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blastall bioActor

Description

This is a demo workflow to run BLAST program (http://blast.ncbi.nlm.nih.gov/).

Execution Choices

  • CrossReduce
  • HadoopMapOnly
  • JobSubmission
  • LocalExecution
  • MapReduce
  • StratosphereMapOnly

Inputs

referenceFileThe input file for reference sequences.
queryFileThe input file for query sequences.

Outputs

alignmentFileThe output file that contains the alignment results.

Parameters

eValueExpectation value.
outputFormatThe format option for output, namely alignment view options.
programNameThe name of blast program to be executed.
programThe command line program to execute.
checkOutputTimestampIf true, verify the last modification timestamp for each output file has increased after execution. If the timestamp has not increased, throw an error.
additionalOptionsAdditional command line options to run blastall
ChoiceThe execution choice to run.

bioKepler is funded by NSF DBI-1062565 under CI Reuse and Advances in Bioinformatics programs. Any opinions, findings and conclusions or recomendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation (NSF).