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Install the DIAMOND aligner into the user cache

Source: R/diamond_install.R
diamond_install.Rd

Downloads a pre-compiled DIAMOND2 binary from the official GitHub releases (https://github.com/bbuchfink/diamond/releases) that matches the operating system of the user and stores it in a user-level cache directory (see R_user_dir). No administrator rights are required. Once installed, diamond, diamond_best, diamond_rec, set_diamond, deepclust and deepclust_realign find the cached binary automatically whenever path = NULL and no diamond is available on the PATH.

Usage

diamond_install(version = "latest", force = FALSE, quiet = FALSE)

Arguments

version

a DIAMOND release tag, e.g. "v2.1.9". The default "latest" uses the most recent release.

force

logical; re-download even if DIAMOND is already cached.

quiet

logical; suppress progress messages.

Value

Invisibly, the directory containing the diamond executable. This can be passed to the path argument of the DIAMOND functions.

Details

Pre-compiled binaries are provided upstream for Linux (x86_64), macOS and Windows (x86_64). On other platforms (e.g. Linux ARM) please install DIAMOND via conda: conda install -c bioconda diamond.

See also

diamond_path, diamond

Examples

if (FALSE) { # \dontrun{
diamond_install()
diamond_path()
} # }