A simple command line interface (CLI) for {scdrake}
is available. It is already installed in the Docker image,
otherwise it can be installed with
scdrake::install_cli()
See the above function's help page for possible parameters. By default, the CLI is installed in user's home as
~/.local/bin/scdrake
.
You can display the help message by running scdrake
or scdrake -h
.
The CLI offers several commands which wrap the most frequently used {scdrake}
functions.
Some options and flags are command-specific.
The usage is:
scdrake [OPTIONS/FLAGS] <COMMAND>
Current commands are listed below.
Initializes a new {scdrake}
project, by default in the current working directory. It will also download example data
if you specify the --download-example-data
tag.
Wraps init_project()
.
Runs a pipeline according to --pipeline-type
parameter which can be currently single_sample
or integration
.
Wraps run_single_sample_r()
and run_integration_r()
.
Updates the project files, by default in the current working directory.
Wraps update_project()
.
Downloads example data: PBMC 1k and 3k from 10x Genomics.
Wraps download_pbmc1k()
and download_pbmc3k()
.
Checks for {scdrake}
dependencies.
Wraps check_scdrake()
.
The CLI actually consists of two scripts:
scdrake
is a shell script which forwards parameters to r --interactive -t path/to/scdrake.R ...
r
is called littler and it is basically a more friendly and robust
alternative to Rscript
.scdrake.R
is the R part of the CLI and parses command line arguments using the
argparser package.r --interactive
and in that case
we cannot use the shebang line (#!/usr/bin/env r --interactive
) because then the script
doesn't accept additional parameters.
That's why we are using the intermediate shell script.Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.