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0
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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2
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3 <package name="numpy" version="1.7.1">
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17
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4 <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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4
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6 <package name="scipy" version="0.12.0">
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17
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7 <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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2
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8 </package>
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17
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9 <package name="R_3_0_1" version="3.0.1">
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20
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10 <repository changeset_revision="1c0e86a44f73" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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0
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11 </package>
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17
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12 <package name="gnu_awk" version="4.1.0">
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13 <repository changeset_revision="cbe9f1c8c98b" name="package_gnu_awk_4_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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16
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14 </package>
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17
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15 <set_environment version="1.0">
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16 <environment_variable action="set_to" name="MACS2_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
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17 </set_environment>
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18 <!-- 2.0.10 12162013 -->
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19 <package name="macs2" version="2.0.10.3">
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20 <install version="1.0">
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21 <actions>
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17
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22 <action type="shell_command">git clone --recursive https://github.com/taoliu/MACS.git</action>
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23 <!-- Galaxy tries to change automatically to the directory "macs2" (name of the package).
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24 But we need to change to MACS. Go one level back and enter MACS -->
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25 <action type="change_directory">../MACS</action>
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26 <action type="shell_command">git checkout 7ccb571d2f2dcb5be1d75f323b1d17a59b926deb</action>
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27 <action type="shell_command">git submodule update --recursive</action>
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12
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28
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3
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29 <action type="set_environment_for_install">
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30 <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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31 <package name="numpy" version="1.7.1" />
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32 </repository>
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4
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33 <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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34 <package name="scipy" version="0.12.0" />
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3
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35 </repository>
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36 </action>
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37 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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19
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38 <!-- exporting the CFLAGS and CPPFLAGS are due to http://stackoverflow.com/questions/22313407/clang-error-unknown-argument-mno-fused-madd-python-package-installation-fa -->
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3
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39 <action type="shell_command">
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19
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40 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
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41 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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3
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42 </action>
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43 <action type="set_environment">
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17
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44 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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45 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
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46 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
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5
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47 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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17
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48 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_SCIPY]</environment_variable>
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49 <environment_variable action="set_to" name="PYTHONPATH_MACS2">$INSTALL_DIR/lib/python</environment_variable>
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50 </action>
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51 </actions>
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52 </install>
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53 <readme>Macs2 installation instructions. MACS2 can be found at https://github.com/taoliu/MACS</readme>
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54 </package>
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55 </tool_dependency>
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