run: Run shmootl pipeline from the command line.
In gact/shmootl: QTL Analysis Utilities for Yeast

Description Usage Package Pipelines Examples

This is the general shmootl pipeline-running function, which provides a basic interface for standard QTL analysis pipelines to be run from a command line. It cannot be called interactively within R.

run()

Within shmootl, package pipelines are fully-documented functions that follow specific conventions regarding function name and formal arguments. Pipeline function names are of the form 'run_<pipeline>' (where '<pipeline>' is replaced by the pipeline name).

Package pipelines can be run from a command line with Rscript as follows:

Rscript -e 'library(shmootl)' -e 'run()' <pipeline> [-h] [<args>]

...where run is the general shmootl pipeline-running function, <pipeline> is the name of the pipeline to run, and <args> represents any arguments to be passed to the given pipeline. To see the available options for a pipeline, input the help flag (-h) after the name of the pipeline. To list all available pipelines, input the help flag (-h) without a pipeline name. (See usage examples below.)

## Not run: 
# To list available pipelines from the command line.
Rscript -e 'library(shmootl)' -e 'run()' -h

# To run the 'scanone' pipeline from the command line.
Rscript -e 'library(shmootl)' -e 'run()' scanone \
    --infile input.csv --h5file output.hdf5

# To run the 'scanone' pipeline from within R.
run_scanone(infile='input.csv', h5file='output.hdf5')

## End(Not run)