sal2bash.RdThis function takes a SYSargsList object and translate it to an executable bash script, so one can run the workflow without loading SPR or using an R console.
sal2bash(sal, out_dir = ".", bash_path = "/bin/bash", stop_on_error = TRUE)SYSargsList object.
string, a relative or absolute path to a directory. If the directory does not exist, this function will first try to create it.
string, the path to the bash executable program
bool, should the bash script stop if any error happens in running
## out files
1. The main executable bash file will be created to the root of `out_dir`
2. All R steps will be stored as R scripts and along with other supporting files inside a folder called `spr_bash` under `out_dir`
3. Not all R steps will have an individual file. This function will "collapse" adjacent R steps into one file as much as possible. Namely, if there is no sysArgs steps in between, R steps will be merged into one file, otherwise they will be in different files.
## R steps
Similarly as running the workflow in R console, all R steps will share the same environment variables and loaded packages. This is done by loading and saving the R environment into a file `spr_wf.RData` before and after the R script execution. Therefore, it will be good to keep all R steps bundle together as much as possible to avoid the package and environment loading/saving overhead time.
Initially, this environment only contains the SYSargsList object that was used to create the bash script. Note: the SYSargsList object name will be the same as what you pass to `sal2bash`. If you have `sal2bash(my_sal)`, then in the `spr_wf.RData` there will be an object called `my_sal` saved there. It is important to keep using the same name for the SYSargsList object managing the workflow and in workflow running. For example, if you have an R step that requires to query a column from the outfiles of the SAL, `getColumn(sal, "FileName1")`, but you pass `my_sal` to `sal2bash(my_sal)`, this will cause this R step cannot find the SAL object when run the workflow from bash.
## Execution
This way of execution is not able to handle complex dependency graphs. The original step dependencies from SAL object will be ignored, so all steps will be executed in a linear manner. It is recommended to adjust the workflow order before using this function.
no return
file_path <- system.file("extdata/spr_simple_wf.Rmd", package="systemPipeR")
sal <- SPRproject(overwrite = TRUE)
#> Recreating directory '/home/runner/work/systemPipeR/systemPipeR/docs/reference/.SPRproject'
#> Creating file '/home/runner/work/systemPipeR/systemPipeR/docs/reference/.SPRproject/SYSargsList.yml'
sal <- importWF(sal, file_path)
#> Reading Rmd file
#>
#>
#> ---- Actions ----
#> Checking chunk eval values
#> Checking chunk SPR option
#> Ignore non-SPR chunks: 17
#> Parse chunk code
#> Checking preprocess code for each step
#> No preprocessing code for SPR steps found
#> Now importing step 'load_library'
#> Now importing step 'export_iris'
#> Now importing step 'gzip'
#> Now importing step 'gunzip'
#> Now importing step 'stats'
#> Now back up current Rmd file as template for `renderReport`
#> Template for renderReport is stored at
#> /home/runner/work/systemPipeR/systemPipeR/docs/reference/.SPRproject/workflow_template.Rmd
#> Edit this file manually is not recommended
#> Now check if required tools are installed
#> Check if they are in path:
#> Checking path for gzip
#> PASS
#> Checking path for gunzip
#> PASS
#> step_name tool in_path
#> 1 gzip gzip TRUE
#> 2 gunzip gunzip TRUE
#> All required tools in PATH, skip module check. If you want to check modules use `listCmdModules`Import done
#>
sal2bash(sal)
#> Success: Make sure the script 'spr_wf.sh' and directory ./spr_bash is there before executing.