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<?xml version="1.0"?>
<tool_dependency>
    <package name="vienna_rna" version="2.1">
        <repository changeset_revision="3b53eda26527" name="package_vienna_rna_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="gnu_coreutils" version="8.22">
        <repository changeset_revision="ac64dfe4b1fb" name="package_gnu_coreutils_8_22" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="kinwalker" version="1.0">
        <install version="1.0">
            <actions>
                <action target_filename="kinwalker.tar.gz" type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/kinwalker/kinwalker-patched.tar.gz</action>
                <action type="set_environment_for_install">
                    <repository changeset_revision="3b53eda26527" name="package_vienna_rna_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="vienna_rna" version="2.1" />
                    </repository>
                </action> 
                <action type="shell_command">make VRNA_INC="-I$ROOT_VIENNA_RNA_DIR/include/ViennaRNA" VRNA_LIB="-L$ROOT_VIENNA_RNA_DIR/lib -lRNA" LDFLAGS="-fopenmp"</action>
                <action type="move_file">
                    <source>kinwalker</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>

The  Kinwalker  algorithm performs cotranscriptional folding of RNAs, 
starting at a user a specified structure (default: open chain) and 
ending at the minimum free energy structure. Folding events are 
performed between transcription of additional bases and are regulated 
by barrier heights between the source and target structure.

        </readme>
    </package>
</tool_dependency>