view tool_dependencies.xml @ 10:08e9244aeab8

Change dependency for kent (blat faToTwoBit) to latest since versions not available at UCSC

<?xml version="1.0"?>
<tool_dependency>
    <package name="boost" version="1.53.0">
        <repository changeset_revision="f5b13e56a321" name="package_boost_1_53" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="samtools" version="0.1.18">
        <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="bowtie" version="1.0.0">
        <repository changeset_revision="e682af6a72cd" name="package_bowtie_1_0_0" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="gmap" version="2013-05-09">
        <repository changeset_revision="03bb09b717ae" name="package_gmap_2013_05_09" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="kent" version="latest">
        <repository changeset_revision="b05b788e3989" name="package_kent" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="defuse" version="0.6.1">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/defuse/files/defuse/0.6/defuse-0.6.1.tar.gz</action>
                <!-- populate the environment variables from the dependent repos -->
                <action type="set_environment_for_install">
                    <repository changeset_revision="f5b13e56a321" name="package_boost_1_53" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" >
                        <package name="boost" version="1.53.0" />
                    </repository>
                </action>
                <action type="shell_command">export CPLUS_INCLUDE_PATH=$BOOST_ROOT_DIR:$CPLUS_INCLUDE_PATH &amp;&amp; cd tools &amp;&amp; make</action>
                <action type="move_directory_files">
                    <source_directory>.</source_directory>
                    <destination_directory>$INSTALL_DIR</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable name="DEFUSE_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
deFuse code
To build the deFuse toolset you must have the boost c++ development libraries installed. If they are not installed on your system you can download them from the boost website. A full install of boost is not required. The easiest thing to do is to download the latest boost source tar.gz, extract it, then add the extracted path to the CPLUS_INCLUDE_PATH environment variable (in bash, `export CPLUS_INCLUDE_PATH=/boost/directory/:$CPLUS_INCLUDE_PATH`)
        </readme>
    </package>

</tool_dependency>