comparison tool_dependencies.xml @ 7:5cfafaafa263 draft default tip

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6:79f0803e3bbb

      The Python programming language version 3.

      http://www.python.org


      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. 

      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:

      <action type="set_environment_for_install">
        <repository name="python3" owner="wolma">
          <package name="python3" version="3.4.1" />
        </repository>
        <!-- other install time dependencies -->
      </action>

      <action type="shell_command">
        # Unset any saved environment settings from parent virtual
        # environments, e.g. for python 2 or if Galaxy itself is running
        # from within a virtual environment.
        unset _OLD_VIRTUAL_PATH; unset _OLD_VIRTUAL_PYTHONHOME
        # Create virtual environment MY_TOOL_venv
        pyvenv MY_TOOL_venv
        # install python packages
        MY_TOOL_venv/bin/pip3 install {{NEEDED_PYTHON_PACKAGES}}
      </action>

      <action type="set_environment">

	<!-- Setting the PYTHONPATH correctly can be a bit tricky, because you must
             make sure that the runtime PYTHONPATH from galaxy itself is not
             included, as it probably points to python 2 code that can crash a
             program if python 3 tries to load it.

             If you only use a single virtual environment that is created
             specifically for a tool you are creating, you can just use a set_to
             like below.

             If you create a virtual environment installation that is meant to be
             reused by other packages, the virtual environment should probably
             prepend its site-packages to the PYTHONPATH since a tool could be
             using python modules from several virtual environments. But in such a
             scenario the tool that uses these virtual environments should also
             depend directly on the python3 package, and this dependency should be
             listed before any virtual environment dependencies. This ensures that
             the python3 environment settings that clear PYTHONPATH are sourced
             first so galaxy's runtime PYTHONPATH is excluded. Virtual environments
             can then prepend their PYTHONPATHs to each other. -->
        <environment_variable name="PYTHONPATH" action="set_to">$INSTALL_DIR/MY_TOOL_venv/lib/python3.4/site-packages</environment_variable>
        <!-- All that is really needed to use a specific virtual environment is that the
             python interpreter in that environment is used, so add it to PATH -->
        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/MY_TOOL_venv/bin</environment_variable>
        <!-- Clear incoming PYTHONHOME just like the venv's 'activate' command does -->
        <environment_variable name="PYTHONHOME" action="set_to"></environment_variable>
        <!-- To find shared libraries for python built-in modules such as libssl or libsqlite3
             we need to re-export LD_LIBRARY_PATH -->
        <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$ENV[LD_LIBRARY_PATH]</environment_variable>
      </action>


      Then, in your MY_TOOL.xml add the following requirement:

      <requirements>
        <requirement name="package" version="XXX">MY_TOOL_venv</requirement>
      </requirements>
      
    </readme>

  </package>
</tool_dependency>

7:5cfafaafa263

      The Python programming language version 3.

      http://www.python.org


      A lean build of python 3.4.1. It does not include modules with external dependencies except for the zlib module (handled in here by depending on package_zlib_1_2_8). 
      
      In particular, this build does not compile Python's ssl module, which would cause dependency on openssl and, in turn, on Perl. This means that **the pip installation tool will not be available with this build**. 
      
      For a build with more modules (and also ssl) 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. 

      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:

      <action type="set_environment_for_install">
        <repository name="package_python3_zlib_dependent_1_0" owner="wolma">
          <package name="python3" version="3.4.1" />
        </repository>
        <!-- other install time dependencies -->
      </action>

      <action type="shell_command">        
        
        # Create virtual environment MY_TOOL_venv
        # pip cannot be used for installation because it depends on ssl, 
        # which this build does not provide
        
        pyvenv --without-pip $INSTALL_DIR/MY_TOOL_venv
        
        # install python packages
        # assuming you are in the download directory of the package
        
        $INSTALL_DIR/MY_TOOL_venv/bin/python3 setup.py install 
      </action>
      
    For an example of how this could used by a package look at:
    
    https://testtoolshed.g2.bx.psu.edu/view/wolma/package_mimodd_0_1_5
    
    </readme>

  </package>
</tool_dependency>