module load R git git clone git@github.com:sahilseth/flowr.git ## test for roel cd ~/apps rm -rf ~/apps/flowr git clone https://github.com/sahilseth/flowr.git R CMD INSTALL flowr flowr run sleep execute=TRUE platform=torque ## HMS test install.flow; flowr run sleep platform=lsf execute=TRUE Rscript -e 'flowr:::.run_sleep(platform = "moab", execute=TRUE)'
devtools::install_github("sahilseth/flowr") library(flowr) setup()
setwd("~/Dropbox/public/github_flow/") devtools::load_all(".")
library(flowr) setup() platform = "torque" platform = "lsf" platform = "moab" fobj = flowr:::.run_sleep(platform = platform) fobj = flowr:::.run_sleep(platform = platform, execute=TRUE)
fobj = .run_sleep() ## should be local fobj@jobs[[1]]@platform == "local" fobj = .run_sleep(execute = TRUE) fobj = .run_sleep(platform = "lsf") ## should be local fobj = .run_sleep(platform = "sge") ## should be local fobj = .run_sleep(platform = "moab") ## should be local
#exdata = file.path(system.file(package = "flowr"), "extdata") exdata = "~/Dropbox/public/github_flow/inst/extdata" flow_mat = read_sheet(file.path(exdata, "example1_flow_mat.txt")) flow_mat = subset(flow_mat, samplename == "sample1") flow_def = read_sheet(file.path(exdata, "example1_flow_def.txt")) ## remove memory, should detect and throw error: #colnames(flow_def)[6] = "mem" #debug(render_queue_cmd) flowr:::check.flow_def(flow_def) fobj = to_flow(x = flow_mat, def = flow_def, submit = TRUE, platform = "lsf")
extdata = file.path(system.file(package = "flowr"), "extdata") ex = file.path(system.file(package = "flowr"), "examples") flow_mat = read_sheet(file.path(ex, "sleep_pipe.tsv")) flow_def = read_sheet(file.path(ex, "sleep_pipe.def")) fobj <- to_flow(x = flow_mat, def = as.flowdef(flow_def), flowname = "example1", platform = "lsf", execute = t) fobj <- to_flow(x = as.flowmat(flow_mat), def = as.flowdef(flow_def), flowname = "example1", platform = "lsf")
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