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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="samtools" version="0.1.19">
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4 <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" 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="numpy" version="1.9">
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7 <repository changeset_revision="dd91d64330d4" name="package_numpy_1_9" 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="1.4">
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10 <repository changeset_revision="38e91928f905" name="package_matplotlib_1_4" 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="0.14">
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13 <repository changeset_revision="a257ce4d82ad" name="package_scipy_0_14" 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="0.8.1">
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16 <repository changeset_revision="6b6843e15541" name="package_pysam_0_8_1" 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="0.7.2">
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19 <repository changeset_revision="8c4879fee3cc" name="package_bx_python_0_7_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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20 </package>
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21 <package name="python" version="2.7">
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22 <repository changeset_revision="2c52c900e56a" name="package_python_2_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="ucsc_tools" version="0.1">
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25 <install version="1.0">
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26 <actions>
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27 <action type="download_binary">
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28 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
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29 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
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30 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
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31 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
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32 </action>
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33 <action type="chmod">
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34 <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
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35 </action>
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36 <action type="download_binary">
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37 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
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38 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
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39 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
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40 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
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41 </action>
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42 <action type="chmod">
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43 <file mode="755">$INSTALL_DIR/bigWigInfo</file>
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44 </action>
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45 <action type="download_binary">
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46 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph</url_template>
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47 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
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48 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
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49 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigToBedGraph</url_template>
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50 </action>
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51 <action type="chmod">
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52 <file mode="755">$INSTALL_DIR/bigWigToBedGraph</file>
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53 </action>
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54 <action type="set_environment">
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55 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
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56 </action>
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57 </actions>
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58 </install>
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59 <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
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60 </package>
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61
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62 <package name="deepTools" version="1.5.9.1">
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63 <install version="1.0">
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64 <actions>
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65 <action type="set_environment_for_install">
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66 <repository changeset_revision="6b6843e15541" name="package_pysam_0_8_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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67 <package name="pysam" version="0.8.1" />
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68 </repository>
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69 <repository changeset_revision="8c4879fee3cc" name="package_bx_python_0_7_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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70 <package name="bx-python" version="0.7.2" />
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71 </repository>
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72 <repository changeset_revision="dd91d64330d4" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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73 <package name="numpy" version="1.9" />
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74 </repository>
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75 <repository changeset_revision="38e91928f905" name="package_matplotlib_1_4" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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76 <package name="matplotlib" version="1.4" />
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77 </repository>
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78 <repository changeset_revision="a257ce4d82ad" name="package_scipy_0_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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79 <package name="scipy" version="0.14" />
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80 </repository>
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81 </action>
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82 <action type="setup_python_environment">
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83 <repository changeset_revision="2c52c900e56a" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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84 <package name="python" version="2.7" />
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85 </repository>
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86 <!-- allow downloading and installing an Python package from https://pypi.org/ -->
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87 <package>https://pypi.python.org/packages/source/d/deepTools/deepTools-1.5.9.1.tar.gz</package>
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88 </action>
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89
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90 <action type="set_environment">
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91 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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92 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
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93 <!-- disable the config file of deepTools -->
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94 <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
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95 </action>
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96 </actions>
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97 </install>
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98 <readme>
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99 Installation of deepTools from Fidel Ramirez.
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100 https://github.com/fidelram/deepTools
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101 </readme>
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102 </package>
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103 </tool_dependency>
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