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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <!--<set_environment version="1.0">
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4 <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
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5 </set_environment>-->
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6 <package name="macs2" version="2.0.10.2">
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7 <install version="1.0">
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8 <actions>
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9 <action type="download_by_url">http://www.python.org/ftp/python/2.7.3/Python-2.7.3.tar.bz2</action>
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10 <action type="shell_command">`pwd` > ~/test.out</action>
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11 <action type="shell_command">cd Python-2.7.3</action>
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12 <action type="shell_command">./configure</action>
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13 <action type="shell_command">make -j</action>
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14 <action type="shell_command">sudo make install</action>
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15 <action type="shell_command">sudo chmod ag+w /usr/local/lib/python2.7/site-packages</action>
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16 <action type="shell_command">sudo chmod ag+wx /usr/local/bin</action>
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17 </actions>
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18 <actions>
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19 <action type="download_by_url">https://github.com/modENCODE-DCC/Galaxy/blob/master/toolshed/dependencies/macs2/macs2pkg.tar?raw=true</action>
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20 <action type="move_directory_files">
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21 <source_directory>bin</source_directory>
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22 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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23 </action>
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24 <action type="move_directory_files">
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25 <source_directory>lib</source_directory>
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26 <destination_directory>$INSTALL_DIR/lib</destination_directory>
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27 </action>
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28 <action type="set_environment">
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29 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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30 <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib/python2.7/site-packages</environment_variable>
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31 </action>
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32 </actions>
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33 </install>
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34 <readme>Macs2 depends on having python2.7 installed on all nodes of the work cluster</readme>
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35 </package>
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36 </tool_dependency>
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