# HG changeset patch
# User testtool
# Date 1489677818 14400
# Node ID ee3fc24b21082d769bae51998778796190ffd9de
# Parent  53df7871db2187117f6067087b1a08a84e0f51b8
Uploaded

diff -r 53df7871db21 -r ee3fc24b2108 annotate_peak/annotatePeak.R
--- a/annotate_peak/annotatePeak.R	Thu Mar 16 11:03:24 2017 -0400
+++ b/annotate_peak/annotatePeak.R	Thu Mar 16 11:23:38 2017 -0400
@@ -1,3 +1,8 @@
+require("ChIPseeker", quietly = TRUE)
+require("ChIPpeakAnno", quietly = TRUE)
+require("EnsDb.Hsapiens.v75", quietly = TRUE)
+require("GenomicRanges", quietly = TRUE)
+
 options(warn = -1)
 args <- commandArgs(trailingOnly = TRUE)
 DMR = args[1]
@@ -16,10 +21,6 @@
                     ranges = IRanges
                     (start = DMRInfo[, 2], end = DMRInfo[, 3]))
 peaks[1:2]
-## try http:// if https:// URLs are not supported
-source("https://bioconductor.org/biocLite.R")
-biocLite("EnsDb.Hsapiens.v75")
-library(EnsDb.Hsapiens.v75)
 annoData <- toGRanges(EnsDb.Hsapiens.v75)
 annoData[1:2]
 
diff -r 53df7871db21 -r ee3fc24b2108 annotate_peak/tool_dependencies.xml
--- a/annotate_peak/tool_dependencies.xml	Thu Mar 16 11:03:24 2017 -0400
+++ b/annotate_peak/tool_dependencies.xml	Thu Mar 16 11:23:38 2017 -0400
@@ -10,6 +10,7 @@
                       <package>https://www.bioconductor.org/packages/release/bioc/src/contrib/ChIPpeakAnno_3.8.9.tar.gz</package>
                       <package>https://bioconductor.org/packages/release/bioc/src/contrib/GenomicRanges_1.26.3.tar.gz</package>
                       <package>https://bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.20.0.tar.gz</package>
+                      <package>http://bioconductor.org/packages/release/data/annotation/src/contrib/EnsDb.Hsapiens.v75_2.1.0.tar.gz</package>
 
                       <package sha256sum="397c3c90af966f48eebe8f5d9e40c41b17541f0baaa102eec3ea4faae5a2bd49">
                             https://depot.galaxyproject.org/software/munsell/munsell_0.4.3.tar.gz