Contents 1 How do I 1.1 How do I make my own workflow? 1.2 How do I change an existing workflow? 1.3 How do I plug in my own algorithm? 1.4 How do I integrate with my LIMS? 1.5 How do I script the GQ platform

How do I

How do I make my own workflow?

Read the how-to. You may benefit from learning the System Concepts and reading the GQ Engine Primer first.

How do I change an existing workflow?

Become familiar with the workflow framework in the System Concepts and the Workflow How-To - then go at it!

How do I plug in my own algorithm?

That depends. If you want your algorithm to run on Sequences or Alignments that a user is browsing, you might consider to write a Plug-In. If you want to do other fancy things with your algorithm, a Workflow might be better.

See When would I write a plug-in? for more.

How do I integrate with my LIMS?

Your LIMS will be providing sequence data to GenomeQuest, so you need to become familiar with:

• GenomeQuest Sequence Databases
• GenomeQuest Content Manager

Once you understand these concepts, the basic process is:

1. transfer the data to a GQ-aware server
2. format the data in an EMBL+ format with the right annotation in the right fields
3. load the data into GQ with the GenomeQuest Content Manager

How do I script the GQ platform

Everything the user can do in GQ can be done via our URL API and via our remote command line tool, HTx.