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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="deepTools" version="1.5.9">
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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://github.com/fidelram/deepTools/archive/1.5.9.1.tar.gz</action>
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7 <action type="set_environment_for_install">
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8 <repository changeset_revision="64e2daea7b15" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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9 <package name="pysam" version="0.7.7" />
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10 </repository>
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11 <repository changeset_revision="4c15bd2528e1" name="package_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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12 <package name="bx-python" version="0.7.1" />
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13 </repository>
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14 <repository changeset_revision="6a7842f2f960" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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15 <package name="numpy" version="1.7.1" />
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16 </repository>
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17 <repository changeset_revision="b08a9f0f28ec" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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18 <package name="matplotlib" version="1.2.1" />
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19 </repository>
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20 <repository changeset_revision="6d8201c2a767" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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21 <package name="scipy" version="0.12.0" />
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22 </repository>
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23 <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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24 <package name="samtools" version="0.1.19" />
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25 </repository>
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26 <repository changeset_revision="535261946ba0" name="package_ucsc_tools" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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27 <package name="ucsc_tools" version="0.1" />
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28 </repository>
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29 </action>
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30 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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31 <action type="shell_command">
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32 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
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33 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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34 </action>
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35
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36 <action type="set_environment">
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37 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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38 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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39 <environment_variable action="set_to" name="DEEPTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
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40 <environment_variable action="set_to" name="DEEPTOOLS_PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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41 <environment_variable action="set_to" name="DEEPTOOLS_PATH">$INSTALL_DIR/bin</environment_variable>
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42 <!-- include samtools into PATH -->
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43 <environment_variable action="prepend_to" name="PATH">$ENV[BAM_ROOT]/bin</environment_variable>
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44 <!-- include numpy -->
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45 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
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46 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
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47 <!-- include matplotlib -->
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48 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable>
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49 <!-- include scipy -->
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50 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_SCIPY]</environment_variable>
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51 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_SCIPY]</environment_variable>
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52 <!-- include bx-python -->
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53 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[BX_PYTHON_PATH]/lib/python</environment_variable>
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54 <environment_variable action="prepend_to" name="PATH">$ENV[BX_PYTHON_PATH]/bin</environment_variable>
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55 <!-- include pysam -->
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56 <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYSAM_PATH]/lib/python</environment_variable>
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57 <environment_variable action="prepend_to" name="PATH">$ENV[PYSAM_PATH]/bin</environment_variable>
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58 <!-- include ucsc tools -->
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59 <environment_variable action="prepend_to" name="PATH">$ENV[UCSC_TOOLS_ROOT_PATH]</environment_variable>
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60
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61 <!-- disable the config file of deepTools -->
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62 <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
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63 </action>
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64 </actions>
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65 </install>
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66 <readme>
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67 Installation of deepTools from Fidel Ramirez.
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68 https://github.com/fidelram/deepTools
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69 </readme>
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70 </package>
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71 </tool_dependency>
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