(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
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