Mercurial > repos > fubar > differential_count_models

changeset 115:badcd3b0e708 draft

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Uploaded
author fubar
date Thu, 23 Oct 2014 01:31:34 -0400
parents 616c780f69a6
children b0d21688db8e
files rgedgeRpaired_nocamera.xml tool_dependencies.xml
diffstat 2 files changed, 34 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/rgedgeRpaired_nocamera.xml	Thu Oct 23 00:05:56 2014 -0400
+++ b/rgedgeRpaired_nocamera.xml	Thu Oct 23 01:31:34 2014 -0400
@@ -1,10 +1,11 @@
 <tool id="rgDifferentialCount" name="Differential_Count" version="0.26">
   <description>models using BioConductor packages</description>
   <requirements>
-      <requirement type="package" version="2.14">biocbasics</requirement>
+      <requirement type="package" version="2.9.1">libxml2</requirement>
       <requirement type="package" version="3.1.1">R_3_1_1</requirement>
       <requirement type="package" version="1.3.18">graphicsmagick</requirement>
-      <requirement type="package" version="9.10">ghostscript</requirement>
+      <requirement type="package" version="9.10">ghostscript</requirement> <package name="libxml2" version="2.9.1">
+      <requirement type="package" version="2.14">biocbasics</requirement>
   </requirements>
   
   <command interpreter="python">
--- a/tool_dependencies.xml	Thu Oct 23 00:05:56 2014 -0400
+++ b/tool_dependencies.xml	Thu Oct 23 01:31:34 2014 -0400
@@ -9,6 +9,9 @@
     <package name="ghostscript" version="9.10">
         <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
+    <package name="libxml2" version="2.9.1">
+        <repository changeset_revision="926b471a2e43" name="package_libxml2_2_9_1" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
 
     <package name="biocbasics" version="2.14">
         <install version="1.0">
@@ -18,34 +21,52 @@
                         <package name="R_3_1_1" version="3.1.1" />
                     </repository>                    
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/getopt_1.20.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/digest_0.6.4.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/labeling_0.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/colorspace_1.2-4.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/munsell_0.4.2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/dichromat_2.0-0.tar.gz?raw=true</package>
+
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/Rcpp_0.11.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/RcppArmadillo_0.4.450.1.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/plyr_1.8.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/statmod_1.4.20.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/proto_0.3-10.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rjson_0.2.14.tar.gz?raw=true</package>                    
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/stringr_0.6.2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/gtable_0.1.2.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/locfit_1.5-9.1.tar.gz?raw=true</package>
+
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/xtable_1.7-4.tar.gz?raw=true</package>                    
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/BiocGenerics_0.10.0.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/IRanges_1.22.10.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/GenomicRanges_1.16.4.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/RcppArmadillo_0.4.450.1.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/Rcpp_0.11.3.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/GenomeInfoDb_1.0.2.tar.gz?raw=true</package>
 
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/Biobase_2.24.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/XVector_0.4.0.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/RColorBrewer_1.0-5.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/locfit_1.5-9.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/GenomicRanges_1.16.4.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/reshape2_1.4.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/scales_0.2.4.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/DBI_0.3.1.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/RSQLite_0.11.4.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/XML_3.98-1.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/xtable_1.7-4.tar.gz?raw=true</package>
 
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/AnnotationDbi_1.26.1.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/annotate_1.42.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/AnnotationDbi_1.26.1.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/rjson_0.2.14.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/geneplotter_1.42.0.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/genefilter_1.46.1.tar.gz?raw=true</package>
+                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/limma_3.20.9.tar.gz?raw=true</package>
+
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/DESeq2_1.4.5.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/edgeR_3.6.8.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/genefilter_1.46.1.tar.gz?raw=true</package>
                     <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/ggplot2_1.0.0.tar.gz?raw=true</package>
-                    <package>https://github.com/fubar2/galaxy_tool_source/blob/master/RELEASE_2_14/limma_3.20.9.tar.gz?raw=true</package>
                 </action>
             </actions>
         </install>
         <readme>
-        Differential gene expression analysis 
+        Differential gene expression analysis
+        You may need libxml2-dev for XML to compile
         Ubuntu has a bug with libgfortran. To fix that create a symlink like: sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.3 /usr/lib/x86_64-linux-gnu/libgfortran.so
         </readme>
     </package>