Mercurial > repos > pieterlukasse > prims_metabolomics_r_dependencies

changeset 0:d57322d79cfe

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initial
author pieter.lukasse@wur.nl
date Thu, 06 Nov 2014 16:04:57 +0100
parents
children e6171a39dd04
files INSTALL.r tool_dependencies.xml
diffstat 2 files changed, 60 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/INSTALL.r	Thu Nov 06 16:04:57 2014 +0100
@@ -0,0 +1,16 @@
+# get R http://cran.r-project.org/src/base/R-3/R-3.0.3.tar.gz
+
+# installs Bioconductor
+source("http://bioconductor.org/biocLite.R")
+biocLite()
+
+# upgrage? Some packages are "old"  and can be upgraded with: biocLite("BiocUpgrade")
+
+
+#  install metaMS and multtest for differential analysis tool (from xcms)
+biocLite("metaMS")
+biocLite("multtest")
+
+# for "multi-threading"  (actually starts multiple R processes for parallel processing):
+install.packages("snow", repos="http://cran.rstudio.com/")
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Nov 06 16:04:57 2014 +0100
@@ -0,0 +1,44 @@
+<?xml version="1.0"?>
+<tool_dependency>
+<!-- see also http://wiki.galaxyproject.org/ToolShedToolFeatures for syntax help
+  partly based on : https://toolshed.g2.bx.psu.edu/repos/iuc/package_r_3_0_3
+   -->
+  	<package name="R_bioc_metams" version="3.1.1">
+      <install version="1.0">
+          <actions_group>
+                <actions>
+                    <action type="download_by_url">http://cran.r-project.org/src/base/R-3/R-3.1.1.tar.gz</action>
+                    <action type="move_directory_files">
+	                  	<source_directory>.</source_directory>
+	                    <destination_directory>$INSTALL_DIR</destination_directory>
+	                </action>
+                    <action type="shell_command">
+                        cd $INSTALL_DIR; $INSTALL_DIR/configure --libdir=$INSTALL_DIR/lib --prefix=$INSTALL_DIR
+                    </action>
+                    <action type="shell_command">make -C $INSTALL_DIR</action>
+                </actions>
+                <action type="set_environment">
+                    <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/doc</environment_variable>
+                    <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable>
+                    <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/share</environment_variable>
+                    <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="set_to" name="RHOME">$INSTALL_DIR</environment_variable>
+                    <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/library</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+                <!-- the Bioconductor and metaMS part -->
+                <action type="shell_command">wget -P $INSTALL_DIR http://toolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_metabolomics_r_dependencies/raw-file/tip/INSTALL.r</action>
+                <action type="shell_command">$INSTALL_DIR/bin/Rscript $INSTALL_DIR/INSTALL.r</action>
+            </actions_group>
+        </install>
+        <readme>
+				Ensures R 3.1.1 is installed. 
+				Ensures Bioconductor 3.0 and package metaMS, multtest and snow are installed. 
+                R is a free software environment for statistical computing and graphics.
+        </readme>
+    </package>
+
+
+</tool_dependency>
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