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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="python_mysqldb" version="1.2.5">
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4 <install version="1.0">
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5 <actions>
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6 <action type="download_by_url">https://pypi.python.org/packages/source/M/MySQL-python/MySQL-python-1.2.5.zip</action>
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7 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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8 <action type="shell_command">
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9 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
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10 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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11 </action>
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12 <action type="set_environment">
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13 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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14 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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15 </action>
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16 </actions>
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17 </install>
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18 <readme>Installs Python module MySQLdb 1.2.5</readme>
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19 </package>
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20 <!-- bx_python
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21 This is cribbed from devteam's 'package_bx_python_0_7' in the main
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22 toolshed:
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23 https://toolshed.g2.bx.psu.edu/view/devteam/package_bx_python_0_7
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24 -->
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25 <package name="bx_python" version="0.7.1">
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26 <install version="1.0">
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27 <actions>
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28 <action type="setup_virtualenv">
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29 numpy==1.7.1
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30 bx-python==0.7.1
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31 </action>
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32 <action type="set_environment">
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33 <environment_variable action="set_to" name="BX_PYTHON_PATH">$INSTALL_DIR</environment_variable>
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34 </action>
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35 </actions>
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36 </install>
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37 <readme>
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38 Installation of bx-python 0.7.1 along with numpy 1.7.1. The installation can be
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39 accessed via BX_PYTHON_PATH.
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40 </readme>
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41 </package>
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42 <!-- cistrome_ceas
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43 Installs the version of CEAS package found in the Cistrome
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44 distribution:
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45 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
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46 -->
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47 <package name="cistrome_ceas" version="1.0.2.d8c0751">
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48 <install version="1.0">
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49 <actions>
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50 <action type="shell_command">
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51 hg clone https://bitbucket.org/cistrome/cistrome-applications-harvard cistrome_ceas
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52 </action>
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53 <action type="shell_command">
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54 hg update d8c0751
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55 </action>
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56 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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57 <action type="shell_command">
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58 cd published-packages/CEAS/
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59 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
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60 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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61 </action>
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62 <action type="set_environment">
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63 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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64 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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65 </action>
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66 </actions>
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67 </install>
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68 <readme>Installs version 1.0.2 of CEAS from cistrome (commit id d8c0751,
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69 datestamp 20140929), which includes ceasBW (a version of ceas which can
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70 handle bigWig file input from MACS2.
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71
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72 Cistrome code is at
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73 https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
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74
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75 The CEAS code is under the published-packages/CEAS/ subdirectory
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76
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77 Cistrome data files and documentation can be found at
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78 http://liulab.dfci.harvard.edu/CEAS/index.html
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79 </readme>
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80 </package>
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81 </tool_dependency>
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