- Amazon Web Services (AWS)
A cloud provider, Amazon provides on demand instances and storage and
is the cloud system on which we deploy SeqWare.
A template system for Java’s build system Maven. We use it in SeqWare
as a template tool to quickly generate new Workflow Bundles, Modules, etc.
- FreeMarker template language (FTL)
A simple markup language for Java previously used by our older, legacy workflow engine.
- High Performance Computing (HPC)
A term that describes traditional cluster compute environments common at Universities and
large research organizations.
- Indivisible Unit of Sequence (IUS)
A term to describe de-multiplexed sequence from a sequencer run.
The SeqWare MetaDB tracks both experimental events (studies, samples, experiments, etc) and computational events (workflows, workflow runs, and processing events).
Loosely based on MIME types, a unique identifier that describes the format of the file produced by a SeqWare Pipeline workflow.
An API for steps in a workflow. Can be used to extend the SeqWare system by core developers. Most workflow developers
will simply use the BashJob to run command line tools as steps in workflows.
- Next Generation Sequencing (NGS)
A collection of high-throughput sequencing technologies.
- Processing Event
Information about individual steps in a workflow are saved in the MetaDB using the processing table.
- Sequencer Run
The Sequencer Run table in the MetaDB stores information about physical runs of the sequencer.
- Virtual Machine (VM)
A virtualized OS running on another machine. We use VirtualBox to redistribute SeqWare for use locally and an AMI for use on Amazon’s cloud.
- Workflow Bundle
A zip file (using Zip64) that contains the workflow definition,
binary files, data files, etc. Everything that needs to be included
to run the workflow.
- Workflow Engine
There are two main sets of workflow engines in SeqWare 1) Oozie and 2) Whitestar. The first uses the Hadoop system for running jobs while the second is a group of workflow engines that can run workflows directly for debugging purposes.
- Workflow Run
Represents a run of a given workflow in the MetaDB.
- More To Come…
We will add more in the near future, please suggest terms you would like defined in the comments section below.