Technical Notes on Integrating Nozzle into Firehose Modules
The path to nozzle libraries can be passed into your R script using the special variable in your manifest/hydrant.deploy file: <nozzle.path> (evaluates to /xchip/tcga/Tools/Nozzle/v1.current). In other words, Firehose will take care of providing this value without the need to expose it to the task configuration (just like <libdir>).
To load the libraries in R: require("Nozzle.R1", lib.loc=nozzlePath, quietly=TRUE); Where nozzlePath is a variable passed into the R script containing <nozzle.path>.
All the resources referenced in your report must be in the top directory. For example, nesting of directories for figure image files will not display correctly in the Firehose UI.
The report must be named nozzle.html. This is the default file name produced by writeReport(myReport). However, writeReport(myReport, filename="report.html")will not work.
In some cases, use of the <R> variable in the manifest/hydrant.deploy file has caused problems. When to use <R> and when to use a direct path to Rscript is currently unclear.