annotate tool_dependencies.xml @ 3:b355179ea459 draft

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<tool_dependency>
    <package name="blat" version="35x1">
        <install version="1.0">
            <actions>

                <action type="download_binary">
                    <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</url_template>
                    <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/blat/blat</url_template>
                    <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/blat/blat</url_template>
                    <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/blat/blat</url_template>
                </action>

                <action type="move_file">
                    <source>$INSTALL_DIR/blat</source>
                    <destination>$INSTALL_DIR/blat</destination>
                </action>
                <action type="chmod">
                    <file mode="755">$INSTALL_DIR/blat</file>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="append_to">$INSTALL_DIR</environment_variable>
                    <environment_variable name="BLAT_PATH" action="append_to">$INSTALL_DIR</environment_variable>
                </action>

                <!--
                Alternative version from Nicola Soranzo.
                <action type="download_by_url" target_filename="blatSrc.zip">http://hgwdev.cse.ucsc.edu/~kent/src/blatSrc35.zip</action>
                <action type="shell_command">export MACHTYPE=`uname -m` &amp;&amp; export HOME=$INSTALL_DIR &amp;&amp; mkdir -p $HOME/bin/$MACHTYPE &amp;&amp; make</action>
                <action type="set_environment">
                  <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin/`uname -m`</environment_variable>
                </action>
                -->

            </actions>
        </install>
        <readme>
BLAT sequence aligner from the UCSC: http://genome.ucsc.edu/FAQ/FAQblat.html
Git development repository: http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git

Please note that the BLAT source and executables are freely available for
academic, nonprofit and personal use. Commercial licensing information is
available on the Kent Informatics website (http://www.kentinformatics.com/).
        </readme>
    </package>
</tool_dependency>