Polymarker is an automated bioinformatics pipeline for SNP assay development which increases the probability of generating homoeologue-specific assays for polyploid wheat. Please see http://polymarker.tgac.ac.uk/, http://polymarker.tgac.ac.uk/Markdown?md=About and https://github.com/TGAC/bioruby-polyploid-tools for further instructions.
Before using polymarker.rb you have to source ../.bashrc from the working directory.