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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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4 <repository changeset_revision="12711c8cada7" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6
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7 <package name="readline" version="6.2">
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8 <repository changeset_revision="246f31787ca1" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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9 </package>
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10
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11 <package name="bzlib" version="1.0.6">
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12 <repository changeset_revision="2dec91192fc7" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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13 </package>
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14
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15 <package name="xz" version="5.0.5">
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16 <repository changeset_revision="b6876995a7e8" name="package_xz_5_0_5" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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17 </package>
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18
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19 <package name="openssl" version="1.0.1g">
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20 <repository changeset_revision="1c0d2868aa06" name="package_openssl_1_0" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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21 </package>
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22
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23 <package name="sqlite" version="3.8.3">
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24 <repository changeset_revision="e3729818491f" name="package_sqlite_3_8_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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25 </package>
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26
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27 <package name="gdbm" version="1.11">
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28 <repository changeset_revision="7367119a4afc" name="package_gdbm_1_11" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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29 </package>
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30
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31 <package name="ncurses" version="5.9">
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32 <repository changeset_revision="f62fa47b852d" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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33 </package>
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34
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35
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36 <package name="python3" version="3.4.1">
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37 <install version="1.0">
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38 <actions>
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39 <action type="download_by_url">https://www.python.org/ftp/python/3.4.1/Python-3.4.1.tgz</action>
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40
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41 <action type="set_environment_for_install">
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42 <repository changeset_revision="12711c8cada7" name="package_zlib_1_2_8" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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43 <package name="zlib" version="1.2.8" />
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44 </repository>
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45 <repository changeset_revision="246f31787ca1" name="package_readline_6_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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46 <package name="readline" version="6.2" />
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47 </repository>
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48 <repository changeset_revision="2dec91192fc7" name="package_bzlib_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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49 <package name="bzlib" version="1.0.6" />
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50 </repository>
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51 <repository changeset_revision="b6876995a7e8" name="package_xz_5_0_5" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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52 <package name="xz" version="5.0.5" />
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53 </repository>
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54 <repository changeset_revision="1c0d2868aa06" name="package_openssl_1_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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55 <package name="openssl" version="1.0.1g" />
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56 </repository>
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57 <repository changeset_revision="e3729818491f" name="package_sqlite_3_8_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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58 <package name="sqlite" version="3.8.3" />
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59 </repository>
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60 <repository changeset_revision="7367119a4afc" name="package_gdbm_1_11" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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61 <package name="gdbm" version="1.11" />
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62 </repository>
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63 <repository changeset_revision="f62fa47b852d" name="package_ncurses_5_9" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
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64 <package name="ncurses" version="5.9" />
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65 </repository>
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66 </action>
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67
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68 <action type="shell_command">
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69 # The python build system doesn't check CPATH / C(PLUS)_INCLUDE_PATH which is set by the depended-upon
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70 # tool definitions for these sources, but it does check CPPFLAGS / LDFLAGS
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71 # Currently not whitespace-safe, I haven't found a way yet to quote the *FLAGS values so that they are
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72 # correctly recognized by both the python build process and the compiler. But as galaxy itself isn't
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73 # whitespace-safe either it doesn't really matter (currently).
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74 oldifs="$IFS"
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75 IFS=":"
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76 for p in $CPLUS_INCLUDE_PATH
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77 do
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78 CPPFLAGS="$CPPFLAGS -I$p"
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79 done
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80 for p in $LD_LIBRARY_PATH
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81 do
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82 LDFLAGS="$LDFLAGS -L$p"
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83 done
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84 IFS="$oldifs"
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85 export CPPFLAGS
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86 export LDFLAGS
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87
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88 # Clear variables that may be used in Galaxy's extenal python 2 environment
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89 unset PYTHONPATH
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90 unset PYTHONHOME
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91
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92 ./configure --prefix="$INSTALL_DIR" --with-ensurepip --enable-loadable-sqlite-extensions \
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93 && make \
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94 && make install
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95 </action>
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96
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97 <action type="set_environment">
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98 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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99 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable>
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100 <!-- clear PYTHONPATH, otherwise we will get Galaxy's Python 2 libraries in the Python 3 path. -->
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101 <environment_variable action="set_to" name="PYTHONPATH" />
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102 <environment_variable action="set_to" name="PYTHONHOME">$INSTALL_DIR</environment_variable>
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103 <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable>
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104 </action>
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105 </actions>
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106 </install>
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107
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108 <readme>
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109 Python 3.4.1
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110
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111 The Python programming language version 3.
