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:
check_meme_install(meme_path = NULL)path to "meme/bin" (if unset will search MEME_BIN
environment variable or meme_bin option)
message indicating which MEME utilities are installed and their location on disk
provide the full path to meme/bin to the meme_path argument to each run* function.
set the meme_bin option using options(meme_bin = "path/to/meme/bin") once per R session.
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:
the meme_path function argument if set
the meme_bin option
the MEME_BIN environment variable
the default location at ~/meme/bin
check_meme_install()
#> checking main install
#> ✔ /opt/meme/bin
#> checking util installs
#> ✔ /opt/meme/bin/dreme
#> ✔ /opt/meme/bin/ame
#> ✔ /opt/meme/bin/fimo
#> ✔ /opt/meme/bin/tomtom
#> ✔ /opt/meme/bin/meme
#> ✔ /opt/meme/bin/streme