Mercurial > repos > big-tiandm > mirplant2

diff tool_dependencies.xml @ 50:7b5a48b972e9 draft

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Uploaded
author big-tiandm
date Fri, 05 Dec 2014 00:11:02 -0500
parents f008ab2cadc6
children
line wrap: on
line diff
--- a/tool_dependencies.xml	Wed Dec 03 02:03:27 2014 -0500
+++ b/tool_dependencies.xml	Fri Dec 05 00:11:02 2014 -0500
@@ -26,6 +26,76 @@
 		   </actions>
 	   </install>
 	</package>
+	<package name="R" version="3.0.1">
+	   <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+
+		<install version="1.0">
+		   <actions>
+		      <action type="set_environment_for_install">
+                    <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
+                        <package name="R" version="3.0.1" />
+                    </repository>
+              </action>
+		      <action type="shell_command">R CMD BATCH $REPOSITORY_INSTALL_DIR/install_DEG.R </action>
+		      <action type="shell_command">echo "export PATH=$PATH" &gt; $INSTALL_DIR/env.sh </action>
+			  <action type="shell_command">chmod 755 $INSTALL_DIR/env.sh </action>
+
+		 </actions>
+		</install>
+	</package>
+
+	<package name="threads" version="1.96">
+	   <install version="1.0">
+		   <actions>
+		     <action type="download_by_url">http://www.cpan.org/authors/id/J/JD/JDHEDDEN/threads-1.96.tar.gz</action>
+			<action type="make_directory">$INSTALL_DIR/lib/perl5</action>
+			<action type="shell_command">
+				perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &amp;&amp;
+				make &amp;&amp;
+				make install 
+			</action>
+			<action type="set_environment">
+				<environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>	
+			</action>
+		   </actions>
+	   </install>
+	</package>
+
+
+	<package name="Parallel-ForkManager" version="1.06">
+	   <install version="1.0">
+		   <actions>
+		     <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/Parallel-ForkManager-1.06.tar.gz</action>
+			<action type="make_directory">$INSTALL_DIR/lib/perl5</action>
+			<action type="shell_command">
+				perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &amp;&amp;
+				make &amp;&amp;
+				make install 
+			</action>
+			<action type="set_environment">
+				<environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>	
+			</action>
+		   </actions>
+	   </install>
+	</package>
+
+	<package name="Boost-Graph" version="1.4_001">
+	   <install version="1.0">
+		   <actions>
+		     <action type="download_by_url">http://www.cpan.org/authors/id/D/DU/DUFFEE/Boost-Graph-1.4_001.tar.gz</action>
+			<action type="make_directory">$INSTALL_DIR/lib/perl5</action>
+			<action type="shell_command">
+				perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &amp;&amp;
+				ls &amp;&amp;
+				make &amp;&amp;
+				make install 
+			</action>
+			<action type="set_environment">
+				<environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>	
+			</action>
+		   </actions>
+	   </install>
+	</package>
 
 	<package name="SVG" version="2.59">
 	   <install version="1.0">