# HG changeset patch
# User brenninc
# Date 1460562512 14400
# Node ID 9d4fe3e641c07296b6c4074f462ab4b4f64710b3
# Parent  601f53aa69735ac0778f48dac1fee94675d5b855
Uploaded

diff -r 601f53aa6973 -r 9d4fe3e641c0 packages.R
--- a/packages.R	Tue Apr 12 04:23:41 2016 -0400
+++ b/packages.R	Wed Apr 13 11:48:32 2016 -0400
@@ -1,101 +1,7 @@
-library(BiocGenerics)
-library(S4Vectors)
-library(IRanges)
-library(GenomeInfoDb)
-library(XVector)
-library(GenomicRanges)
-library(Rcpp)
-library(RcppArmadillo)
-library(Biobase)
-library(lambda.r)
-library(futile.options)
-library(futile.logger)
-library(snow)
-library(BiocParallel)
-library(DBI)
-library(RSQLite)
-library(AnnotationDbi)
-library(XML)
-library(xtable)
-library(annotate)
-library(survival)
-library(genefilter)
-library(lattice)
-library(locfit)
-library(RColorBrewer)
-library(geneplotter)
-library(plyr)
-library(digest)
-library(gtable)
-library(stringi)
-library(magrittr)
-library(stringr)
-library(reshape2)
-library(dichromat)
-library(colorspace)
-library(munsell)
-library(labeling)
-library(scales)
-library(proto)
-library(MASS)
-library(ggplot2)
-library(Formula)
-library(latticeExtra)
-library(cluster)
-library(rpart)
-library(nnet)
-library(acepack)
-library(foreign)
-library(gridExtra)
-library(Hmisc)
-library(DESeq2)
-library(modeltools)
-library(flexmix)
-library(brew)
-library(Rook)
-library(rjson)
-library(Cairo)
-library(limma)
-library(edgeR)
-library(RMTstat)
-library(Lmoments)
-library(distillery)
-library(nlme)
-library(Matrix)
-library(mgcv)
-library(minqa)
-library(nloptr)
-library(RcppEigen)
-library(lme4)
-library(pbkrtest)
-library(SparseM)
-library(MatrixModels)
-library(quantreg)
-library(car)
-library(extRemes)
-library(pcaMethods)
-library(scde)
-library(evaluate)
-library(formatR)
-library(highr)
-library(mime)
-library(markdown)
-library(yaml)
-library(knitr)
-library(proxy)
-library(cba)
-library(fastcluster)
-library(dynamicTreeCut)
-library(matrixStats)
-library(impute)
-library(codetools)
-library(iterators)
-library(foreach)
-library(doParallel)
-library(reshape)
-library(preprocessCore)
-library(GO.db)
-library(WGCNA)
+installed_packages_info = installed.packages()
+installed_packages = installed_packages_info[,1]
+
+lapply(installed_packages, require, character.only = TRUE)
 
 args<-commandArgs(TRUE)
 writeLines(capture.output(sessionInfo()), args[1])
diff -r 601f53aa6973 -r 9d4fe3e641c0 r_info.xml
--- a/r_info.xml	Tue Apr 12 04:23:41 2016 -0400
+++ b/r_info.xml	Wed Apr 13 11:48:32 2016 -0400
@@ -1,29 +1,34 @@
 <tool id="r_exended_lister" name="r extended lister" version="0.1.beta">
-  <requirements>
-    <requirement type="package" version="3.2.1">R</requirement>
-    <!--requirement type="package" version="0.0.1">R_extended</requirement-->
-  </requirements>  
-  <description>Lists packages installed into R</description>
-  <stdio>
+    <description>Lists packages installed into R</description>
+    <requirements>
+        <requirement type="package" version="3.2.1">R</requirement>
+        <!--requirement type="package" version="0.0.1">R_extended</requirement-->
+    </requirements>  
+    <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>
+    </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>
+        <test>
+            <output name="out_file1">
+                <assert_contents>
+                    <has_text text="Matrix_1.2-1" />
+                </assert_contents>
+            </output>
+        </test>
+    </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>
-
+    </help>
+    <citations/>
 </tool>
diff -r 601f53aa6973 -r 9d4fe3e641c0 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Apr 12 04:23:41 2016 -0400
+++ b/tool_dependencies.xml	Wed Apr 13 11:48:32 2016 -0400
@@ -1,115 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="R" version="3.2.1">
-        <repository changeset_revision="3f2e129aae27" name="brenninc_r_oct9_2015" owner="brenninc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="1eda5afe26d0" name="package_r_3_2_1" owner="brenninc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <!--package name="R_extended" version="0.0.1">
-        <install version="1.0">
-            <actions>
-                <action type="setup_r_environment">
-                    <repository name="package_r_3_2_1" owner="brenninc" prior_installation_required="True" >
-                        <package name="R" version="3.2.1" />
-                    </repository>  
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/BiocGenerics_0.14.0.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/S4Vectors_0.6.6.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/IRanges_2.2.9.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/GenomeInfoDb_1.4.3.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/XVector_0.8.0.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/GenomicRanges_1.20.8.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/Rcpp_0.12.1.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/RcppArmadillo_0.6.100.0.0.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/Biobase_2.28.0.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/lambda.r_1.1.7.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/futile.options_1.0.0.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/futile.logger_1.4.1.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/snow_0.3-13.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/BiocParallel_1.2.22.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/DBI_0.3.1.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/RSQLite_1.0.0.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/AnnotationDbi_1.30.1.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/XML_3.98-1.3.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/xtable_1.7-4.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/annotate_1.46.1.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/survival_2.38-3.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/genefilter_1.50.0.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/lattice_0.20-33.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/locfit_1.5-9.1.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/RColorBrewer_1.1-2.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/geneplotter_1.46.0.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/plyr_1.8.3.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/digest_0.6.8.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/gtable_0.1.2.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/stringi_0.5-5.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/magrittr_1.5.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/stringr_1.0.0.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/reshape2_1.4.1.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/dichromat_2.0-0.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/colorspace_1.2-6.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/munsell_0.4.2.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/labeling_0.3.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/scales_0.3.0.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/proto_0.3-10.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/MASS_7.3-44.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/ggplot2_1.0.1.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/Formula_1.2-1.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/latticeExtra_0.6-26.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/cluster_2.0.3.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/rpart_4.1-10.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/nnet_7.3-11.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/acepack_1.3-3.3.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/foreign_0.8-66.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/gridExtra_2.0.0.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/Hmisc_3.17-0.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/DESeq2_1.8.2.tar.gz</package>
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-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/brew_1.0-6.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/Rook_1.1-1.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/rjson_0.2.15.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/Cairo_1.5-9.tar.gz</package>
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-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/RMTstat_0.3.tar.gz</package>
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-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/lme4_1.1-10.tar.gz</package>
-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/pbkrtest_0.4-2.tar.gz</package>
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-                    <package>https://github.com/Christian-B/galaxy_shedtools/raw/master/r_extended/WGCNA_1.47.tar.gz</package>
-                </action>
-            </actions>
-        </install>
-    </package-->
+    <!--package name="R_extended" version="3.2.1"-->
 </tool_dependency>