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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="zlib" version="1.2.8">
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2
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4 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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5 </package>
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6
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7 <package name="sqlite" version="3.8.3">
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8 <repository changeset_revision="706b1f3b1fc0" name="package_sqlite_3_8_3" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
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9 </package>
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10
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11 <package name="python3" version="3.4.1">
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12 <install version="1.0">
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13 <actions>
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14 <action type="download_by_url">https://www.python.org/ftp/python/3.4.1/Python-3.4.1.tgz</action>
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15
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16 <action type="set_environment_for_install">
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2
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17 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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18 <package name="zlib" version="1.2.8" />
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19 </repository>
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20
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21 <repository changeset_revision="706b1f3b1fc0" name="package_sqlite_3_8_3" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
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22 <package name="sqlite" version="3.8.3" />
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23 </repository>
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24 </action>
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25
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26 <action type="shell_command">
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27 # The python build system doesn't check CPATH / C(PLUS)_INCLUDE_PATH which is set by the depended-upon
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28 # tool definitions for these sources, but it does check CPPFLAGS / LDFLAGS
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29 # Currently not whitespace-safe, I haven't found a way yet to quote the *FLAGS values so that they are
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30 # correctly recognized by both the python build process and the compiler. But as galaxy itself isn't
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31 # whitespace-safe either it doesn't really matter (currently).
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32 oldifs="$IFS"
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33 IFS=":"
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34 for p in $CPLUS_INCLUDE_PATH
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35 do
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36 CPPFLAGS="$CPPFLAGS -I$p"
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37 done
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38 for p in $LD_LIBRARY_PATH
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39 do
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40 LDFLAGS="$LDFLAGS -L$p"
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41 done
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42 IFS="$oldifs"
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43 export CPPFLAGS
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44 export LDFLAGS
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45
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46 # Clear variables that may be used in Galaxy's extenal python 2 environment
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47 unset PYTHONPATH
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48 unset PYTHONHOME
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49
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50 ./configure --prefix="$INSTALL_DIR" --with-ensurepip \
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51 && make \
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52 && make install
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53 </action>
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54
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55 <action type="set_environment">
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56 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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57 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable>
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58 <!-- clear PYTHONPATH, otherwise we will get Galaxy's Python 2 libraries in the Python 3 path. -->
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59 <environment_variable action="set_to" name="PYTHONPATH" />
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60 <environment_variable action="set_to" name="PYTHONHOME">$INSTALL_DIR</environment_variable>
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61 <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable>
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62 </action>
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63 </actions>
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64 </install>
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65 <readme>
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66 Python 3.4.1
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67
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68 The Python programming language version 3.
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69
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70 http://www.python.org
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71
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72
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73 A lean build of python 3.4.1.
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74 It contains the zlib and sqlite3 modules as the only stdlib modules with
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75 external dependencies (handled in here by depending on package_zlib_1_2_8
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76 and package_sqlite_3_8_3).
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77
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78 In particular, this build does not compile Python's ssl module (which
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79 would cause dependency on openssl and, in turn, on Perl).
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80
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81 This means that **the pip installation tool will not be available with
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82 this build** !!
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83
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84 For a full build (including the ssl module) look at
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85 https://toolshed.g2.bx.psu.edu/view/jankanis/package_python3_4
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86 written by jankanis, of which this package is a shameless plagiarism.
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87
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88 This version of Python includes a built-in virtual environment manager.
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89 To create a Python 3 virtual env, include the following actions in your
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90 tool_dependencies.xml, e.g. for a package MY_TOOL_venv:
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91
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92 <action type="set_environment_for_install">
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93 <repository name="package_python3_zlib_dependent_1_0" owner="wolma">
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94 <package name="python3" version="3.4.1" />
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95 </repository>
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96 <!-- other install time dependencies -->
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97 </action>
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98
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99 <action type="shell_command">
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100
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101 # Create virtual environment MY_TOOL_venv
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102 # pip cannot be used for installation because it depends on ssl,
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103 # which this build does not provide
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104
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105 pyvenv --without-pip $INSTALL_DIR/MY_TOOL_venv
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106
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107 # install python packages
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108 # assuming you are in the download directory of the package
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109
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110 $INSTALL_DIR/MY_TOOL_venv/bin/python3 setup.py install
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111 </action>
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112
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113 For an example of how this could used by a package look at the
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114 tool_dependencies file of:
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115
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116 https://toolshed.g2.bx.psu.edu/view/wolma/mimodd
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117
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118 </readme>
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1
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119 </package>
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120 </tool_dependency>
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