ergatis workflow creation and monitoring interface

selected component list

  • AAT (aa)
  • AAT (na)
  • augustus
  • backupdb
  • BER
  • blast (see ncbi-blast and wu-blast series)
  • bsml -> chado (db loader)
  • bsml -> fasta
  • build supercontig
  • chado -> bsml (dumper)
  • clustalw
  • cogs
  • coordinate adjustment
  • copydb
  • coverage
  • delete analysis (db manip)
  • fasta -> bsml
  • fgenesh
  • genbank -> bsml
  • genemark
  • genewise
  • genezilla
  • genie
  • genscan
  • genscan+
  • gff -> bsml
  • glimmer3
  • glimmerHMM
  • hmmpfam
  • hmmpir
  • hmmsearch
  • hmmsmart
  • hmmtigr
  • infernal
  • initdb (chado db init)
  • iprscan
  • jaccard
  • legacy -> bsml
  • mask analysis
  • mepipe
  • mreps
  • muscle
  • ncbi-blastn
  • ncbi-blastp
  • ncbi-blastx
  • ncbi-tblastn
  • ncbi-tblastx
  • ngap
  • nucmer
  • nucmer SNP detection
  • obo -> chado
  • pangenome
  • pe
  • pepstats
  • phat
  • predotar
  • promer
  • prosite scan
  • psipred
  • region
  • repeatmasker
  • signalp
  • snoscan
  • snp (detection)
  • split fasta
  • split multifasta
  • statistics -> chado
  • subfeature mapping
  • tRNAscan-SE
  • targetp
  • tiling
  • tmhmm
  • translate sequence
  • transterm
  • trf
  • wait (test component)
  • wu-blastn
  • wu-blastp
  • wu-blastx
  • wu-tblastn
  • wu-tblastx
  • xdformat

documentation

Ergatis is a highly scalable and portable architecture for performing high throughput genome annotation and comparative analysis. The architecture supports a large number of commonly used bioinformatics tools and predefines a number of integrated, multi-step pipelines for performing automated gene annotations and comparative analysis. The architecture utilizes a Java based workflow engine and integrates with a popular grid management packages, such as Sun Grid Engine and Condor, in addition to supporting pipeline execution on a stand-alone machine. A web based front-end provides an interface for configuring and monitoring pipelines. The software provides detailed execution status, logging information for process auditing, and facilitates error recovery from point of failure.

Most of the documentation for Ergatis is accessible from a 'documentation' tab like this one but within an actual install of the software. This includes component and pipeline creation tutorials, directory structure convention explanations and component documentation. On this SourceForge site you can find the installation guide and a list of some of the components found within Ergatis (on the right).