view tool_dependencies.xml @ 14:b738c51af132 draft

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<?xml version="1.0"?>
<tool_dependency>
    <package name="perl" version="5.18.1">
        <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="bioperl" version="1.6.922">
        <install version="1.0">
            <actions>
                <!-- install perl -->
                <!--<action type="download_by_url">http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</action>-->
                <!-- populate the environment variables from the dependend repos -->
                <action type="set_environment_for_install">
                    <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                        <package name="perl" version="5.18.1" />
                    </repository>
                </action>

                <action type="shell_command">cpanm --local-lib=$INSTALL_DIR XML::Parser</action>
                <action type="shell_command">cpanm --local-lib=$INSTALL_DIR Bundle::BioPerl</action>


                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5</environment_variable>
                    <environment_variable action="set_to" name="PERL_ROOT_DIR">$INSTALL_DIR/lib</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            Bundle::BioPerl
        </readme>
    </package>
</tool_dependency>