exec: Invoke a System Command

In blit: Bioinformatics Library for Integrated Tools

Invoke a System Command

Description

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()

• cellranger()

• conda()

• fastq_pair()

• gistic2()

• kraken_tools()

• kraken2()

• perl()

• pyscenic()

• python()

• samtools()

• seqkit()

• trust4()

See Also

• cmd_wd()/cmd_envvar()/cmd_envpath()/cmd_conda()

• cmd_on_start()/cmd_on_exit()

• cmd_on_succeed()/cmd_on_fail()

• cmd_parallel()

Examples

cmd_run(exec("echo", "$PATH"))

blit documentation built on April 12, 2025, 1:16 a.m.