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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="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.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="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://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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10 <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" toolshed="http://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="3c1bf479158c" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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14 </package>
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15 <package name="pysam" version="0.7.6">
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16 <repository changeset_revision="247e5e5bee87" name="package_pysam_0_7_6" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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17 </package>
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18
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19 <package name="ucsc_tools" version="0.1">
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20 <install version="1.0">
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21 <actions>
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22 <action type="download_binary">
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23 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
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24 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
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25 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
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26 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
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27 </action>
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28 <action type="chmod">
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29 <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
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30 </action>
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31 <action type="download_binary">
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32 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
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33 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
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34 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
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35 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
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36 </action>
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37 <action type="chmod">
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38 <file mode="755">$INSTALL_DIR/bigWigInfo</file>
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39 </action>
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40 <action type="download_binary">
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41 <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph</url_template>
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42 <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
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43 <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigToBedGraph</url_template>
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44 <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigToBedGraph</url_template>
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45 </action>
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46 <action type="chmod">
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47 <file mode="755">$INSTALL_DIR/bigWigToBedGraph</file>
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48 </action>
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49 <action type="set_environment">
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50 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
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51 </action>
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52 </actions>
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53 </install>
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54 <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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55 </package>
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56
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57 <package name="deepTools" version="1.5.1_91b873c095bb4ca44da99e57d8b49784508aa98b">
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58 <install version="1.0">
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59 <actions>
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60 <!-- populate the environment variables from the dependend repos -->
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61 <action type="set_environment_for_install">
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62 <repository changeset_revision="a4e35f23093f" name="package_pysam_0_7_5" owner="fubar" toolshed="http://testtoolshed.g2.bx.psu.edu">
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63 <package name="pysam" version="0.7.5" />
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64 </repository>
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65 </action>
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66 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
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67 <action type="shell_command">git reset --hard 91b873c095bb4ca44da99e57d8b49784508aa98b</action>
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68 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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69 <action type="shell_command">
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70 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
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71 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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72 </action>
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73
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74 <action type="set_environment">
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75 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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76 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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77 <!-- disable the config file of deepTools -->
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78 <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
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79 </action>
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80 </actions>
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81 </install>
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82 <readme>Installation of deepTools from Fidel Ramirez.</readme>
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83 </package>
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84 </tool_dependency>
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