find_executable_seacr: Find executable: 'SEACR'

In neurogenomics/PeakyFinders: Mining, Calling, and Importing Epigenomic Peaks in R

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 March 24, 2024, 4:28 p.m.