condathis (version 0.1.1)

create_env: Create a Conda Environment

Description

Create Conda Environment with specific packages installed to be used by run().

Usage

create_env(
  packages = NULL,
  env_file = NULL,
  env_name = "condathis-env",
  channels = c("bioconda", "conda-forge"),
  method = c("native", "auto"),
  additional_channels = NULL,
  platform = NULL,
  verbose = "silent",
  overwrite = FALSE
)

Value

An object of class list representing the result of the command execution. Contains information about the standard output, standard error, and exit status of the command.

Arguments

packages

Character vector. Names of the packages, and version strings if necessary, e.g. 'python=3.11'. The use of the packages argument assumes that env_file is not used.

env_file

Character. Path to the YAML file with Conda Environment description. If this argument is used, the packages argument should not be included in the command.

env_name

Character. Name of the Conda environment where the packages are going to be installed. Defaults to 'condathis-env'.

channels

Character vector. Names of the channels to be included. By default 'c("bioconda", "conda-forge")' are used for solving dependencies.

method

Character. Beckend method to run micromamba, the default is "auto" running "native" with the micromamba binaries installed by condathis. This argument is soft deprecated as changing it don't really do anything.

additional_channels

Character. Additional Channels to be added to the default ones.

platform

Character. Platform to search for packages. Defaults to NULL which will use the current platform. E.g. "linux-64", "linux-32", "osx-64", "win-64", "win-32", "noarch". Note: on Apple Silicon MacOS will use "osx-64" instead of "osx-arm64" if Rosetta 2 is available and any of the packages is not available for "osx-arm64".

verbose

Character string specifying the verbosity level of the function's output. Acceptable values are:

• "silent": Suppress all output from internal command-line tools. Equivalent to FALSE.

• "cmd": Print the internal command(s) passed to the command-line tool.

• "output": Print the standard output and error from the command-line tool to the screen. Note that the order of the standard output and error lines may not be correct, as standard output is typically buffered. If the standard output and/or error is redirected to a file or they are ignored, they will not be echoed.

• "full": Print both the internal command(s) ("cmd") and their standard output and error ("output"). Equivalent to TRUE. Logical values FALSE and TRUE are also accepted for backward compatibility but are soft-deprecated. Please use "silent" and "full" respectively instead.

overwrite

Logical. Should environment always be overwritten? Defaults to FALSE.

Examples

if (FALSE) {
condathis::with_sandbox_dir({
  # Create a Conda environment and install the CLI `fastqc` in it.
  condathis::create_env(
    packages = "fastqc==0.12.1",
    env_name = "fastqc-env",
    verbose = "output"
  )
  #> ! Environment fastqc-env succesfully created.
})
}