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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="vienna_rna" version="2.1">
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4 <repository changeset_revision="bb91a5b178e2" name="package_vienna_rna_2_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="gnu_coreutils" version="8.22">
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7 <repository changeset_revision="b638666e399d" name="package_gnu_coreutils_8_22" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="kinwalker" version="1.0">
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10 <install version="1.0">
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11 <actions>
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12 <action target_filename="kinwalker.tar.gz" type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/kinwalker/kinwalker-patched.tar.gz</action>
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13 <action type="set_environment_for_install">
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14 <repository changeset_revision="bb91a5b178e2" name="package_vienna_rna_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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15 <package name="vienna_rna" version="2.1" />
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16 </repository>
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17 </action>
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18 <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>
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19 <action type="move_file">
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20 <source>kinwalker</source>
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21 <destination>$INSTALL_DIR/bin</destination>
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22 </action>
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23 <action type="set_environment">
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24 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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25 </action>
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26 </actions>
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27 </install>
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28 <readme>
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29
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30 The Kinwalker algorithm performs cotranscriptional folding of RNAs,
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31 starting at a user a specified structure (default: open chain) and
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32 ending at the minimum free energy structure. Folding events are
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33 performed between transcription of additional bases and are regulated
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34 by barrier heights between the source and target structure.
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35
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36 </readme>
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37 </package>
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38 </tool_dependency>
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