annotate tool_dependencies.xml @ 4:cc0f4b49b6f1 draft default tip

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<?xml version="1.0"?>
<tool_dependency>
    <package name="libpng" version="1.6.7">
        <repository changeset_revision="51f77dcf27bd" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="blat" version="35x1">
        <install version="1.0">
            <actions>
                <!-- finally go back to the original version and compile blat and the entire server from source 
                    Thanks to Nicola Soranzo.
                    The problem is that the binaries are not versioned and we can't guarantee reproducibility. 
                    The only way to download the source code of minor releases is from the git repository.
                -->
                <action type="shell_command">git clone git://genome-source.cse.ucsc.edu/kent.git blat</action>
                <action type="shell_command">git reset --hard 84614918e462d7750a8f56e5ce9540c623b87b48</action>
                <action type="set_environment_for_install">
                    <repository changeset_revision="51f77dcf27bd" name="package_libpng_1_6_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu">
                        <package name="libpng" version="1.6.7" />
                    </repository>
                </action>
                <action type="shell_command">export HOME=$INSTALL_DIR &amp;&amp; export MACHTYPE=`uname -m` &amp;&amp; export PNGINCL=-I${LIBPNG_ROOT}/include &amp;&amp; export PNGLIB="-L${LIBPNG_ROOT}/lib -lpng" &amp;&amp; mkdir -p $HOME/bin/$MACHTYPE &amp;&amp; make -C src/lib/ &amp;&amp; make -C src/jkOwnLib/ &amp;&amp; make -C src/blat/ &amp;&amp; mv $INSTALL_DIR/bin/$MACHTYPE/* $INSTALL_DIR/bin/ &amp;&amp; rm -rf $INSTALL_DIR/.ccache/</action>
                <action type="set_environment">
                  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable>
                  <environment_variable action="set_to" name="BLAT_PATH">$INSTALL_DIR</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>