1. Introduction to SeqWare
  2. Installation
  3. Getting Started
  4. SeqWare Pipeline
  5. SeqWare MetaDB
  6. SeqWare Portal
  7. SeqWare Web Service
  8. SeqWare Query Engine
  9. Glossary
  10. Frequently Asked Questions
  11. APIs
  12. Source Code
  13. Plugins
  14. Modules
  15. Advanced Topics

Frequently Asked Questions

Is SeqWare right for me?
Take a look at the Introduction which describes why you would want to use SeqWare and why you would not.
Is there a web-based GUI for writing workflows? For launching workflows?
Yes, the SeqWare Portal provides a GUI for launching workflows. Building workflows, however, is a programmatic process.
Do I need to be a programmer to use SeqWare? Do I need to be a bioinformatician?
There are three primary types of SeqWare users, see the main Documentation page for a description for each. For users of workflows, you do not need to be a developer, however to be an effective workflow developer you should be comfortable with bioinformatics tools and have at least very basic Java programming skills.
Can I contribute to the project?
Of course! See our Community page.
How do I report problems?
We use a public bug tracker for user requests and bug reports. See our Community page.
How can I get support for using SeqWare?
We have a mailing list, see our Community page.
Is there a commercially supported version of SeqWare?
Nimbus Informatics provides a workflow creation service and hosts SeqWare on the Amazon cloud.
Is there a VM available?
Yes, a local VM can be downloaded and/or a cloud VM (AMI) can be used on Amazon’s cloud, see the Installation guide.
What is the fastest way to setup SeqWare in my organization?
We recommend using our VM (or AMI on the cloud). For a local VM you can actually connect it to your cluster infrastructure directly.
What workflow language should I use?
Our Java workflow language is the current recommended choice.
What workflow engine should I use?
Our Oozie-SGE workflow engine is the current recommended choice.