From 0e768b5342ea9a1caa292f507d0537b87fa6b46c Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sat, 11 Aug 2018 20:37:26 -0500
Subject: [PATCH] Fix library issues for R.
---
workflow/scripts/annotate_peaks.R | 24 ++++++++----------------
workflow/scripts/dba.R | 6 +-----
2 files changed, 9 insertions(+), 21 deletions(-)
diff --git a/workflow/scripts/annotate_peaks.R b/workflow/scripts/annotate_peaks.R
index 74c60b3..6a0fb4a 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 42986d2..31ccf72 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)
--
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