<tool_dependency>
    <package name="tRNAscan-SE" version="1.3.1">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz</action>
                <action type="make_directory">$INSTALL_DIR/bin/</action>
                <action type="make_directory">$INSTALL_DIR/lib/tRNAscan-SE/</action>
                <action type="make_directory">$INSTALL_DIR/man/</action>
                <!-- replacing the hardcoded pathvariables with the real ones -->
                <action type="shell_command">sed 's%^BINDIR  = .*%BINDIR = $INSTALL_DIR/bin/%' Makefile | sed 's%^LIBDIR  = .*%LIBDIR = $INSTALL_DIR/lib/tRNAscan-SE/%' | sed 's%^MANDIR  = .*%MANDIR = $INSTALL_DIR/man%' > Makefile_new</action>
                <action type="shell_command">rm Makefile &amp;&amp; mv Makefile_new Makefile</action>
                <action type="make_install"/>

                <!-- for some reason infernal needs to be directly under the bin/ from tRNAScan -->
                <action type="shell_command">wget ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz</action>
                <action type="shell_command">tar xfvz infernal-1.0.2.tar.gz</action>
                <action type="shell_command">cd infernal-1.0.2 &amp;&amp; ./configure --prefix=$INSTALL_DIR &amp;&amp; make &amp;&amp; make install</action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable name="PERL5LIB" action="prepend_to">$INSTALL_DIR/bin/</environment_variable>
                </action>
            </actions>
        </install>
        <readme>Compiling and running tRNAScan-SE requires gcc a PERL environment.</readme>
    </package>
</tool_dependency>