<?xml version="1.0"?>
<tool_dependency>
    <package name="stringtie" version="0.97">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="linux">
	                <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.Linux_x86_64.tar.gz</action>
                    <action type="move_file">
                        <source>stringtie</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                </actions>
                <actions architecture="x86_64" os="darwin">
	                <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/stringtie/stringtie-0.97-Darwin-x86_64.tgz</action>
                    <action type="move_file">
                        <source>stringtie</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                </actions>
	            <actions>
                    <package name="samtools" version="0.1.19">
                        <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="true" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                    </package>
	                <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.tar.gz</action>
	                <action type="set_environment_for_install">
	                    <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="true" toolshed="https://testtoolshed.g2.bx.psu.edu">
	                        <package name="samtools" version="0.1.19" />
	                    </repository>
	                </action>
	                <action type="shell_command">ln -s $SAMTOOLS_ROOT_DIR/src samtools</action>
	                <action type="shell_command">cp $SAMTOOLS_ROOT_DIR/lib/libbam.* samtools/</action>
	                <action type="shell_command">make</action>
	                <action type="move_file">
	                    <source>stringtie</source>
	                    <destination>$INSTALL_DIR/bin</destination>
	                </action>
	            </actions>
	            <action type="set_environment">
	                <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
	            </action>
	        </actions_group>
        </install>
        <readme>StringTie is a fast and highly efficient assembler of RNA-Seq
        alignments into potential transcripts. It is primarily a genome-guided
        transcriptome assembler, although it can borrow algorithmic techniques
        from de novo genome assembly to help with transcript assembly. Its input
        can include not only the spliced read alignments used by reference-based
        assemblers, but also longer contigs that were assembled de novo from
        unambiguous, non-branching parts of a transcript.</readme>
    </package>
</tool_dependency>