Get started • lineaGT

Installation of the package

You can install LineaGT from GitHub using devtools.

devtools::install_github("caravagnalab/lineaGT")

Load the package.

library(lineaGT)

Python dependencies installation

When the package is loaded, the package will automatically check whether:

a version of Anaconda or Miniconda is available, otherwise a Miniconda installation will be started,
if there is no conda environment loaded, the package will check if the lineagt-env is present, otherwise it will be created,
to use an existing conda environment, it can be loaded before loading the package, either through the reticulate function reticulate::use_condaenv() or by using the lineaGT function load_conda_env():

reticulate::use_condaenv("env-name", required=TRUE)
load_conda_env(envname="env-name")

eventually, if the required Python dependencies are not installed in the loaded environment, they will be installed.

Functions to manually configure an environment

The function pylineaGT can also be used interactively to manually configure an existing environment, or to create one from scratch.

configure_environment(env_name="lineaget-env", use_default=F)

The function will first check if a Anaconda or Miniconda installation is available, otherwise it will prompt a Miniconda installation. The input name of the environment is either the name of an existing environment or the name of the environment to be created. The environment will be loaded or created, and the required Python dependencies will be installed.

Check the loaded Python version and environment

The package provides also a set of helper functions to check if an environment is loaded.

have_loaded_env() to check if an environment is already loaded,
which_conda_env() to check which environment is loaded.
have_python_deps() to check if a Python packages list is installed in the specified environment.
load_conda_env() to load the specified environment.