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26
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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="00e17a794a2e" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="numpy" version="1.7.1">
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7 <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.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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27
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10 <repository changeset_revision="d639ff3d6b6e" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
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26
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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="984d208b0808" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.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="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.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="f938170835cc" name="package_bx_python_12_2013" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
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20 </package>
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21
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22 <package name="ucsc_tools" version="0.1">
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23 <install version="1.0">
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24 <actions>
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25 <action type="download_binary">
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26 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
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27 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
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28 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
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29 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
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30 </action>
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31 <action type="chmod">
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32 <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
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33 </action>
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34 <action type="download_binary">
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35 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
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36 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
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37 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
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38 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
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39 </action>
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40 <action type="chmod">
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41 <file mode="755">$INSTALL_DIR/bigWigInfo</file>
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42 </action>
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43 <action type="download_binary">
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44 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph</url_template>
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45 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
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46 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
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47 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigToBedGraph</url_template>
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48 </action>
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49 <action type="chmod">
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50 <file mode="755">$INSTALL_DIR/bigWigToBedGraph</file>
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51 </action>
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52 <action type="set_environment">
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53 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
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54 </action>
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55 </actions>
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56 </install>
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57 <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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58 </package>
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59
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27
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60 <package name="deepTools" version="1.5.4_43d3b51b3c3ab71dc07f31fefe6b3492226cc217">
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26
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61 <install version="1.0">
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62 <actions>
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63 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
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64 <!-- populate the environment variables from the dependend repos -->
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65 <action type="set_environment_for_install">
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66 <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
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67 <package name="pysam" version="0.7.7" />
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68 </repository>
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69 <repository changeset_revision="f938170835cc" name="package_bx_python_12_2013" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
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70 <package name="bx-python" version="12-2013" />
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71 </repository>
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72 <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
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73 <package name="numpy" version="1.7.1" />
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74 </repository>
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27
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75 <repository changeset_revision="d639ff3d6b6e" name="package_matplotlib_1_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
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26
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76 <package name="matplotlib" version="1.2.1" />
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77 </repository>
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78 <repository changeset_revision="984d208b0808" name="package_scipy_0_12" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
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79 <package name="scipy" version="0.12.0" />
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80 </repository>
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81 </action>
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27
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82 <action type="shell_command">git reset --hard 43d3b51b3c3ab71dc07f31fefe6b3492226cc217</action>
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26
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83 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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84 <action type="shell_command">
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85 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
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86 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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87 </action>
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88 <action type="set_environment">
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89 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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90 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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91 <!-- disable the config file of deepTools -->
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92 <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
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93 </action>
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94 </actions>
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95 </install>
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96 <readme>
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97 Installation of deepTools from Fidel Ramirez.
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98 https://github.com/fidelram/deepTools
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99 </readme>
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100 </package>
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101 </tool_dependency>
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