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112
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113 http://www.python.org
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114
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115
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116 This build of python is configured with --enable-loadable-sqlite-extensions, any other settings are default. This build does not include modules for lzma and Tkinter, but does include ssl, (g)dbm and sqlite. Adding the missing modules should not be very difficult but requires wrapping the external sources that these modules require inside galaxy.
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117
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118 Python as of version 3.3 includes a built-in virtual environment manager. To create a python 3 virtual env, include the following actions in your tool_dependencies.xml, e.g. for a package MY_TOOL_venv:
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119
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120 <action type="set_environment_for_install">
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121 <repository name="python3" owner="jankanis">
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122 <package name="python3" version="3.4.1" />
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123 </repository>
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124 <!-- ... other install time dependencies ... -->
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125 </action>
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126
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127 <action type="shell_command">
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128 # Unset any saved environment settings from parent virtual
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129 # environments, e.g. for python 2 or if Galaxy itself is running
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130 # from within a virtual environment.
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131 unset _OLD_VIRTUAL_PATH; unset _OLD_VIRTUAL_PYTHONHOME
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132 # Create virtual environment MY_TOOL_venv
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133 pyvenv MY_TOOL_venv
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134 # install python packages
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135 MY_TOOL_venv/bin/pip3 install {{NEEDED_PYTHON_PACKAGES}}
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136 </action>
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137
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138 <action type="set_environment">
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139
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140 <!-- Setting the PYTHONPATH correctly can be a bit tricky, because you must
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141 make sure that the runtime PYTHONPATH from galaxy itself is not
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142 included, as it probably points to python 2 code that can crash a
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143 program if python 3 tries to load it.
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144
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145 If you only use a single virtual environment that is created
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146 specifically for a tool you are creating, you can just use a set_to
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147 like below.
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148
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149 If you create a virtual environment installation that is meant to be
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150 reused by other packages, the virtual environment should probably
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151 prepend its site-packages to the PYTHONPATH since a tool could be
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152 using python modules from several virtual environments. But in such a
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153 scenario the tool that uses these virtual environments should also
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154 depend directly on the python3 package, and this dependency should be
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155 listed before any virtual environment dependencies. This ensures that
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156 the python3 environment settings that clear PYTHONPATH are sourced
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157 first so galaxy's runtime PYTHONPATH is excluded. Virtual environments
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158 can then prepend their PYTHONPATHs to each other. -->
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159 <environment_variable name="PYTHONPATH" action="set_to">$INSTALL_DIR/MY_TOOL_venv/lib/python3.4/site-packages</environment_variable>
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160 <!-- All that is really needed to use a specific virtual environment is that the
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161 python interpreter in that environment is used, so add it to PATH -->
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162 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/MY_TOOL_venv/bin</environment_variable>
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163 <!-- Clear incoming PYTHONHOME just like the venv's 'activate' command does -->
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164 <environment_variable name="PYTHONHOME" action="set_to"></environment_variable>
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165 <!-- To find shared libraries for python built-in modules such as libssl or libsqlite3
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166 we need to re-export LD_LIBRARY_PATH -->
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167 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$ENV[LD_LIBRARY_PATH]</environment_variable>
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168 </action>
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169
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170
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171 Then, in your MY_TOOL.xml add the following requirement:
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172
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173 <requirements>
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174 <requirement name="package" version="XXX">MY_TOOL_venv</requirement>
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175 </requirements>
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176
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177 </readme>
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178
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179 </package>
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180 </tool_dependency>
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