<?xml version="1.0"?>
<tool_dependency>
    <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="bedtools" version="2.18.2">
	<install version="1.0">
		<actions>
			<action type="download_by_url" target_filename="bedtools-2.18.2.tar.gz" >https://github.com/arq5x/bedtools2/releases/download/v2.18.2/bedtools-2.18.2.tar.gz</action>
			<action type="shell_command">make</action>
			<action type="move_file">
				<source>bin/</source>	
				<destination>$INSTALL_DIR/bin</destination>
			</action>
			<action type="set_environment">
				<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
               		</action>
            	</actions>
        </install>
        <readme>
		Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.
     	</readme>
   </package>
   <package name="samtools" version="0.1.18">
	<repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
   </package>
</tool_dependency>