changeset 0:07d42414fcee draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/error.txt	Thu Aug 27 11:19:53 2015 -0400
@@ -0,0 +1,12 @@
+https://toolshed.g2.bx.psu.edu/repository?repository_id=f55e08d70b8fd026&changeset_revision=b39299b4b6e1
+checking if R was compiled with the RConn patch... no
+install_environment.STDOUT DEBUG 2015-08-25 17:43:55,657 checking cairo.h presence... no
+checking cairo.h usability... no
+checking cairo.h presence... no
+checking for cairo.h... no
+configure: error: Cannot find cairo.h! Please install cairo (http://www.cairographics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly.
+ERROR: configuration failed for package ‘Cairo’
+* removing ‘/home/christian/galaxy/dependency_dir/R_cairo/0.0.1/brenninc/r_packages/99051bae79b0/Cairo’
+Warning message:
+
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/packages.R	Thu Aug 27 11:19:53 2015 -0400
@@ -0,0 +1,5 @@
+library(Cairo)
+
+args<-commandArgs(TRUE)
+writeLines(capture.output(sessionInfo()), args[1])
+sessionInfo()

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/r_info.sh	Thu Aug 27 11:19:53 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	Thu Aug 27 11:19:53 2015 -0400
@@ -0,0 +1,30 @@
+<tool id="brenninc_r_test" name="r_test" version="0.1.beta">
+  <requirements>
+    <requirement type="package" version="3.2.1">R</requirement>
+    <requirement type="package" version="0.0.2">R_cairo</requirement>
+    <requirement type="package" version="1.12.14">cairo</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	Thu Aug 27 11:19:53 2015 -0400
@@ -0,0 +1,28 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="3.2.1">
+        <repository toolshed="https://testtoolshed.g2.bx.psu.edu/" name="package_r_3_2_1" owner="iuc" changeset_revision="3d28600fc82c" />
+    </package>    
+    <package name="cairo" version="1.12.14">
+        <repository name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True"  
+                    changeset_revision="5c25a57405a9" toolshed="https://testtoolshed.g2.bx.psu.edu/" />
+    </package>
+    <package name="R_cairo" version="0.0.2">
+        <install version="1.0">
+            <actions>
+               <action type="setup_r_environment">
+                    <repository changeset_revision="3d28600fc82c" name="iuc" owner="brenninc" toolshed="https://testtoolshed.g2.bx.psu.edu/">
+                        <package name="R" version="3.2.1" />
+                    </repository>  
+                    <repository name="package_cairo_1_12_14" owner="iuc" prior_installation_required="True" 
+                                changeset_revision="5c25a57405a9" toolshed="https://testtoolshed.g2.bx.psu.edu/" >
+                        <package name="cairo" version="1.12.14" />
+                    </repository>
+                    <package>https://cran.r-project.org/src/contrib/Cairo_1.5-8.tar.gz</package>
+                </action>            
+            </actions>
+        </install>
+    </package>
+</tool_dependency>
+
+