Create a Conda environment

Creates a Conda environment managed by condathis and installs dependencies from package specs or from an environment file.

Usage

create_env(
  packages = NULL,
  env_file = NULL,
  env_name = "condathis-env",
  channels = c("conda-forge", "bioconda"),
  method = c("native", "auto"),
  channel_priority = c("disabled", "strict", "flexible"),
  additional_channels = NULL,
  platform = NULL,
  verbose = c("output", "silent", "cmd", "spinner", "full"),
  overwrite = FALSE
)

Arguments

packages

Character vector of package MatchSpec strings. Examples: "python=3.13", "bioconda::fastqc==0.12.1". Defaults to NULL.

env_file

Character string with the path to an environment YAML file. Defaults to NULL. When provided, it is passed to micromamba create -f.

env_name

Character string with the target environment name. Defaults to "condathis-env".

channels

Character vector with channel names used for dependency resolution. Defaults to c("conda-forge", "bioconda").

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.

channel_priority

Character string with channel priority mode. Supported values are "disabled", "strict", and "flexible". Defaults to "disabled".

additional_channels

Character vector of additional channels appended to channels. Defaults to NULL.

platform

Character string with the platform used for dependency solving (for example, "linux-64", "osx-64", "osx-arm64", "win-64", "noarch"). Defaults to NULL. On Apple Silicon, condathis may fall back to "osx-64" when Rosetta 2 is available and packages are not available for "osx-arm64".

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".

overwrite

Logical value that controls whether an existing environment should always be recreated. Defaults to FALSE.

Value

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

Examples

if (FALSE) { # \dontrun{
condathis::with_sandbox_dir({
  # Create a Conda environment and install the CLI `fastqc` in it.
  # Explicitly using the channel `bioconda` and version `0.12.1`.
  condathis::create_env(
    packages = "bioconda::fastqc==0.12.1",
    env_name = "fastqc-env",
    verbose = "output"
  )
})
} # }