(cc'ing the dev list and updating the subject line in case others are 

> I have been looking for Java related API's to run workflows externally and
> haven't found anything searching message forums etc. Would like to
> automate data coming off up hiseq uploaded to Amazon S3 and then
> programmatically from external process import the fastq files and kick off
> a workflow to process. If you know of any docs or Java API for doing this
> kind of external control can you point me to it.

John Chilton has a Java library to access the API through Java:

which should cover lots of this. If you're interested in other JVM
languages, I built a small Clojure wrapper around this to simplify some

We'd definitely love to have more people involved, so if any
functionality you need is missing please feel free to submit
pull requests.

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