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# Moves BLAT files to the package location for straight BLAT usage
# http://genome.ucsc.edu/goldenPath/help/blatSpec.html
# Author : Sylvain Mareschal <mareschal@ovsa.fr>
blatInstall = function(
blat,
cygwin
)
{
# Directory
package = find.package("cghRA", quiet=TRUE, verbose=FALSE)
dir.create(sprintf("%s/blat", package), showWarnings=FALSE)
# Cygwin DLL
message("Cygwin DLL : ", appendLF=FALSE)
if(.Platform$OS.type == "windows") {
# Windows
if(missing(cygwin)) {
message("WARNING (missing and required if Cygwin is not installed)")
} else {
if(basename(cygwin) != "cygwin1.dll") {
message("ERROR (incorrect file name, should be 'cygwin1.dll')")
} else if(!file.exists(cygwin)) {
message("ERROR (file not found)")
} else if(!suppressWarnings(file.copy(cygwin, sprintf("%s/blat/cygwin1.dll", package), overwrite=TRUE))) {
message("ERROR (copy failure at file system level)")
} else {
message("OK (valid and copied)")
}
}
} else {
# UNIX
if(missing(cygwin)) message("OK (missing and not required)")
else message("OK (provided and ignored)")
}
# BLAT exe
message("BLAT exe : ", appendLF=FALSE)
if(missing(blat)) {
message("ERROR (not provided)")
} else if(!file.exists(blat)) {
message("ERROR (file not found)")
} else if(!suppressWarnings(file.copy(blat, sprintf("%s/blat/blat.exe", package), overwrite=TRUE))) {
message("ERROR (copy failure at file system level)")
} else {
message("OK (valid and copied)")
}
}
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