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## ----load_libs, echo = FALSE, message = FALSE---------------------------------
library(knitr)
library(flowr)
## ----load_flowr, message=FALSE------------------------------------------------
library(flowr)
## ----setup, eval=FALSE--------------------------------------------------------
# setup()
## ----echo=FALSE, eval=FALSE---------------------------------------------------
# #We have a quite handy command-line-interface for flowr, which exposes all functions of the package to terminal. Such that we dont have to open a interactive R session each time. To make this work, run a setup function which copies the 'flowr' helper script to your `~/bin` directory.
#
## ----message=FALSE, echo=FALSE, fig.height=1.5, fig.width=5, eval=FALSE-------
# library(DiagrammeR)
# mermaid("
# graph LR
# A(sleep)-->B(create_few_files)
# B-->C{merge them}
# C-->D[get size]
# ")
## ----echo=FALSE, message=FALSE------------------------------------------------
ex = file.path(system.file(package = "flowr"), "pipelines")
flow_mat = as.flowmat(file.path(ex, "sleep_pipe.tsv"))
flow_def = as.flowdef(file.path(ex, "sleep_pipe.def"))
## ----echo=FALSE---------------------------------------------------------------
kable(flow_mat)
## ----message=FALSE, echo=FALSE------------------------------------------------
kable(flow_def)
## ----message=FALSE------------------------------------------------------------
ex = file.path(system.file(package = "flowr"), "pipelines")
flowmat = as.flowmat(file.path(ex, "sleep_pipe.tsv"))
flowdef = as.flowdef(file.path(ex, "sleep_pipe.def"))
fobj <- to_flow(x = flowmat,
def = flowdef,
flowname = "example1", ## give it a name
platform = "lsf") ## override platform mentioned in flow def
## ----plotit, fig.cap="Flow chart describing process for example 1", message=FALSE----
plot_flow(fobj) # ?plot_flow for more information
plot_flow(flowdef) # plot_flow works on flow definition as well
## ----eval=FALSE---------------------------------------------------------------
# submit_flow(fobj)
## ----eval=FALSE---------------------------------------------------------------
# submit_flow(fobj, execute = TRUE)
## ----build_pipe_exdata, message=FALSE-----------------------------------------
ex = file.path(system.file(package = "flowr"), "pipelines")
flow_mat = as.flowmat(file.path(ex, "sleep_pipe.tsv"))
flow_def = as.flowdef(file.path(ex, "sleep_pipe.def"))
## ----build_pipe_ex1, eval=FALSE, echo=FALSE-----------------------------------
# #flow_def = read_sheet(file.path(exdata, "example1_flow_def2.txt"))
# fobj = suppressMessages(to_flow(flow_mat, def = flow_def, platform = "torque"))
# fobj@jobs[[1]]@nodes
# #debug(submit_flow)
# fobj = submit_flow(fobj)
## ----build_pipe_exmat, echo=FALSE---------------------------------------------
kable(subset(flow_mat, samplename == "sample1"))
## ----build_pipe_exdef, echo=FALSE---------------------------------------------
kable(head(flow_def))
## ----plot_one_one, echo=FALSE, message=FALSE----------------------------------
qobj <- queue(platform = "lsf", queue = "normal", verbose = FALSE)
A <- job(name = "A", cmds = "sleep1", q_obj = qobj,
submission_type = "scatter")
B <- job(name = "B", cmds = "sleep2", q_obj = qobj,
previous_job = "A",
dependency_type = "serial", submission_type = "scatter")
C <- job(name = "C", cmds = "sleep2", q_obj = qobj,
previous_job = "B",
dependency_type = "gather", submission_type = "serial")
D <- job(name = "D", cmds = "sleep2", q_obj = qobj,
previous_job = "C",
dependency_type = "burst", submission_type = "scatter")
pab <- plot_flow(flow(jobs = list(A, B)))
## ----plot_many_one, echo=FALSE, message=FALSE, eval=FALSE---------------------
# pbc <- plot_flow(flow(jobs = list(B, C)))
## ----plot_one_many, echo=FALSE, message=FALSE, eval=FALSE---------------------
# pcd <- plot_flow(flow(jobs = list(C, D)))
## ----plot_abcd, message=FALSE-------------------------------------------------
ex2def = as.flowdef(file.path(ex, "abcd.def"))
ex2mat = as.flowmat(file.path(ex, "abcd.tsv"))
kable(ex2def[, 1:4])
plot_flow(ex2def)
## ----echo=FALSE, results='asis', message=TRUE, eval=FALSE---------------------
# # Available Pipelines
#
# Here are some of the available pipelines along with their respective locations
#
# pipes = try(fetch_pipes(silent = TRUE))
# #message(pipes)
# if(class(pipes) != "try-error")
# if(nrow(pipes) > 0){
# pipes$pipe = basename(pipes$pipe)
# pipes$def = basename(pipes$def)
# pipes$conf = basename(pipes$conf)
# params::kable(pipes)
# }
#
## ----echo=FALSE---------------------------------------------------------------
#exdata = file.path(system.file(package = "flowr"), "extdata")
plat <- params::read_sheet("files/platforms_supported.txt", id_column = "Platform")
kable(plat)
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