Mercurial > repos > testtool > geo_data
changeset 43:660897ee0d12 draft
Uploaded
| author | testtool |
|---|---|
| date | Mon, 24 Apr 2017 10:31:20 -0400 |
| parents | 4987433afb56 |
| children | 1edbb29139af |
| files | GRsetFromGEO/GRsetFromGEO.R GRsetFromGEO/tool_dependencies.xml |
| diffstat | 2 files changed, 14 insertions(+), 3 deletions(-) [+] |
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--- a/GRsetFromGEO/GRsetFromGEO.R Mon Apr 24 10:09:39 2017 -0400 +++ b/GRsetFromGEO/GRsetFromGEO.R Mon Apr 24 10:31:20 2017 -0400 @@ -1,9 +1,10 @@ -require("BiocGenerics", quietly = TRUE) -require("data.table", quietly = TRUE) require("GEOquery", quietly = TRUE) require("minfi", quietly = TRUE) require("FDb.InfiniumMethylation.hg19", quietly = TRUE) +options(warn = -1) +options("download.file.method"="wget") + args <- commandArgs(trailingOnly = TRUE) GSE = args[1] output = args[2] @@ -26,7 +27,13 @@ mergeManifest = FALSE i = 1 -gset <- GEOquery::getGEO(GSE) +gset <- getGEO(GSE) + +if (is.null(GSE)) { + stop("Must specify GSE") +} else { + options(download.file.method.GEOquery = "wget")} + gset <- gset[[1]] platform <- annotation(gset)
--- a/GRsetFromGEO/tool_dependencies.xml Mon Apr 24 10:09:39 2017 -0400 +++ b/GRsetFromGEO/tool_dependencies.xml Mon Apr 24 10:31:20 2017 -0400 @@ -6,6 +6,10 @@ <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="R" version="3.2.1"/> </repository> + <package>https://bioarchive.galaxyproject.org/minfi_1.21.6.tar.gz</package> + + <package>https://bioarchive.galaxyproject.org/GEOquery_2.41.0.tar.gz</package> + <package sha256sum="397c3c90af966f48eebe8f5d9e40c41b17541f0baaa102eec3ea4faae5a2bd49"> https://depot.galaxyproject.org/software/munsell/munsell_0.4.3.tar.gz </package>