Mercurial > repos > deepakjadmin > rcpp_edger_limma_test2
changeset 0:7171114c3734 draft
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 23 Sep 2015 14:24:35 -0400 |
| parents | |
| children | 5e3fd49af978 |
| files | rtest.xml test.R tool_dependencies.xml |
| diffstat | 3 files changed, 52 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rtest.xml Wed Sep 23 14:24:35 2015 -0400 @@ -0,0 +1,20 @@ +<tool id="djvfdgkdls" name="R 3.2.0 test" version="1.0.0"> + <description>R version and installation test</description> +<requirements> + <requirement type="set_environment">R_ROOT_DIR</requirement> + <requirement type="package" version="3.2.0">R</requirement> + <requirement type="package" version="3.24.12">limma</requirement> +</requirements> + <command> GALAXY_ROOT_DIR=`pwd`; + cd ../../../../; + GALAXY_ROOT_DIR=`pwd`; + \$R_ROOT_DIR/bin/Rscript \${GALAXY_ROOT_DIR}/tools/toop2/test.R $output; + </command> + <outputs> + <data type="data" name="output" label ="outputfile" /> + </outputs> + <help> + + </help> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test.R Wed Sep 23 14:24:35 2015 -0400 @@ -0,0 +1,6 @@ +args <- commandArgs(T) +arg1 <- args[1] ## Reae Input prediction file +library("Rcpp") +library("edgeR") +asd <- sessionInfo() +save(asd,file=arg1)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Sep 23 14:24:35 2015 -0400 @@ -0,0 +1,26 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="R" version="3.2.0"> + <repository changeset_revision="d973c8e9b29e" name="package_r_3_2_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + + <package name="limma" version="3.24.12"> + <install version="1.0"> + <actions> + <action type="setup_r_environment"> + <repository changeset_revision="d973c8e9b29e" name="package_r_3_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="R" version="3.2.0" /> + </repository> + <package>https://bioarchive.galaxyproject.org/limma_3.25.3.tar.gz?raw=true</package> + <package>http://bioconductor.org/packages/release/bioc/src/contrib/edgeR_3.10.2.tar.gz?raw=true</package> + <package>https://cran.r-project.org/src/contrib/Rcpp_0.12.1.tar.gz?raw=true</package> + </action> + </actions> + + </install> + <readme> +limma_3.24.12 installed now try edgeR + </readme> + </package> + +</tool_dependency>