find_executable_seacr: Find executable: 'SEACR'

View source: R/find_executable_seacr.R

find_executable_seacrR Documentation

Find executable: SEACR

Description

Find path to the executable file for SEACR.

Usage

find_executable_seacr(
  packages = c("SEACR_1.3.sh", "SEACR_1.3.R"),
  outdir = tempdir(),
  fix_script = TRUE,
  verbose = TRUE,
  ...
)

Arguments

packages

A package (e.g. "pandas") or a list of packages (e.g. c("pandas","r-dplyr","bgzip")). Will recognize R packages with or without the prefixes "r-" and "bioconductor-" (i.e. "r-dplyr" is equivalent to "dplyr").

verbose

Print messages.

...

Arguments passed on to echoconda::find_packages

conda_env

Conda environments to search in. If NULL (default), will search all conda environments.

conda

The path to a conda executable. Use "auto" to allow reticulate to automatically find an appropriate conda binary. See Finding Conda and conda_binary() for more details.

method

Method to use:

  • "basilisk"

  • "reticulate"

types

Path type to search for and include in the table.

return_path

Return only the path to each package.

robust

Uses a more robust (but slower) method for identifying paths to conda environments and package executables (default: FALSE). When robust=FALSE, only executables in the main "bin" directory will be detected. When robust=TRUE, additional executables to R packages, Python packages, and executables in nested subdirectories will be detected.

filter_paths

Filter out packages without callable executable paths from the table.

sort_names

Sort packages alphanumerically by their name.

nThread

Number of threads to use when parallelizing searches across multiple conda envs.

Value

Path to SEACR executable.

Source

GitHub Issue: illegal byte sequence


neurogenomics/PeakyFinders documentation built on Oct. 14, 2024, 3:09 p.m.