<?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">http://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.2.5-linux-x86_64.zip</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>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme></readme>
    </package>
</tool_dependency>

Correct download link for precompiled bowtie.
Correct download link for precompiled bowtie.