Create a Shell Script

Create a shell script for a data analysis workflow consisting of commands extracted from existing R files.

Usage

shell_script(
  path_files,
  dir_shell = NULL,
  name_shell = "workflow.sh",
  overwrite = FALSE,
  quiet = FALSE
)

Arguments

path_files: A path from dir_shell to a directory with R scripts containing calls to cmd_assign() or cmd_assign_collect().
dir_shell: The directory where shell_script() will create the shell script. If no value is supplied, then shell_script() creates the shell script in the current working directory.
name_shell: The name of the shell script. The default is "workflow.sh".
overwrite: Whether to overwrite an existing shell script. Default is FALSE.
quiet: Whether to suppress progress messages. Default is FALSE.

Value

shell_script() is called for its side effect, which is to create a file. However, shell_script() also returns a string with the contents of the shell script.

Details

shell_script() tries to put the commands in the order they need to run, by matching each script's output path with the input paths of the other scripts. It can get this order wrong, so the shell script may still need editing.

To create a shell script in the files directory, set files to ".".

To obtain the contents of the shell script without creating a file on disk, creating the file on disk, set name_shell to NULL.

Supplying a value for files is compulsory for shell_script(), but optional for makefile(). The output from shell_script() is generated entirely from files while the output from makefile() also includes some general-purpose Makefile commands.

References

Episodes 1–3 of The Unix Shell Introduction to the command line
Command-Line Programs Introduction to Rscript

Examples

library(withr)

with_tempdir({

  ## create 'src'  directory
  dir.create("src")

  ## put R scripts containing calls to
  ## 'cmd_assign' in the 'src' directory
  writeLines(c("cmd_assign(x = 1, .out = 'out/results.rds')",
               "results <- x + 1",
               "saveRDS(results, file = .out)"),
             con = "src/results.R")
  writeLines(c("cmd_assign(.results = 'out/results.rds', .out = 'out/more_results.rds')",
               "results <- readRDS(.results)",
               "more_results <- results + 2",
               "saveRDS(more_results, file = .out)"),
             con = "src/more_results.R")

  ## the shell script runs 'results.R' first, because
  ## 'more_results.R' reads the file that 'results.R' writes

  ## call 'shell_script()'
  shell_script(path_files = "src",
               dir_shell = ".")

  ## shell script has been created
  list.files()

  ## print contents of shell script
  cat(readLines("workflow.sh"), sep = "\n")

})
#> ✔ Extracted call to `cmd_assign()` in src/more_results.R.
#> ✔ Extracted call to `cmd_assign()` in src/results.R.
#> 
#> Rscript src/results.R \
#>   out/results.rds \
#>   --x=1
#> 
#> Rscript src/more_results.R \
#>   out/results.rds \
#>   out/more_results.rds
#> 
#>