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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="grabix" version="0.1.3">
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1
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4 <repository changeset_revision="8a1184d30e64" name="package_grabix_0_1_3" 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="tabix" version="0.2.6">
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7 <repository changeset_revision="c1743e071a28" name="package_tabix_0_2_6" 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="samtools" version="0.1.19">
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10 <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="bedtools" version="2.19.1">
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13 <repository changeset_revision="3ad963111153" name="package_bedtools_2_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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14 </package>
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15 <package name="pybedtools" version="0.6.6">
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16 <repository changeset_revision="cc2ed79fc537" name="package_pybedtools_0_6_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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17 </package>
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18 <package name="bx-python" version="12-2013">
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19 <repository changeset_revision="5457e32b427c" name="package_bx_python_12_2013" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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20 </package>
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21 <package name="numpy" version="1.7.1">
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22 <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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23 </package>
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24 <package name="scipy" version="0.12.0">
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25 <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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26 </package>
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27 <package name="pandas" version="0.14.1">
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28 <repository changeset_revision="21afd61aae1e" name="package_pandas_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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29 </package>
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0
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30 <package name="gemini" version="0.9.1">
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31 <install version="1.0">
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32 <actions>
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33 <!-- first action is always downloading -->
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34 <action type="download_by_url">https://github.com/arq5x/gemini/archive/v0.9.1.tar.gz</action>
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35
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36 <!-- populate the environment variables from the dependend repos -->
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37 <action type="set_environment_for_install">
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1
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38 <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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39 <package name="numpy" version="1.7.1" />
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40 </repository>
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41 <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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42 <package name="scipy" version="0.12.0" />
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43 </repository>
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44 <repository changeset_revision="21afd61aae1e" name="package_pandas_0_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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45 <package name="pandas" version="0.14.1" />
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46 </repository>
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0
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47 <repository changeset_revision="c1743e071a28" name="package_tabix_0_2_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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48 <package name="tabix" version="0.2.6" />
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49 </repository>
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1
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50 <repository changeset_revision="8a1184d30e64" name="package_grabix_0_1_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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0
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51 <package name="grabix" version="0.1.3" />
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52 </repository>
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53 <repository changeset_revision="cc2ed79fc537" name="package_pybedtools_0_6_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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54 <package name="pybedtools" version="0.6.6" />
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55 </repository>
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1
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56 <repository changeset_revision="5457e32b427c" name="package_bx_python_12_2013" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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57 <package name="bx-python" version="12-2013" />
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58 </repository>
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59 <repository changeset_revision="5457e32b427c" name="package_bx_python_12_2013" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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60 <package name="bx-python" version="12-2013" />
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61 </repository>
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0
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62 </action>
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63
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64 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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65 <action type="shell_command">
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66 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
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67 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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68 </action>
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69
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70 <action type="set_environment">
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71 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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72 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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73 <environment_variable action="set_to" name="PYTHONPATH_GEMINI">$INSTALL_DIR/lib/python</environment_variable>
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74 <environment_variable action="set_to" name="PATH_GEMINI">$INSTALL_DIR/bin</environment_variable>
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75 <environment_variable action="set_to" name="GEMINI_ROOT_DIR">$INSTALL_DIR</environment_variable>
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76 </action>
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77 </actions>
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78 </install>
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79 <readme>Compiling GEMINI requires a recent c++ compiler, usually gcc.</readme>
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80 </package>
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81 </tool_dependency>
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