Nozzle R Package
Download and Installation
Nozzle is available on CRAN and can be installed directly from the R shell.
install.packages( "Nozzle.R1" );
For reference only. As of version 1.0-0 Nozzle should be obtained from CRAN. Please note that the releases before 1.0-0 do not contain any documentation within the R package.
The GitHub repository for Nozzle is at http://github.com/parklab/nozzle.
Nozzle is open source software and licensed under the LGPL version 2.1.
All questions related to Nozzle should be sent directly to Nils Gehlenborg (firstname.lastname@example.org). Questions about Nozzle related to the Firehose Analysis pipeline should be directed to email@example.com.
Nozzle & Firehose
Nozzle Reports for Monthly TCGA Firehose Analysis Runs
- Dashboard (public reports available starting January 2012)
Guidelines for Firehose Developers
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.