Mercurial > repos > testtool > annotate_peak
changeset 16:ee3fc24b2108 draft
Uploaded
| author | testtool |
|---|---|
| date | Thu, 16 Mar 2017 11:23:38 -0400 |
| parents | 53df7871db21 |
| children | 982a01524118 |
| files | annotate_peak/annotatePeak.R annotate_peak/tool_dependencies.xml |
| diffstat | 2 files changed, 6 insertions(+), 4 deletions(-) [+] |
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--- 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]
--- 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