make_vignette.R

#' @title make_vignette
#' @name make_vignette
#' @description This function tries to build the prerequisite last-1595,
#' KaKs_calculator2.0 and DAGchainer from source code forked within CRBHits
#' @return path of prerequisites
#' @references Kiełbasa SM et al. (2011) Adaptive seeds tame genomic sequence
#' comparison. \bold{Genome Res.} \bold{21} \bold{(3)}, 487-93.
#' @references Wang D, Zhang Y et al. (2010) KaKs_Calculator 2.0: a toolkit
#' incorporating gamma-series methods and sliding window strategies.
#' \emph{Genomics Proteomics Bioinformatics.} \bold{8(1)}, 77-80.
#' @references Haas BJ et al. (2004) DAGchainer: a tool for mining segmental
#' genome duplications and synteny. \bold{Bioinformatics}
#' \bold{20} \bold{(18)}, 3643-6.
#' @export make_vignette
#' @author Kristian K Ullrich

make_vignette <- function(){
    CRBHits_root <- system.file(package="CRBHits")
    LastTempDir <- tempdir()
    system2(command="unzip", args=c("-o",
        paste0(CRBHits_root, "/extdata/last-1595.zip"), "-d", LastTempDir))
    system2(command="cd", args=c(paste0(LastTempDir, "/last-1595/;"), "make"))
    #KaKsCalcTempDir <- tempdir()
    #system2(command="tar", args=c("-C", KaKsCalcTempDir, "-xvf",
    #    paste0(CRBHits_root, "/extdata/KaKs_Calculator2.0_src.tar.gz")))
    #system2(command="cd", args=c(
    #    paste0(KaKsCalcTempDir, "/KaKs_Calculator2.0_src/src/;"),
    #    "make", "clean;", "make"))
    DAGchainerTempDir <- tempdir()
    system2(command="unzip", args=c("-o", paste0(CRBHits_root,
        "/extdata/dagchainer.zip"), "-d", DAGchainerTempDir))
    system2(command="cd", args=c(paste0(DAGchainerTempDir, "/dagchainer/;"),
        "make"))
    return(c(
        paste0(LastTempDir, "/last-1595/bin/"),
        #paste0(KaKsCalcTempDir, "/KaKs_Calculator2.0_src/src/"),
        paste0(DAGchainerTempDir, "/dagchainer/")))
}