Pre-install UCSC's gff3ToGenePred binary — gdb.install_gff3

Downloads UCSC's gff3ToGenePred static binary (~25 MB) into tools::R_user_dir("misha", "cache")/bin/, verifies its SHA256, and makes it executable. Used by gdb.build_genome when the ncbi backend (or the manual backend with genes_format: gff3) is invoked. Calling it directly is useful in CI or in non-interactive scripts where the consent prompt would otherwise fail.

gdb.install_gff3_converter(force = FALSE)

Arguments

force: If TRUE, skip the consent prompt and re-download even if the binary is already cached.

Value

The cache path of the installed binary (invisibly).

Details

Override the binary location by setting environment variable MISHA_GFF3_TO_GENEPRED to a binary you provide (for example, one installed via conda install -c bioconda ucsc-gff3togenepred). This is the recommended workaround on systems whose glibc is older than the one UCSC's prebuilt binary requires.

Examples

if (FALSE) { # \dontrun{
gdb.install_gff3_converter()
Sys.setenv(MISHA_GFF3_TO_GENEPRED = "/path/to/your/gff3ToGenePred")
} # }