comparison tool_dependencies.xml @ 1:c322db44259d draft

build sqlite3; updated readme

0:1c337560fa56

<?xml version="1.0"?>
<tool_dependency>
  <package name="zlib" version="1.2.8">
      <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="python3" version="3.4.1">
      <install version="1.0">
          <actions>
              <action type="download_by_url">https://www.python.org/ftp/python/3.4.1/Python-3.4.1.tgz</action>
                <action type="set_environment_for_install">
                  <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
                      <package name="zlib" version="1.2.8" />
                    </repository>
                </action>
                <action type="shell_command">
          # The python build system doesn't check CPATH / C(PLUS)_INCLUDE_PATH which is set by the depended-upon
          # tool definitions for these sources, but it does check CPPFLAGS / LDFLAGS
          # Currently not whitespace-safe, I haven't found a way yet to quote the *FLAGS values so that they are
          # correctly recognized by both the python build process and the compiler. But as galaxy itself isn't

          unset PYTHONHOME

          ./configure --prefix="$INSTALL_DIR" --with-ensurepip \
          && make \
          && make install
        </action>
                <action type="set_environment">
                  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable>
                    <!-- clear PYTHONPATH, otherwise we will get Galaxy's Python 2 libraries in the Python 3 path. -->
                    <environment_variable action="set_to" name="PYTHONPATH" />

      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>

        # 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>

1:c322db44259d

<?xml version="1.0"?>
<tool_dependency>
  <package name="zlib" version="1.2.8">
      <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
  </package>
  
  <package name="sqlite" version="3.8.3">
    <repository changeset_revision="706b1f3b1fc0" name="package_sqlite_3_8_3" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
  </package>
  
  <package name="python3" version="3.4.1">
      <install version="1.0">
          <actions>
              <action type="download_by_url">https://www.python.org/ftp/python/3.4.1/Python-3.4.1.tgz</action>
              
                <action type="set_environment_for_install">
                  <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
                      <package name="zlib" version="1.2.8" />
                  </repository>
                    
                  <repository changeset_revision="706b1f3b1fc0" name="package_sqlite_3_8_3" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
                    <package name="sqlite" version="3.8.3" />
                  </repository>
                </action>
                
                <action type="shell_command">
          # The python build system doesn't check CPATH / C(PLUS)_INCLUDE_PATH which is set by the depended-upon
          # tool definitions for these sources, but it does check CPPFLAGS / LDFLAGS
          # Currently not whitespace-safe, I haven't found a way yet to quote the *FLAGS values so that they are
          # correctly recognized by both the python build process and the compiler. But as galaxy itself isn't

          unset PYTHONHOME

          ./configure --prefix="$INSTALL_DIR" --with-ensurepip \
          && make \
          && make install
                </action>
                
                <action type="set_environment">
                  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable>
                    <!-- clear PYTHONPATH, otherwise we will get Galaxy's Python 2 libraries in the Python 3 path. -->
                    <environment_variable action="set_to" name="PYTHONPATH" />

      The Python programming language version 3.

      http://www.python.org


      A lean build of python 3.4.1. 
      It contains the zlib and sqlite3 modules as the only stdlib modules with 
      external dependencies (handled in here by depending on package_zlib_1_2_8 
      and package_sqlite_3_8_3). 
      
      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 full build (including the ssl module) look at 
      https://toolshed.g2.bx.psu.edu/view/jankanis/package_python3_4 
      written by jankanis, of which this package is a shameless plagiarism. 

      This version of Python 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>

        # 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 the 
    tool_dependencies file of:
    
    https://toolshed.g2.bx.psu.edu/view/wolma/mimodd
    
    </readme>
  </package>
</tool_dependency>