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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3
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4 <package name="samtools" version="0.1.18">
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5 <install version="1.0">
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6 <actions>
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7 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
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8 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
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9 <action type="shell_command">make</action>
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10 <action type="move_file">
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11 <source>samtools</source>
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12 <destination>$INSTALL_DIR/bin</destination>
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13 </action>
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14 <action type="move_file">
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15 <source>misc/maq2sam-long</source>
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16 <destination>$INSTALL_DIR/bin</destination>
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17 </action>
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18 <action type="set_environment">
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19 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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20 </action>
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21 </actions>
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22 </install>
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23 <readme>
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24 Compiling SAMtools requires the ncurses and zlib development libraries.
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25 </readme>
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26 </package>
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27
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28 <package name="python" version="2.7">
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29 <readme>
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30 JointSNVMix requires Python >= 2.7
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31 </readme>
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32 </package>
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33
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34 <package name="cython" version="0.19.1">
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35 <install version="1.0">
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36 <actions>
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37 <action type="download_by_url">http://cython.org/release/Cython-0.19.1.tar.gz</action>
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38 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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39 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
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40 <action type="set_environment">
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41 <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
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42 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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43 </action>
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44 </actions>
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45 </install>
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46 <readme>
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47 </readme>
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48 </package>
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49
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50 <package name="pysam" version="0.5">
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51 <install version="1.0">
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52 <actions>
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53 <action type="download_by_url">http://pysam.googlecode.com/files/pysam-0.5.tar.gz</action>
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54 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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55 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
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56 <action type="set_environment">
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57 <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
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58 </action>
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59 </actions>
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60 </install>
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61 <readme>
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62 </readme>
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63 </package>
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64 <package name="jointsnvmix" version="0.7.5">
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65 <install version="1.0">
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66 <actions>
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67 <action type="download_by_url">http://joint-snv-mix.googlecode.com/files/JointSNVMix-0.7.5.tar.gz</action>
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68 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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69 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
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70 <action type="set_environment">
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71 <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
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72 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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73 </action>
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74 </actions>
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75 </install>
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76 <readme>
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77 </readme>
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78 </package>
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79
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80
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81
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82 </tool_dependency>
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