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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="9d017266c41e" name="package_zlib_1_2_8" owner="wolma" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
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5 </package>
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6
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7 <package name="python3" version="3.4.1">
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8 <install version="1.0">
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9 <actions>
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10 <action type="download_by_url">https://www.python.org/ftp/python/3.4.1/Python-3.4.1.tgz</action>
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11
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12 <action type="set_environment_for_install">
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13 <repository changeset_revision="31f1e69aae89" name="package_zlib_1_2_8" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
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14 <package name="zlib" version="1.2.8" />
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15 </repository>
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16 </action>
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17
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18 <action type="shell_command">
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19 # The python build system doesn't check CPATH / C(PLUS)_INCLUDE_PATH which is set by the depended-upon
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20 # tool definitions for these sources, but it does check CPPFLAGS / LDFLAGS
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21 # Currently not whitespace-safe, I haven't found a way yet to quote the *FLAGS values so that they are
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22 # correctly recognized by both the python build process and the compiler. But as galaxy itself isn't
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23 # whitespace-safe either it doesn't really matter (currently).
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24 oldifs="$IFS"
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25 IFS=":"
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26 for p in $CPLUS_INCLUDE_PATH
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27 do
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28 CPPFLAGS="$CPPFLAGS -I$p"
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29 done
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30 for p in $LD_LIBRARY_PATH
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31 do
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32 LDFLAGS="$LDFLAGS -L$p"
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33 done
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34 IFS="$oldifs"
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35 export CPPFLAGS
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36 export LDFLAGS
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37
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38 # Clear variables that may be used in Galaxy's extenal python 2 environment
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39 unset PYTHONPATH
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40 unset PYTHONHOME
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41
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42 ./configure --prefix="$INSTALL_DIR" --with-ensurepip \
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43 && make \
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44 && make install
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45 </action>
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46
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47 <action type="set_environment">
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48 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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49 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable>
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50 <!-- clear PYTHONPATH, otherwise we will get Galaxy's Python 2 libraries in the Python 3 path. -->
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51 <environment_variable action="set_to" name="PYTHONPATH" />
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52 <environment_variable action="set_to" name="PYTHONHOME">$INSTALL_DIR</environment_variable>
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53 <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable>
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54 </action>
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55 </actions>
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56 </install>
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57
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58 <readme>
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59 Python 3.4.1
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60
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61 The Python programming language version 3.
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62
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63 http://www.python.org
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64
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65
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66 A lean build of python 3.4.1. It does not include modules with external dependencies except for the zlib module, which requires the zlib library installed on your system. For a build with more such modules included look at https://toolshed.g2.bx.psu.edu/view/jankanis/package_python3_4 written by jankanis, of which this package is a shameless plagiarism.
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67
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68 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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69
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70 <action type="set_environment_for_install">
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71 <repository name="python3" owner="wolma">
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72 <package name="python3" version="3.4.1" />
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73 </repository>
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74 <!-- other install time dependencies -->
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75 </action>
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76
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77 <action type="shell_command">
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78 # Unset any saved environment settings from parent virtual
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79 # environments, e.g. for python 2 or if Galaxy itself is running
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80 # from within a virtual environment.
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81 unset _OLD_VIRTUAL_PATH; unset _OLD_VIRTUAL_PYTHONHOME
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82 # Create virtual environment MY_TOOL_venv
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83 pyvenv MY_TOOL_venv
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84 # install python packages
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85 MY_TOOL_venv/bin/pip3 install {{NEEDED_PYTHON_PACKAGES}}
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86 </action>
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87
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88 <action type="set_environment">
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89
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90 <!-- Setting the PYTHONPATH correctly can be a bit tricky, because you must
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91 make sure that the runtime PYTHONPATH from galaxy itself is not
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92 included, as it probably points to python 2 code that can crash a
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93 program if python 3 tries to load it.
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94
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95 If you only use a single virtual environment that is created
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96 specifically for a tool you are creating, you can just use a set_to
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97 like below.
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98
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99 If you create a virtual environment installation that is meant to be
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100 reused by other packages, the virtual environment should probably
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101 prepend its site-packages to the PYTHONPATH since a tool could be
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102 using python modules from several virtual environments. But in such a
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103 scenario the tool that uses these virtual environments should also
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104 depend directly on the python3 package, and this dependency should be
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105 listed before any virtual environment dependencies. This ensures that
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106 the python3 environment settings that clear PYTHONPATH are sourced
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107 first so galaxy's runtime PYTHONPATH is excluded. Virtual environments
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108 can then prepend their PYTHONPATHs to each other. -->
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109 <environment_variable name="PYTHONPATH" action="set_to">$INSTALL_DIR/MY_TOOL_venv/lib/python3.4/site-packages</environment_variable>
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110 <!-- All that is really needed to use a specific virtual environment is that the
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111 python interpreter in that environment is used, so add it to PATH -->
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112 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/MY_TOOL_venv/bin</environment_variable>
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113 <!-- Clear incoming PYTHONHOME just like the venv's 'activate' command does -->
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114 <environment_variable name="PYTHONHOME" action="set_to"></environment_variable>
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115 <!-- To find shared libraries for python built-in modules such as libssl or libsqlite3
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116 we need to re-export LD_LIBRARY_PATH -->
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117 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$ENV[LD_LIBRARY_PATH]</environment_variable>
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118 </action>
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119
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120
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121 Then, in your MY_TOOL.xml add the following requirement:
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122
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123 <requirements>
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124 <requirement name="package" version="XXX">MY_TOOL_venv</requirement>
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125 </requirements>
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126
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127 </readme>
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128
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129 </package>
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130 </tool_dependency>
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