UseEnvironments: Use Conda environments.

In Herper: The Herper package is a simple toolset to install and manage conda packages and environments from R

Description

Use Conda environments

Use Conda environments

Usage

with_CondaEnv(
  new,
  code,
  pathToMiniConda = NULL,
  path_action = "prefix",
  pythonpath_action = "replace",
  perl5lib_action = "replace",
  path_additional = NULL,
  pythonpath_additional = NULL,
  perl5lib_additional = NULL
)

local_CondaEnv(
  new,
  pathToMiniConda = NULL,
  path_action = "prefix",
  pythonpath_action = "replace",
  perl5lib_action = "replace",
  path_additional = NULL,
  pythonpath_additional = NULL,
  perl5lib_additional = NULL,
  .local_envir = parent.frame()
)

Arguments

new	The name of conda environment to include in the temporary R environment.
code	Code to execute in the temporary R environment
pathToMiniConda	Path to miniconda.
path_action	Should new values "replace", "prefix" or "suffix" existing PATH variable.
pythonpath_action	Should new values "replace", "prefix" or "suffix" existing PYTHONPATH variable.
perl5lib_action	Should new values "replace", "prefix" or "suffix" existing PERL5LIB variable.
path_additional	Additional paths to suffix to existing PATH variable.
pythonpath_additional	Additional paths to suffix to existing PYTHONPATH variable.
perl5lib_additional	Additional paths to suffix to existing PERL5LIB variable.
.local_envir	The environment to use for scoping.

Value

Nothing returned.

Author(s)

Thomas Carroll

Examples

testYML <- system.file("extdata/test.yml",package="Herper")
condaDir <- file.path(tempdir(),"r-miniconda")
import_CondaEnv(testYML,"HerperTest",pathToMiniConda=condaDir)
with_CondaEnv("HerperTest",system2(command = "multiqc",args = ,"--version"),
    pathToMiniConda = condaDir)
## Not run: 
  install_CondaTools("cytoscape","cytoscape",updateEnv = TRUE,pathToMiniConda = condaDir)
  with_CondaEnv("cytoscape",system2(command = "cytoscape.sh"),pathToMiniConda = condaDir)

## End(Not run)

Herper documentation built on Feb. 28, 2021, 2:02 a.m.