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1 <?xml version="1.0"?>
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2 <tool_dependency>
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1
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3 <package name="samtools" version="0.1.19">
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5
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4 <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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1
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5 </package>
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6 <package name="numpy" version="1.7.1">
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5
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7 <repository changeset_revision="11099cc214d5" name="package_numpy_1_7" 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="matplotlib" version="1.2.1">
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6
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10 <repository changeset_revision="9f3e58477115" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="scipy" version="0.12.0">
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13 <repository changeset_revision="d607515b0510" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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14 </package>
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15 <package name="pysam" version="0.7.7">
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16 <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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17 </package>
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18 <package name="bx-python" version="0.7.1">
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19 <repository changeset_revision="ec30e3f438f4" name="package_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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1
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20 </package>
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21 <package name="ucsc_tools" version="0.1">
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22 <repository changeset_revision="535261946ba0" name="package_ucsc_tools" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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2
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23 </package>
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24 <package name="deepTools" version="1.5.9">
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25 <install version="1.0">
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26 <actions>
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27 <action type="download_by_url">https://github.com/fidelram/deepTools/archive/1.5.9.1.tar.gz</action>
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28 <action type="set_environment_for_install">
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29 <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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30 <package name="pysam" version="0.7.7" />
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31 </repository>
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5
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32 <repository changeset_revision="ec30e3f438f4" name="package_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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33 <package name="bx-python" version="0.7.1" />
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34 </repository>
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5
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35 <repository changeset_revision="11099cc214d5" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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36 <package name="numpy" version="1.7.1" />
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37 </repository>
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6
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38 <repository changeset_revision="9f3e58477115" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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39 <package name="matplotlib" version="1.2.1" />
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40 </repository>
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5
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41 <repository changeset_revision="d607515b0510" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" 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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6
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44 <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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45 <package name="samtools" version="0.1.19" />
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46 </repository>
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47 <repository changeset_revision="535261946ba0" name="package_ucsc_tools" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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48 <package name="ucsc_tools" version="0.1" />
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49 </repository>
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50 </action>
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51 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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52 <action type="shell_command">
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53 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
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54 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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55 </action>
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56
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57 <action type="set_environment">
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58 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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59 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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60 <environment_variable action="set_to" name="DEEPTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
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61 <environment_variable action="set_to" name="DEEPTOOLS_PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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62 <environment_variable action="set_to" name="DEEPTOOLS_PATH">$INSTALL_DIR/bin</environment_variable>
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63 <!-- include samtools into PATH -->
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64 <environment_variable action="prepend_to" name="PATH">$ENV[BAM_ROOT]/bin</environment_variable>
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65 <!-- include numpy -->
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66 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
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67 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
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68 <!-- include matplotlib -->
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69 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable>
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70 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[MATPLOTLIB_LIB_PATH]</environment_variable>
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71 <!-- include scipy -->
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72 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_SCIPY]</environment_variable>
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73 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_SCIPY]</environment_variable>
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74 <!-- include bx-python -->
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75 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[BX_PYTHON_PATH]/lib/python</environment_variable>
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76 <environment_variable action="prepend_to" name="PATH">$ENV[BX_PYTHON_PATH]/bin</environment_variable>
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77 <!-- include pysam -->
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78 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYSAM_PATH]/lib/python</environment_variable>
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79 <environment_variable action="prepend_to" name="PATH">$ENV[PYSAM_PATH]/bin</environment_variable>
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80 <!-- include ucsc tools -->
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81 <environment_variable action="prepend_to" name="PATH">$ENV[UCSC_TOOLS_ROOT_PATH]</environment_variable>
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82
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83 <!-- disable the config file of deepTools -->
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84 <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
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85 </action>
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86 </actions>
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87 </install>
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88 <readme>
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89 Installation of deepTools from Fidel Ramirez.
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90 https://github.com/fidelram/deepTools
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91 </readme>
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92 </package>
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93 </tool_dependency>
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