<?xml version="1.0"?>
<tool_dependency>
    <package name="bowtie2" version="2.2.5">
        <install version="1.0">
            <actions_group>
                <actions os="linux" architecture="x86_64">
                    <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.2.5-Linux-x86_64.tar.gz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme></readme>
    </package>
</tool_dependency>

<?xml version="1.0"?>
<tool_dependency>
    <package name="bowtie2" version="2.2.5">
        <install version="1.0">
            <actions_group>
                <actions os="linux" architecture="x86_64">
                    <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.2.5-Linux-x86_64.tar.gz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <actions>
                    <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-source.zip</action>
                    <action type="shell_command">make</action>
                    <action type="move_file">
                        <source>bowtie2</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="move_file">
                        <source>bowtie2-build</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="move_file">
                        <source>bowtie2-inspect</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="move_file">
                        <source>bowtie</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="move_file">
                        <source>bowtie-build</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="move_file">
                        <source>bowtie-inspect</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                </actions>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme></readme>
    </package>
</tool_dependency>

Fix compilation recipe for bowtie.
Fix compilation recipe for bowtie.
