with remote index
Is it possible to perform an alignment with bowtie 2 where the reference index is stored somewhere not in the file system? For example, I am thinking of several docker containers that all use the same index stored in something like AWS S3.
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If they can be accessed by referring to them as a file/directory path then it should work. (https://docs.docker.com/storage/volumes/ and https://stackoverflow.com/questions/52041550/mount-s3-bucket-as-filesystem-on-aws-ecs-container )
You need to be very cautious about using cloud buckets mounted via fuse etc. They are not suitable for high performance computation. So be aware of this.
Set up a NAS if all the containers are to be deployed in local network.
You'll be paying for the data egress every time you use it then unless you're running the compute on AWS too (and then why not just mount the storage?).