# HG changeset patch
# User brenninc
# Date 1443691399 14400
# Node ID d03274c7c54685df38ea12a8935de751681964c2

Uploaded

diff -r 000000000000 -r d03274c7c546 packages.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/packages.R	Thu Oct 01 05:23:19 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()
diff -r 000000000000 -r d03274c7c546 r_info.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/r_info.sh	Thu Oct 01 05:23:19 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"
diff -r 000000000000 -r d03274c7c546 r_info.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/r_info.xml	Thu Oct 01 05:23:19 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_mulitple</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>
diff -r 000000000000 -r d03274c7c546 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Oct 01 05:23:19 2015 -0400
@@ -0,0 +1,74 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="3.1.2">
+        <repository toolshed="http://l-unxx4770.it.manchester.ac.uk:9009/" name="package_r_3_1_2" owner="brenninc" changeset_revision="6c7b9b5dfcae" prior_installation_required="True" />
+    </package>
+    <package name="R_extend_level_one" version="0.0.1">
+        <install version="1.0">
+            <actions>
+                <action type="setup_r_environment">
+                    <repository changeset_revision="6c7b9b5dfcae" name="package_r_3_1_2" owner="brenninc" toolshed="http://l-unxx4770.it.manchester.ac.uk:9009/">
+                        <package name="R" version="3.1.2" />
+                        <!-- includes base, boot, 
+                                      class, cluster, codetools, compiler, 
+                                      datasets, 
+                                      foreign, 
+                                      graphics, grDevices, grid, 
+                                      KernSmooth, 
+                                      lattice, 
+                                      MASS, Matrix, methods, mgcv, 
+                                      nlme, nnet, 
+                                      parallel, 
+                                      rpart,
+                                      spatial, splines, stats, stats4, survival,
+                                      tcltk, tools,
+                                      utils-->
+
+                    </repository>  
+                    <!--No dependencies Not on https://bioarchive.galaxyproject.org -->
+                    <package>https://cran.r-project.org/src/contrib/acepack_1.3-3.3.tar.gz</package> 
+                    <package>https://cran.r-project.org/src/contrib/colorspace_1.2-6.tar.gz</package> 
+                        <!-- Imports graphics 
+                             Suggests: KernSmooth, MASS, kernlab, mvtnorm, vcd, dichromat, tcltk-->
+                    <package>https://cran.r-project.org/src/contrib/digest_0.6.8.tar.gz</package> 
+                    <package>https://cran.r-project.org/src/contrib/dichromat_2.0-0.tar.gz</package> 
+                        <!-- Depends stats -->
+                    <package>https://cran.r-project.org/src/contrib/Formula_1.2-1.tar.gz</package> 
+                        <!-- Depends stats -->
+                    <package>https://cran.r-project.org/src/contrib/gtable_0.1.2.tar.gz</package> 
+                        <!-- Depends grid 
+                             Suggests: testthat, plyr-->
+                    <package>https://cran.r-project.org/src/contrib/labeling_0.3.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/magrittr_1.5.tar.gz</package>
+                        <!-- Suggests: 	testthat, knitr -->
+                    <package>https://cran.r-project.org/src/contrib/proto_0.3-10.tar.gz</package>
+                        <!-- Suggests: 	graph, Rgraphviz -->
+                    <package>https://cran.r-project.org/src/contrib/Rcpp_0.12.0.tar.gz</package>
+                        <!-- Imports: 	methods, utils
+                             Suggests: 	RUnit, inline, rbenchmark, highlight, pkgKitten (≥ 0.1.2) -->
+                    <package>https://cran.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/rjson_0.2.15.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/snow_0.3-13.tar.gz</package>
+                        <!-- Depends: R (≥ 2.12.1), utils
+                             Suggests: Rmpi, rpvm, rlecuyer, rsprng, nws -->
+                    <package>https://cran.r-project.org/src/contrib/SparseM_1.7.tar.gz</package>
+                        <!-- Depends: R (≥ 2.15), methods
+                             Imports: graphics, stats, utils -->
+                    <package>https://cran.r-project.org/src/contrib/stringi_0.5-5.tar.gz</package>
+                        <!-- Depends: R (≥ 2.13.1)
+                             Imports: tools, utils, stats -->
+                    <package>https://cran.r-project.org/src/contrib/XML_3.98-1.3.tar.gz</package>
+                        <!-- Depends: R (≥ 2.13.0), methods, utils
+                             Suggests: bitops, RCurl -->
+                    <package>https://cran.r-project.org/src/contrib/xtable_1.7-4.tar.gz</package>
+                    <package>https://cran.r-project.org/src/contrib/stringr_1.0.0.tar.gz</package>
+                        <!-- Depends: R (≥ 2.14)
+                             Imports: stringi (≥ 0.4.1), magrittr
+                             Suggests: testthat, knitr -->
+                </action>            
+            </actions>
+        </install>
+    </package>
+</tool_dependency>
+
+