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3 votes

Accessing .bam/.cram files from AWS S3?

You could set up a public read-only bucket in an S3 account and put your files there. URLs would look like: https://${username}.s3.amazonaws.com/public/${filename} ...
Alex Reynolds's user avatar
2 votes

Downloading SRA Files from AWS

A member of the SRA submission staff pointed out that using prefetch --type all SRR5253957 will download the original files. In this case, it means running the ...
merv's user avatar
  • 651
1 vote

Increasing memory usage in AWS instance

You need to diagnose for low memory and consider switching to an R5 processor that prioritises memory. Basically it's easily solvable by switching hardware. There are certainly alot of other ...
M__'s user avatar
  • 12.5k
1 vote

How does cromwell and AWS batch decide which compute environment (on-demand or spot) to use?

Cromwell will send jobs to the AWS Batch queue ARN defined in the cromwell.conf file in the Cromwell server. To use Spot instances you can create an AWS Batch ...
Mark's user avatar
  • 141
1 vote

Accessing .bam/.cram files from AWS S3?

I have recently open sourced a Java NIO SPI for S3 that allows direct reads from S3 using Java applications that use the NIO model. This allows applications like GATK and some parts of Picard to ...
Mark's user avatar
  • 141
1 vote

Accessing .bam/.cram files from AWS S3?

Doo you have your heart set on AWS, or are you open to using Google Cloud Platform (GCP)? If you're open to using GCP, there are some advantages. For example GATK can read and write directly to and ...
Geraldine_VdAuwera's user avatar

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