check_meme_install: Check user's MEME install

In snystrom/memes: motif matching, comparison, and de novo discovery using the MEME Suite

Check user's MEME install

Description

In order to use the run* family of functions, memes must detect a local install of the MEME Suite. MEME is installed in a directory named meme/bin/ which can be located anywhere on the filesystem, but is typically found in ⁠~/meme/bin⁠. If the MEME Suite is installed at ⁠~/meme/bin⁠, memes can autodetect the install. However, in the case that the MEME Suite is found at a nonstandard location, the user may specify the location of their meme/bin in three ways:

Usage

check_meme_install(meme_path = NULL)

Arguments

meme_path

path to "meme/bin" (if unset will search MEME_BIN environment variable or meme_bin option)

Details

1. provide the full path to meme/bin to the meme_path argument to each ⁠run*⁠ function.

2. set the meme_bin option using options(meme_bin = "path/to/meme/bin") once per R session.

3. set the MEME_BIN environment variable either in .Renviron or ⁠~/.bashrc⁠ with the path to meme/bin

To aid the user in determining if memes can detect their meme/bin install, check_meme_install() will search the aforementioned locations for a valid meme/bin, returning green checks for each detected tool, or red X's for undetected tools. Alternatively, users can run meme_is_installed() to get a boolean value indicating whether their MEME Suite can be detected.

check_meme_install() searches using the following heirarchy. This heirarchy mimics how all ⁠run*⁠ functions search for meme/bin, thus the paths printed from check_meme_install() will indicate the paths used by each ⁠run*⁠ function. The heirarchy is as follows:

1. the meme_path function argument if set

2. the meme_bin option

3. the MEME_BIN environment variable

4. the default location at ⁠~/meme/bin⁠

Value

message indicating which MEME utilities are installed and their location on disk

Examples

check_meme_install()

snystrom/memes documentation built on Oct. 12, 2024, 2:42 a.m.