Mercurial > repos > testtool > geo_data
changeset 42:4987433afb56 draft
Uploaded
| author | testtool |
|---|---|
| date | Mon, 24 Apr 2017 10:09:39 -0400 |
| parents | 1ed398538e91 |
| children | 660897ee0d12 |
| files | GRsetFromGEO/GRsetFromGEO.R GRsetFromGEO/tool_dependencies.xml |
| diffstat | 2 files changed, 7 insertions(+), 9 deletions(-) [+] |
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--- a/GRsetFromGEO/GRsetFromGEO.R Mon Apr 24 10:04:18 2017 -0400 +++ b/GRsetFromGEO/GRsetFromGEO.R Mon Apr 24 10:09:39 2017 -0400 @@ -1,5 +1,7 @@ +require("BiocGenerics", quietly = TRUE) +require("data.table", quietly = TRUE) +require("GEOquery", quietly = TRUE) require("minfi", quietly = TRUE) -require("GEOquery", quietly = TRUE) require("FDb.InfiniumMethylation.hg19", quietly = TRUE) args <- commandArgs(trailingOnly = TRUE) @@ -24,7 +26,7 @@ mergeManifest = FALSE i = 1 -gset <- getGEO(GSE) +gset <- GEOquery::getGEO(GSE) gset <- gset[[1]] platform <- annotation(gset)
--- a/GRsetFromGEO/tool_dependencies.xml Mon Apr 24 10:04:18 2017 -0400 +++ b/GRsetFromGEO/tool_dependencies.xml Mon Apr 24 10:09:39 2017 -0400 @@ -1,5 +1,6 @@ -<?xml version='1.0' encoding='utf-8' ?> +<?xml version="1.0"?> <tool_dependency> + <install version="1.0"> <actions> <action type="setup_r_environment"> <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> @@ -267,11 +268,6 @@ https://depot.galaxyproject.org/software/FDb.InfiniumMethylation.hg19/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz </package> </action> - <action type="download_by_url" > - https://depot.galaxyproject.org/software/bioconductor-minfi/bioconductor-minfi_1.20.0_src_all.tar.gz -</action> -<action type="download_by_url" > - https://depot.galaxyproject.org/software/bioconductor-geoquery/bioconductor-geoquery_2.38.4_src_all.tar.gz -</action> </actions> + </install> </tool_dependency>