## This code is part of the megaptera package
## © C. Heibl 2019 (last update 2019-10-30)
#' @title Initialize MEGAPTERA
#' @description Creates a consist system of folders where data and metadata are
#' stored.
#' @param path A vector of mode \code{"character"} that gives the directory
#' where megaptera should store data and results.
#' @details \code{"megapteraInit"} creates a file system that is designed to
#' keep memory requirements and execution times at the necessary minimum
#' during subsequent runs of the MEGAPTERA pipeline. Individula projects can
#' be created with \code{\link{megapteraProj}}.
#' @return None, \code{megapteraInit} is called for its side effects.
#' @seealso \code{\link{megapteraProj}}, \code{\link{ncbiTaxonomy}}
#' @import DBI
#' @importFrom restez db_download restez_path_set
#' @export
megapteraInit <- function(path){
megaptera_path <- file.path(path, "megaptera_data")
taxonomy_path <- file.path(megaptera_path, "gb_taxonomy")
sequence_path <- file.path(megaptera_path, "gb_sequence")
project_path <- file.path(megaptera_path, "project")
## root directory 'megaptera_data'
## -------------------------------
if (!dir.exists(megaptera_path)){
dir.create(megaptera_path)
info <- c(as.character(Sys.time()),
packageDescription("megaptera")$Version)
info <- paste(info, collapse = "\n")
write(info, file.path(megaptera_path, "INFO"))
} else {
info <- scan(file.path(megaptera_path, "INFO"),
what = "c", sep = "\n", quiet = TRUE)
message("megaptera file system was already initialized on ",
info[1], " by package version ", info[2])
}
## Make sure that subdirectories exist
## -----------------------------------
if (!dir.exists(taxonomy_path)){
dir.create(taxonomy_path)
}
if (!dir.exists(sequence_path)){
dir.create(sequence_path)
}
if (!dir.exists(project_path)){
dir.create(project_path)
}
}
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