Find an external tool — find

Locates an external bioinformatics tool using a hybrid resolution strategy:

Explicit path if provided
Conda prefix (direct path to environment) if specified
Conda environment name if specified
System PATH as fallback

Usage

find_tool(
  tool,
  tool_path = NULL,
  conda_prefix = NULL,
  conda_env = NULL,
  error = TRUE
)

Arguments

tool: Character. Name of the tool (e.g., "diamond", "mmseqs").
tool_path: Character. Optional explicit path to the tool binary.
conda_prefix: Character. Optional direct path to a conda/mamba environment (e.g., "./this_project_env"). The tool is expected at <prefix>/bin/<tool>.
conda_env: Character. Optional conda environment name (looked up in standard conda envs directory).
error: Logical. Whether to error if tool not found (default: TRUE).

Value

Character path to the tool, or NULL if not found and error = FALSE.

Examples

if (FALSE) { # \dontrun{
find_tool("diamond")
find_tool("diamond", conda_prefix = "./this_project_env")
find_tool("diamond", conda_env = "bioinf")
find_tool("diamond", tool_path = "/opt/diamond/diamond")
} # }