Package 'Herper'

Search package availabilty

Description

Search package availabilty

Usage

conda_search(package, channel = NULL, print_out = TRUE, pathToMiniConda = NULL)

Arguments

package	Package to search for. If an exact match is found, the funtion will return true (assuming 'package_version' is left NULL or is a valid entry). If there is not an exact match and other packages contain this text, the function will return FALSE but the alternative options will be printed if print_out = TRUE.
channel	Channels for to search in (bioconda and conda-forge are defaults).
print_out	Either True or FALSE indicating whether to print out information about available builds and channels for the search entry.
pathToMiniConda	Path to miniconda installation. If this is set to NULL (default), then the output of 'reticulate::miniconda_path()' is used.

Value

TRUE/FALSE

Author(s)

Doug Barrows and Matt Paul

Examples

condaPaths <- install_CondaTools("salmon", "herper_env")
conda_search("salmon")

---

Export Conda environment.

Description

Export Conda environment

Import Conda environment

Usage

export_CondaEnv(
  env_name,
  yml_export = NULL,
  pathToMiniConda = NULL,
  depends = TRUE
)

import_CondaEnv(
  yml_import,
  name = NULL,
  pathToMiniConda = NULL,
  install = TRUE,
  channels = NULL
)

Arguments

env_name	Name of environment you want to save
yml_export	Destination for exported environment yml file
pathToMiniConda	NULL Path to miniconda installation
depends	if FALSE will only include packages explicitly installed and not dependencies
yml_import	conda environment yml file
name	Name of the environment to create.
install	TRUE/FALSE whether to install miniconda at path if it doesn't exist.
channels	Channels for miniconda (bioconda and conda-forge are defaults).

Value

Nothing returned. Output written to file.

Nothing returned. Output written to file.

Author(s)

Matt Paul

---

Install Conda requirements listed in the System Requirement field of description

Description

Install Conda requirements

Usage

install_CondaSysReqs(
  pkg,
  channels = NULL,
  env = NULL,
  pathToMiniConda = NULL,
  updateEnv = FALSE,
  SysReqsAsJSON = FALSE,
  SysReqsSep = ",",
  verbose = FALSE
)

Arguments

pkg	Package to install Conda System Requirements from.
channels	Channels for miniconda (bioconda and conda-forge are defaults).
env	Name of Conda environment to install tools into.
pathToMiniConda	NULL Path to miniconda installation
updateEnv	Update existing package's conda environment if already installed.
SysReqsAsJSON	Parse the SystemRequirements in JSON format (see Details). Default is TRUE.
SysReqsSep	Separator used in SystemRequirement field.
verbose	Print system messages from conda on progress (Default is FALSE). There is a third option "silent" which suppresses Herper and Conda messaging.

Value

Nothing returned. Output written to file.

Author(s)

Thomas Carroll

Examples

testPkg <- system.file("extdata/HerperTestPkg", package = "Herper")
install.packages(testPkg, type = "source", repos = NULL)
condaPaths <- install_CondaSysReqs("HerperTestPkg", SysReqsAsJSON = FALSE)
system2(file.path(condaPaths$pathToEnvBin, "samtools"), args = "--help")

---

Install Conda requirements.

Description

Install Conda requirements

Usage

install_CondaTools(
  tools,
  env,
  channels = NULL,
  pathToMiniConda = NULL,
  updateEnv = FALSE,
  search = FALSE,
  verbose = FALSE
)

Arguments

tools	Vector of software to install using conda.
env	Name of Conda environment to install tools into.
channels	Channels for miniconda (bioconda and conda-forge are defaults).
pathToMiniConda	NULL Path to miniconda installation
updateEnv	Update existing package's conda environment if already installed.
search	Whether to search for the package name and version before installing. It is highly recommended this be set to TRUE as information about available versions or similar packages will be included in the output if the exact match is not found.
verbose	Print system messages from conda on progress (Default is FALSE). There is a third option "silent" which suppresses Herper and Conda messaging.

Value

Nothing returned. Output written to file.

Author(s)

Thomas Carroll

Examples

condaPaths <- install_CondaTools("salmon", "herper_env")
system2(file.path(condaPaths$pathToEnvBin, "salmon"), args = "--help")

---

List Conda environments.

Description

List Conda environments

Usage

list_CondaEnv(pathToMiniConda = NULL, allCondas = FALSE, env = NULL)

Arguments

pathToMiniConda	NULL Path to miniconda installation
allCondas	Logical. Whether to return conda environments, for all discoverable conda installs, or just the conda specified in pathToMiniConda.
env	Environment name. If this is supplied to list_CondaEnv, it will query whether that environment is present in the given conda.

Value

Conda environment names and the file paths to their conda installation are printed to the screen. If environment name is supplied a TRUE/FALSE will be returned depending on whether that environment is present or not.

Author(s)

Matt Paul

Examples

condaPaths <- install_CondaTools("salmon", "herper_env")
list_CondaEnv()
list_CondaEnv( env = "herper_env")

---

List Conda packages.

Description

List Conda packages

Usage

list_CondaPkgs(env, pathToMiniConda = NULL, pkg = NULL)

Arguments

env	environment to look in
pathToMiniConda	NULL Path to miniconda installation
pkg	Package name. If this is supplied to list_CondaPkg, it will query whether that package is present in the given environment.

Value

Conda package information is printed to the screen. If package name is supplied a TRUE/FALSE will be returned depending on whether that package is present or not.

Author(s)

Matt Paul

Examples

condaPaths <- install_CondaTools("salmon", "herper_env")
list_CondaPkgs("herper_env")

---

Use Conda environments.

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 = list(),
  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

local_CondaEnv(new = "herper_env")

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