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

library(sevenbridges)
a <- Auth(token = "fake_token", url = "https://cgc-api.sbgenomics.com/v2/")
p = a$project('RWorkshop2')

Copy the get s3 file app

app.gets3fl <- a$copyApp(id =  "tsang/temp/txfr/2", project = pid, name = "copytxfrforbatch")
apid <- app.gets3fl$id

Run the app for the number of files listed in input file

fileName <- "S3Links.txt"
conn <- file(fileName,open="r")
linn <-readLines(conn)
for (i in 1:length(linn)){
  url = (linn[i])
  ## print(url)
  fn <- tail(strsplit(url,split="/")[[1]],1)
  ##print(fn)

tsk <-p$task_add(name= "s3upload-file-links",
           description='File upload from S3, with input from a file',
           app=apid,
           inputs=list(url = url, ofname = fn))

tsk$run()

}
close(conn)

teamcgc/cgcR documentation built on May 31, 2019, 7:56 a.m.