Run a command inside a Conda environment

Executes a command in a Conda environment managed by condathis. The command is run through micromamba run using the internal Conda root.

Usage

run(
  cmd,
  ...,
  env_name = "condathis-env",
  method = c("native", "auto"),
  verbose = c("output", "silent", "cmd", "spinner", "full"),
  error = c("cancel", "continue"),
  stdout = "|",
  stderr = "|",
  stdin = NULL
)

Arguments

cmd: Character string with the command to execute.
...: Additional unnamed command arguments passed to cmd.
env_name: Character string with the target environment name. Defaults to "condathis-env". If the default environment does not exist, it is created automatically.
method: Character string with the backend execution strategy. Supported values are "native" and "auto". Defaults to "native". This argument is soft-deprecated and currently does not change behavior.
verbose: Character string controlling console output. Supported values are "output", "silent", "cmd", "spinner", and "full". Defaults to "output". Logical values are accepted for backward compatibility: TRUE maps to "output" and FALSE maps to "silent".
error: Character string that controls error behavior. Supported values are "cancel" and "continue". Defaults to "cancel".
stdout: Standard output target. Defaults to "|" (capture stdout in the returned object). Provide a file path to redirect stdout to a file.
stderr: Standard error target. Defaults to "|" (capture stderr in the returned object). Provide a file path to redirect stderr to a file.
stdin: Standard input source. Defaults to NULL (no stdin stream). Provide a file path to use file contents as stdin.

Value

A process result list (from processx::run()) with command output, error output, exit status, and timeout information.

Details

This function is the main execution entry point in condathis. Use it to run CLI tools with reproducible dependencies isolated in Conda environments.

Examples

if (FALSE) { # \dontrun{
condathis::with_sandbox_dir({
  ## Create env
  create_env("bioconda::samtools", env_name = "samtools-env")

  ## Run a command in a specific Conda environment
  samtools_res <- run(
    "samtools", "view",
    fs::path_package("condathis", "extdata", "example.bam"),
    env_name = "samtools-env",
    verbose = "silent"
  )
  parse_output(samtools_res)[1]
  #> [1] "SOLEXA-1GA-1_6_FC20ET7:6:92:473:531\t0\tchr1\t10156..."
})
} # }