Use Cases

This is a short note on use cases we want to support in the MOLGENIS processing extension

• Share my pipeline
• Add new module
• List my data items
• Incorporate Galaxy or GenePattern? modules in my pipeline
• How did I produce this result file?
• Autogenerate a R-suave (?) document that is executable documentation?
• Export R data annotation packages?

Notes

• We use Freemarker to define templates
• We use shell scripts to execute jobs
• PBS supports dependencies
• Each step should check for completion and have proper return values (so PBS knows and can cancel dependent jobs)