Mercurial > repos > nml > package_python_3_4_hivtrace_0_1_4

annotate tool_dependencies.xml @ 1:af0cf1f508fa draft

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planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa-dirty
author nml
date Thu, 07 Jul 2016 13:43:14 -0400
parents 38541eaf0d20
children 8ba7ea2370cb
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38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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1 <?xml version="1.0"?>
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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2 <tool_dependency>
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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3 <package name="python" version="3.4">
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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4 <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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5 </package>
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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6 <package name="cmake" version="3.2.3">
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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7 <repository changeset_revision="1aea698a1c63" name="package_cmake_3_2_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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8 </package>
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af0cf1f508fa planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa-dirty
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9 <package name="hyphy-python" version="0.1.3">
af0cf1f508fa planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa-dirty
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38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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11 </package>
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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12 <package name="pysam" version="0.8.3">
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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13 <repository changeset_revision="085a17b297b1" name="package_python_3_4_pysam_0_8_3" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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14 </package>
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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15 <package name="numpy" version="1.10.1">
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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17 </package>
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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18 <package name="biopython" version="1.66">
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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20 </package>
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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21 <package name="bioext" version="0.17.3">
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af0cf1f508fa planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa-dirty
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af0cf1f508fa planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa-dirty
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23 </package>
af0cf1f508fa planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa-dirty
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24 <package name="cython" version="0.23.4">
af0cf1f508fa planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa-dirty
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af0cf1f508fa planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa-dirty
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26 </package>
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27 <package name="fakemp" version="0.9.1">
af0cf1f508fa planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa-dirty
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38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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29 </package>
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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30 <package name="hppy" version="0.9.6">
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af0cf1f508fa planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa-dirty
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38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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32 </package>
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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33 <package name="hivclustering" version="1.2.3">
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af0cf1f508fa planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa-dirty
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38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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35 </package>
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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36 <package name="tn93" version="1.0.2">
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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38 </package>
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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39 <package name="hivtrace" version="0.1.4">
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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40 <install version="1.0">
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41 <actions>
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42 <action type="download_by_url">https://github.com/veg/hivtrace/archive/0.1.4.tar.gz</action>
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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43 <action type="set_environment_for_install">
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44 <repository changeset_revision="5c14a49141f0" name="package_python_3_4_hyphy_python_0_1_3" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
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45 <package name="hyphy-python" version="0.1.3" />
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46 </repository>
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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47 <repository changeset_revision="085a17b297b1" name="package_python_3_4_pysam_0_8_3" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
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48 <package name="pysam" version="0.8.3" />
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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49 </repository>
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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50 <repository changeset_revision="f182da2b1d78" name="package_python_3_4_numpy_1_10_1" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
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51 <package name="numpy" version="1.10.1" />
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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52 </repository>
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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53 <repository changeset_revision="cb43753d0467" name="package_python_3_4_biopython_1_66" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
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54 <package name="biopython" version="1.66" />
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55 </repository>
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57 <package name="bioext" version="0.17.3" />
38541eaf0d20 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
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58 </repository>
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59 <repository changeset_revision="eda1cbde6572" name="package_python_3_4_hivclustering_1_2_3" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
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60 <package name="hivclustering" version="1.2.3" />
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61 </repository>
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62 <repository changeset_revision="52c11d398790" name="package_python_3_4_cython_0_23_4" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
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63 <package name="cython" version="0.23.4" />
af0cf1f508fa planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_hivtrace_0_1_4 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa-dirty
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64 </repository>
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65 <repository changeset_revision="13da2754601c" name="package_python_3_4_fakemp_0_9_1" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
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66 <package name="fakemp" version="0.9.1" />
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67 </repository>
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68 <repository changeset_revision="46decde5b780" name="package_python_3_4_hppy_0_9_6" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
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69 <package name="hppy" version="0.9.6" />
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70 </repository>
0
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71 <repository changeset_revision="e1abbe60f3d4" name="package_tn93_1_0_2" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
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72 <package name="tn93" version="1.0.2" />
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73 </repository>
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74 <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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75 <package name="python" version="3.4" />
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76 </repository>
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77 </action>
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78 <action type="make_directory">$INSTALL_DIR/lib/python</action>
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79 <action type="make_directory">$INSTALL_DIR/bin</action>
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80 <action type="shell_command">
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81 ln -s $PATH_PYTHON3/python3 $INSTALL_DIR/bin/python3 &amp;&amp;
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82 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
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83 export PATH=$PATH:$PATH_NUMPY &amp;&amp;
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84 export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp;
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85 $INSTALL_DIR/bin/python3 setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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86 </action>
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87 <action type="set_environment">
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88 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
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89 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
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90 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_BIOPYTHON]</environment_variable>
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91 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_BIOEXT]</environment_variable>
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92 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
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93 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_PYSAM]</environment_variable>
1
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94 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_HYPHY_PYTHON]</environment_variable>
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95 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_CYTHON]</environment_variable>
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96 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_HIVCLUSTERING]</environment_variable>
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97 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_FAKEMP]</environment_variable>
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98 <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_HPPY]</environment_variable>
0
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99 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
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100 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_PYSAM]</environment_variable>
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101 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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102 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_HIVCLUSTERING]</environment_variable>
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103 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_BIOEXT]</environment_variable>
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104 <environment_variable action="prepend_to" name="PATH">$ENV[PATH_TN93]</environment_variable>
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105 </action>
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106 </actions>
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107 </install>
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108 <readme>
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109 This installs hivtrace 0.1.4 (and all its dependencies).
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110
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111 See usage instructions here: https://github.com/veg/hivtrace
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112 </readme>
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113 </package>
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114 </tool_dependency>