diff offtarget/tool_dependencies.xml @ 0:94332d4947cb draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/offtarget/tool_dependencies.xml	Thu Mar 13 19:43:26 2014 -0400
@@ -0,0 +1,23 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="2.15.1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.gz</action>
+                <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
+                <action type="shell_command">make</action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+                <action type="setup_r_environment">
+                    <package>http://www.bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.8.0.tar.gz</package>
+                    <package>http://www.bioconductor.org/packages/release/bioc/src/contrib/Biobase_2.22.0.tar.gz</package>
+                    <package>http://bioinformatics.mdanderson.org/OOMPA/2.15/src/contrib/oompaBase_3.0.1.tar.gz</package>
+                    <package>http://bioinformatics.mdanderson.org/OOMPA/2.15/src/contrib/ClassComparison_3.0.0.tar.gz</package>
+                    <package>http://cran.r-project.org/src/contrib/glmnet_1.9-5.tar.gz</package>
+                </action>
+            </actions>
+        </install>
+        <readme>You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R.</readme>
+    </package>
+</tool_dependency>
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