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1 <?xml version="1.0"?>
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2 <!--
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3
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4 <requirement type="package">deepTools</requirement>
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5 <requirement type="python-module">deepTools</requirement>
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6 <requirement type="python-module">matplotlib</requirement> -> toolshed
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7 <requirement type="python-module">argsparse</requirement> -> is in python 2.7 or?
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8 <requirement type="python-module">itertools</requirement> -> is in standard python?
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9 <requirement type="python-module">pysam</requirement> -> is also shipped with galaxy
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10 <requirement type="python-module">numpy</requirement> -> toolshed
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11 <requirement type="python-module">pylab</requirement> -> scipy toolshed
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12 <requirement type="python-module">bx.intervals.io</requirement> -> bx-python is shipped with galaxy afaik
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13 -->
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14
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15 <tool_dependency>
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16 <package name="samtools" version="0.1.18">
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17 <repository name="package_samtools_0_1_18" owner="devteam" />
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18 </package>
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19 <package name="numpy" version="1.7.1">
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20 <repository name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" />
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21 </package>
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22 <package name="matplotlib" version="1.2.1">
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23 <repository name="package_matplotlib_1_2" owner="bgruening" prior_installation_required="True" />
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24 </package>
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25 <package name="scipy" version="0.12.0">
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26 <repository name="package_scipy_0_12" owner="bgruening" prior_installation_required="True" />
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0
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27 </package>
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28
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29 <package name="ucsc_tools" version="0.1">
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30 <install version="1.0">
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31 <actions>
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32 <action type="download_binary">
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33 <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
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34 <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
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35 <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
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36 <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
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0
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37 </action>
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38 <action type="chmod">
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39 <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
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40 </action>
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41 <action type="download_binary">
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42 <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
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43 <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
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44 <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
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45 <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
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0
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46 </action>
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47 <action type="chmod">
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48 <file mode="755">$INSTALL_DIR/bigWigInfo</file>
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49 </action>
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50 <action type="set_environment">
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51 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
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0
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52 </action>
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53 </actions>
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54 </install>
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55 <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
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56 </package>
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57
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58 <package name="deepTools" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">
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59 <install version="1.0">
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60 <actions>
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61 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
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62 <action type="shell_command">git reset --hard 98e5d8a61431ea8605c0643d991a1a5d8999b4dc</action>
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63 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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64 <action type="shell_command">
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65 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
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66 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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67 </action>
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68
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69 <action type="set_environment">
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70 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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71 <environment_variable name="PYTHONPATH" action="append_to" >$INSTALL_DIR/lib/python</environment_variable>
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72 <!-- disable the config file of deepTools -->
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73 <environment_variable name="DEEP_TOOLS_NO_CONFIG" action="set_to">TRUE</environment_variable>
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0
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74 </action>
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75 </actions>
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76 </install>
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77 <readme>Installation of deepTools from Fidel Ramirez.</readme>
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78 </package>
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79 </tool_dependency>
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