In teamcgc/cgcR: NCI Cancer Genomics Cloud examples in R

This is the second workshop for the NCI Cancer Genomic Cloud Pilots. This document includes instructions to do the following tasks using the Seven Bridges API with the R client.

This is a work-in-progress.

Material for this workshop
Additional information can be found here - (Follow API V2)

Pre-requisite
R studio https://www.rstudio.com/products/rstudio/download/
Seven Bridges CGC account https://cgc.sbgenomics.com/login/
Login and retrieve your authorization token

Installation

Make sure you have the latest verion of bioconductor installed. (Updated 5/3/2016)

#source("http://bioconductor.org/biocLite.R")
#useDevel(devel = TRUE)
#biocLite("sevenbridges")

For now, use github

Authorization

library(sevenbridges) 
a<-Auth(user="tsang", platform = "cgc", token = "XXX")

Navigate the CGC

p<- a$project(id="tsang/hackathon")
##a$project()
##p$file()
p$file()[[1]]
p$file()[[1]]$download_url()

Download Files

fid = p$file()[[1]]$id
a$project("hackathon")[[2]]$file(id = fid)$download("~/Downloads/")

fls <-a$project("hackathon")$file()
download(fls, "~/Downloads/")

Upload files

from my computer

fl = "~/Downloads/count000.csv"
> p$upload(fl, overwrite=FALSE)

dir <- "~/Downloads/temp/"
list.files(dir)
p$upload(dir, overwrite=TRUE)

Start a task with apps

p<-a$project(id="tsang/temp-1")
p$app()
ap <- p$app()[[1]]
#RNAseq STAR DEseq2

a$project("temp-1")$app_add(name= "Draft rnaseq",
                            description = "test",
                            app = tsang/temp-1/rna-seq-STAR-deseq2,
                            inputs = list(min=1, max=10))