Install a tool or environment

Install a bioinformatics tool using mamba/micromamba. Can install either: - A single tool by name and version - A complete environment from YAML file

Usage

sn_install_tool(
  tool_name,
  version = NULL,
  base_dir = NULL,
  channel = "bioconda",
  yaml = NULL,
  overwrite = FALSE,
  mamba = NULL
)

Arguments

tool_name

Character. Tool name (used for environment naming and tool installation).

version

Character. Version to install (NULL for latest). Ignored if yaml is provided.

base_dir

Character. Base directory for installations.

channel

Character. Conda channel to use. Ignored if yaml is provided.

yaml

Character. Path to YAML environment file (optional). If provided, installs the environment to base_dir/tool_name.

overwrite

Logical. Force reinstallation.

mamba

Character. Path to mamba/micromamba executable.

Value

Character. Path to the installed environment.

See also

Other tool management: .sn_validate_tool_legacy(), sn_add_tool(), sn_diagnose_tool(), sn_initialize_toolbox(), sn_install_micromamba(), sn_remove_tool(), sn_reset_toolbox(), sn_validate_tool()

Other tool management: .sn_validate_tool_legacy(), sn_add_tool(), sn_diagnose_tool(), sn_initialize_toolbox(), sn_install_micromamba(), sn_remove_tool(), sn_reset_toolbox(), sn_validate_tool()

Examples

if (FALSE) { # \dontrun{
# Install a single tool
sn_install_tool("fastqc")

# Install with specific version
sn_install_tool("samtools", version = "1.16")

# Install from YAML file to custom environment name
sn_install_tool("bioinformatics", yaml = "path/to/environment.yaml")
} # }