Mercurial > repos > deepakjadmin > rcpp_edger_limma_test3

changeset 0:6bca60a11948 draft

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Uploaded
author deepakjadmin
date Thu, 24 Sep 2015 03:03:08 -0400
parents
children 3e852cd7f528
files rtest.xml tool_dependencies.xml yueer.R
diffstat 3 files changed, 55 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rtest.xml	Thu Sep 24 03:03:08 2015 -0400
@@ -0,0 +1,23 @@
+<tool id="djvytfdgkdls" 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`; 
+  		 echo \$GALAXY_ROOT_DIR &gt; $log 2 &gt;&amp;1;
+                 cd ../../../../;
+                 GALAXY_ROOT_DIR=`pwd`;
+                 echo \$GALAXY_ROOT_DIR &gt; $log 2 &gt;&amp;1;
+                 \$R_ROOT_DIR/bin/Rscript \${GALAXY_ROOT_DIR}/tools/toop2/test.R $output  &gt; $log 2 &gt;&amp;1
+   </command>
+  <outputs>
+    <data type="data" name="output" label ="outputfile" />
+    <data type="text" name="log" label ="packages loaded" />
+  </outputs>
+  <help>
+ 
+  </help>
+</tool>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Sep 24 03:03:08 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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/yueer.R	Thu Sep 24 03:03:08 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)