diff --git a/workflow/scripts/annotate_peaks.R b/workflow/scripts/annotate_peaks.R index 74c60b3a137144c3335d1dc7a14ac45f3e308d7f..6a0fb4aaa82dde146a1606e886b264b0b309e3e3 100644 --- a/workflow/scripts/annotate_peaks.R +++ b/workflow/scripts/annotate_peaks.R @@ -1,26 +1,18 @@ #!/bin/Rscript # Load libraries +library("ChIPseeker") + +# Currently mouse or human + +library("TxDb.Hsapiens.UCSC.hg19.knownGene") +library("TxDb.Mmusculus.UCSC.mm10.knownGene") +library("TxDb.Hsapiens.UCSC.hg38.knownGene") + source("http://bioconductor.org/biocLite.R") if(!require("ChIPseeker")){ biocLite("ChIPseeker") - library("ChIPseeker") -} - -# Currently mouse or human -if (!require("TxDb.Hsapiens.UCSC.hg19.knownGene")){ - biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene") - library("TxDb.Hsapiens.UCSC.hg19.knownGene") -} -if (!require("TxDb.Mmusculus.UCSC.mm10.knownGene")){ - biocLite("TxDb.Mmusculus.UCSC.mm10.knownGene") - library("TxDb.Mmusculus.UCSC.mm10.knownGene") } -if (!require("TxDb.Hsapiens.UCSC.hg38.knownGene")){ - biocLite("TxDb.Hsapiens.UCSC.hg38.knownGene") - library("TxDb.Hsapiens.UCSC.hg38.knownGene") -} - # Create parser object diff --git a/workflow/scripts/dba.R b/workflow/scripts/dba.R index 42986d23afa1b5cc0c699ad27ec68468be8ea9df..31ccf7239017efa9013e6c5201318f27795b2fef 100644 --- a/workflow/scripts/dba.R +++ b/workflow/scripts/dba.R @@ -1,11 +1,7 @@ #!/bin/Rscript # Load libraries -source("http://bioconductor.org/biocLite.R") -if(!require("DiffBind")){ - biocLite("DiffBind") - library("DiffBind") -} +library("DiffBind") # Create parser object args <- commandArgs(trailingOnly=TRUE)