<?xml version="1.0"?>
<tool_dependency>
    <package name="fastx_toolkit" version="0.0.13">
        <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="bowtie" version="0.12.7">
        <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <set_environment version="1.0">
        <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>
	<!--package name="R" version="3.0.1">
	   <repository name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
	</package!-->

	<package name="ViennaRNA" version="2.1.8">
	   <install version="1.0">
		   <actions>
		     <action type="download_by_url">http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-2.1.8.tar.gz</action>
			 <action type="shell_command">./configure --prefix=$INSTALL_DIR </action>
			 <action type="shell_command">make</action>
			 <action type="shell_command">make install</action>
			 <action type="set_environment">
			   <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
			 </action>
		   </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">
		   <actions>
		     <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/SVG-2.59.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>


</tool_dependency>