changeset 24:1c8ae2960409 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/packages.R	Fri Oct 02 11:46:51 2015 -0400
@@ -0,0 +1,22 @@
+library(acepack)
+library(colorspace)
+library(dichromat)
+library(digest)
+library(Formula)
+library(gtable)
+library(labeling)
+library(magrittr)
+library(proto)
+library(Rcpp)
+library(RColorBrewer)
+library(rjson)
+library(snow)
+library(SparseM)
+library(stringi)
+library(stringr)
+#library(XML)
+library(xtable)
+
+args<-commandArgs(TRUE)
+writeLines(capture.output(sessionInfo()), args[1])
+sessionInfo()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/r_info.sh	Fri Oct 02 11:46:51 2015 -0400
@@ -0,0 +1,30 @@
+#!/bin/sh
+
+
+#Copied from https://github.com/galaxyproject/galaxy/blob/dev/tools/stats/r_wrapper.sh
+
+### Run R providing the R script in $1 as standard input and passing 
+### the remaining arguments on the command line
+
+# Function that writes a message to stderr and exits
+fail()
+{
+    echo "$@" >&2
+    exit 1
+}
+
+# Ensure R executable is found
+which R > /dev/null || fail "'R' is required by this tool but was not found on path" 
+
+# Extract first argument
+rfile=$1
+package_file=$2
+version_file=$3
+
+# Ensure the file exists
+test -f $infile || fail "R input file '$infile' does not exist"
+
+# Invoke R passing file named by first argument to stdin
+#Remove --slave for full R output
+R --vanilla --slave --args $package_file < $rfile
+echo "done"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/r_info.xml	Fri Oct 02 11:46:51 2015 -0400
@@ -0,0 +1,30 @@
+<tool id="r_extended_level_one_sessioninfo" name="r_extended_level_one sessionInfo" version="0.1.beta">
+  <requirements>
+    <requirement type="package" version="3.1.2">R</requirement>
+    <requirement type="package" version="0.0.1">R_extend</requirement>
+    <!--requirement type="package" version="2.0-0">R_dichroma</requirement-->
+  </requirements>  
+  <description>Lists packages installed into R</description>
+  <stdio>
+        <exit_code range="1" level="fatal" description="Error code 1 occurred" />
+        <exit_code range="2:255" level="fatal" description="Unknown error occurred" />
+  </stdio>
+  <command   interpreter="bash">
+    r_info.sh $__tool_directory__/packages.R $packages
+  </command>
+  <outputs>
+    <data format="txt" name="packages" label="R Session Info"/>
+  </outputs>
+
+  <tests>
+  </tests>
+
+  <help>
+<![CDATA[
+This is a verification tool to see exactly which R this galaxy server is using.
+
+It will outout the R version info and the R packages installed.
+    ]]>
+  </help>
+
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Oct 02 11:46:51 2015 -0400
@@ -0,0 +1,20 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="3.1.2">
+        <repository toolshed="https://testtoolshed.g2.bx.psu.edu/" name="brenninc_r_sept32105" owner="brenninc" changeset_revision="1d7f08f14e93" prior_installation_required="True" />
+    </package>
+    <package name="R_extend" version="0.0.1">
+        <install version="1.0">
+            <actions>
+                <action type="setup_r_environment">
+                    <repository changeset_revision="1d7f08f14e93" name="brenninc_r_sept32105" owner="brenninc" toolshed="https://testtoolshed.g2.bx.psu.edu/">
+                        <package name="R" version="3.1.2" />
+                    </repository>  
+                    <package>https://cran.r-project.org/src/contrib/acepack_1.3-3.3.tar.gz</package> 
+                </action>            
+            </actions>
+        </install>
+    </package>
+</tool_dependency>
+
+