view tool_dependencies.xml @ 3:8fbe25248354

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<?xml version="1.0"?>
<tool_dependency>

    <set_environment version="1.0">
        <environment_variable action="set_to" name="LINKYX_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>

    <package name="perl" version="5.18.1">
        <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>

    <package name="samtools-fpic" version="0.1.19">
        <repository changeset_revision="a6c82a5d0b51" name="package_samtools_0_1_19_custom" owner="biomonika" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>

    <package name="bioperl" version="1.6.922">
        <install version="1.0">
            <actions>
                <action type="set_environment_for_install">
                    <repository changeset_revision="a6c82a5d0b51" name="package_samtools_0_1_19_custom" owner="biomonika" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="samtools-fpic" version="0.1.19" />
                    </repository>
                    <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="perl" version="5.18.1" />
                    </repository>
                </action>
                <action type="setup_perl_environment">
                    
                    <!-- allow downloading and installing an Perl package from cpan.org-->
                    <package>XML::Parser</package>
                    <package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</package>
                    <package>Bio::DB::Fasta</package>
                    <package>File::Slurp</package>
                    <package>Bio::DB::Sam</package>
                    <package>PerlIO::gzip</package>
                </action>
            </actions>
        </install>
        <readme>
            Bundle::BioPerl
        </readme>
    </package>
</tool_dependency>