diff tool_dependencies.xml @ 7:eda59b985b1c draft default tip

Uploaded

--- a/tool_dependencies.xml	Tue Jun 28 02:59:32 2016 -0400
+++ b/tool_dependencies.xml	Mon Mar 13 08:21:19 2017 -0400
@@ -12,17 +12,13 @@
             <package name="perl" prior_installation_required="True" version="5.18.1" />
           </repository> 
 
-          <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-            <package name="R" version="3.0.1" />
-          </repository>
-
           <!-- allow downloading and installing an Perl package from cpan.org-->
           <package>http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/IPC-Run-0.94.tar.gz</package>
           <package>http://search.cpan.org/CPAN/authors/id/A/AB/ABIGAIL/Regexp-Common-2013031301.tar.gz</package>
-          <package>http://search.cpan.org/CPAN/authors/id/F/FA/FANGLY/Statistics-R-0.33.tar.gz</package>
           <package>http://search.cpan.org/CPAN/authors/id/J/JM/JMCNAMARA/OLE-Storage_Lite-0.19.tar.gz</package>
           <package>http://search.cpan.org/CPAN/authors/id/J/JM/JMCNAMARA/Spreadsheet-WriteExcel-2.40.tar.gz</package>
           <package>http://search.cpan.org/CPAN/authors/id/D/DL/DLUX/Parallel-ForkManager-0.7.5.tar.gz</package>
+          <package>http://search.cpan.org/CPAN/authors/id/G/GR/GROMMEL/Math-Round-0.06.tar.gz</package>
         </action>
       <action type="set_environment">
         <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
@@ -34,21 +30,42 @@
   <package name="perl" version="5.18.1">
     <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-    
-  <package name="weblogo" version="3.3">
-    <repository changeset_revision="648e4b32f15c" name="package_weblogo_3_3" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+
+  <!-- package_weblogo_3_3 has broken link in main Galaxy toolshed (February 2017) -->
+  <package name="weblogo" version="3.5">
+    <install version="1.0">
+      <actions>
+       <action type="download_by_url">https://github.com/WebLogo/weblogo/archive/master.zip</action>                               
+        <!-- Use screen instead of printer to work around a color bug in ghostscript. -->
+        <action type="shell_command">sed -i.bak 's#"-dPDFSETTINGS=/printer",#"-dPDFSETTINGS=/screen",#' weblogolib/__init__.py</action>
+          <action type="move_directory_files">
+            <source_directory>.</source_directory>
+              <destination_directory>$INSTALL_DIR</destination_directory>
+          </action>
+          <action type="set_environment">
+            <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
+            <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
+          </action>
+        </actions>
+      </install>
+    <readme />
   </package>
-    
+
   <package name="numpy" version="1.9">
     <repository changeset_revision="f24fc0b630fc" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
 
-  <package name="R" version="3.1.2">
-    <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+  <package name="R" version="3.2.1">
+    <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-    
+
+  <!-- package_R_3_2_1 doesn't load fontconfig, load it manually -->
+  <package name="fontconfig" version="2.11.1">
+    <repository changeset_revision="d88d844df0cb" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+
   <package name="mutspec" version="0.1">
-    <repository changeset_revision="63cc1719e1aa" name="package_r_mutspec_0_1" owner="iarc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="47d4bc32a67c" name="package_r_mutspec_0_1" owner="iarc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
     
 </tool_dependency>