post_install() { script=$(cat <<-EOF # CountsQC if(!require("optparse")) { install.packages("optparse", repos = "http://cran.r-project.org") } if(!require("NOISeq")) { source("http://bioconductor.org/biocLite.R"); biocLite("NOISeq") } # Epigenetics if(!require("XML")) { install.packages("XML", repos = "http://cran.r-project.org") } if(!require("Repitools")) { source("http://bioconductor.org/biocLite.R"); biocLite("Repitools") } if(!require("Rsamtools")) { source("http://bioconductor.org/biocLite.R"); biocLite("Rsamtools") } if(!require("rtracklayer")) { source("http://bioconductor.org/biocLite.R"); biocLite("rtracklayer") } EOF ) echo "${script}" > /tmp/qualimap-install-dependencies.R export R_USER=root Rscript /tmp/qualimap-install-dependencies.R }