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TIGR-Workflow / Ergatis

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Status
  • Mature release
  • Active development
  • Active support
Resources

What is it?

Screenshot of the Ergatis pipeline monitor

(From http://ergatis.sourceforge.net) :

Ergatis is a web-based utility that is used to create, run, and monitor reusable computational analysis pipelines. It contains pre-built components for common bioinformatics analysis tasks. These components can be arranged graphically to form highly-configurable pipelines. Each analysis component supports multiple output formats, including the Bioinformatic Sequence Markup Language (BSML). The current implementation includes support for data loading into project databases following the Chado schema, a highly normalized, community-supported schema for storage of biological annotation data.

Ergatis uses the Workflow engine to process its work on a compute grid. Workflow provides an XML language and processing engine for specifying the steps of a computational pipeline. It provides detailed execution status and logging for process auditing, facilitates error recovery from point of failure, and is highly scalable with support for distributed computing environments. The XML format employed enables commands to be run serially, in parallel, and in any combination or nesting level.

This framework has been employed in the annotation of several large, eukaryotic organisms, including Aedes aegypti and Trichomonas vaginalis.

Screenshot of the Ergatis pipeline builder

More information is available at:

http://ergatis.sourceforge.net

How is it a part of GMOD?

Currently, only loosely. As described above, Ergatis has been used at TIGR (now part of JCVI) for the majority of annotation and comparative genomics computation and the output of many of the components (such as blast, gene predictions, clustering etc.) can be loaded automatically into a chado database instance. In the past, due to its primary use at TIGR/JCVI, the database support was limited to Sybase, though flat-files could also be generated. Development is now underway to port this to also support PostgreSQL and Oracle.

Joshua Orvis is the lead developer of Ergatis and is currently at the Institute for Genome Sciences at the University of Maryland School of Medicine.

Mailing Lists

Mailing List Link Description Archive(s)
Ergatis ergatis-users Ergatis users mailing list. Nabble (2010/05+), Sourceforge
announcement Ergatis announcements. Nabble (2010/05+), Sourceforge
ergatis-devel Ergatis developers. Nabble (2010/05+), Sourceforge