<?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="http://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="http://toolshed.g2.bx.psu.edu" />
    </package>
    <set_environment version="1.0">
        <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>
    <package name="R" version="2.11.0">
        <repository changeset_revision="8d0a55bf7aaf" name="package_r_2_11_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>
	<package name="ViennaRNA" version="2.1.7">
	   <!--install version="1.0">
		   <actions>
		     <action type="download_by_url">http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-2.1.7.tar.gz</action>
			 <action type="shell_command">./configure</action>
			 <action type="shell_command">make</action>
			 <action type="shell_command">make install</action>
			 <action type="set_environment">
			   <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
			 </action>
		   </actions>
	   </install-->
	</package>
</tool_dependency>