test driving the Seven Bridges Genomics bioinformatics platform

I recently examined the Seven Bridges Genomics (SBG) platform, building and running a short-read alignment pipeline. Overall, I am impressed by the software. Here I describe my test of the program and then report on my investigation of how it works. Test Drive The test pipeline I devised consisted of two steps, FastQC analysis of […]

listing an Amazon S3 directory’s contents in Java

After much struggle, I have figured out how to list an Amazon S3 directory’s contents in Java using the AWS SDK. Here is how to do it: First, you need to import the following libraries: Then, in your main function (or elsewhere in your code) you need: Be sure to change the “prefix” variable to […]

test driving Amazon Web Services’ Elastic MapReduce

Hadoop provides software infrastructure for running MapReduce tasks, but it requires substantial setup time and availability of a compute cluster to take full advantage of. Amazon’s Elastic MapReduce (EMR) solves these problems; delivering pre-configured Hadoop virtual machines running on the cloud for only the time they are required, and billing only for the computation minutes […]