Invoke a System Command

Invoke a System Command

Usage

exec(cmd, ...)

Arguments

cmd

Command to be invoked, as a character string.

...

<dynamic dots> Additional arguments passed to cmd command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using shQuote().

Value

A command object.

command collections

• allele_counter()

• bcftools()

• bedtools()

• bowtie2()

• bwa()

• cellranger()

• conda()

• fastp()

• fastq_pair()

• gistic2()

• kraken_tools()

• kraken2()

• perl()

• pyscenic()

• python()

• samtools()

• seqkit()

• snpEff()

• trust4()

• varscan()

See also

• cmd_wd()/cmd_envvar()/cmd_envpath()/cmd_condaenv()

• cmd_on_start()/cmd_on_exit()

• cmd_on_succeed()/cmd_on_fail()

• cmd_parallel()

Examples

cmd_run(exec("echo", "$PATH"))
#> Running command (2025-09-29 09:06:13): echo $PATH
#> 
#> Running scheduled exit task
#> Command process finished
#> System command succeed