annotate tool_dependencies.xml @ 2:0fef99b5f63f draft default tip

apply patch from Nicola Soranzo

<tool_dependency>
    <package name="aragorn" version="1.2.36">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn1.2.36.tgz</action>
                <action type="make_directory">$INSTALL_DIR/bin/</action>
                <action type="shell_command">gcc -O3 -ffast-math -finline-functions -o aragorn aragorn1.2.36.c</action>
                <action type="move_file">
                    <source>aragorn</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>Compiling ARAGORN requires gcc.</readme>
    </package>
    <package name="tRNAscan-SE" version="1.3.1">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz</action>
                <action type="make_directory">$INSTALL_DIR/bin/</action>
                <action type="make_directory">$INSTALL_DIR/lib/tRNAscan-SE/</action>
                <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; make</action>
                <!-- replacing the hardcoded pathvariables with the real ones -->
                <action type="shell_command">sed -i 's%^our $lib_dir.*%our $lib_dir="$INSTALL_DIR/lib/tRNAscan-SE/";%'  ./tRNAscan-SE-1.3.1/tRNAscan-SE</action>
                <action type="shell_command">sed -i 's%^our $bindir.*%our $bindir="$INSTALL_DIR/bin/";%'  ./tRNAscan-SE-1.3.1/tRNAscan-SE</action>
                <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; cp trnascan-1.4 covels-SE coves-SE eufindtRNA tRNAscan-SE $INSTALL_DIR/bin/</action>
                <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; cp -R tRNAscanSE $INSTALL_DIR/bin/</action>
                <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; cp TPCsignal Dsignal *.cm gcode.* $INSTALL_DIR/lib/tRNAscan-SE/</action>
                <!-- for some reason infernal needs to be directly under the bin/ from tRNAScan -->
                <action type="shell_command">wget ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz</action>
                <action type="shell_command">tar xfvz infernal-1.0.2.tar.gz</action>
                <action type="shell_command">cd infernal-1.0.2 &amp;&amp; ./configure --prefix=$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>