view tool_dependencies.xml @ 14:59b33d253163 draft

re-export LD_LIBRARY_PATH so that the required libraries can also be found at runtime

<?xml version="1.0"?>
<tool_dependency>
  <package name="openssl" version="1.0.1g">
    <repository changeset_revision="23ebff671a20" name="package_openssl" owner="jankanis" prior_installation_required="True" toolshed="http://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="gdbm" version="1.11">
    <repository changeset_revision="15e7435c2663" name="package_gdbm_1_11" 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="23ebff671a20" name="package_openssl" owner="jankanis" toolshed="http://toolshed.g2.bx.psu.edu">
            <package name="openssl" version="1.0.1g" />
          </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>
          <repository changeset_revision="15e7435c2663" name="package_gdbm_1_11" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
            <package name="gdbm" version="1.11" />
          </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, but galaxy itself isn't whitespace-safe either so it doesn't matter (yet)
          oldifs="$IFS"
          IFS=:
          for p in $CPLUS_INCLUDE_PATH
          do
              CPPFLAGS="$CPPFLAGS -I$p"
          done
          for p in $LD_LIBRARY_PATH
          do
              LDFLAGS="$LDFLAGS -L$p"
          done
          IFS="$oldifs"
          export CPPFLAGS
          export LDFLAGS

          # Clear variables that may be used in Galaxy's extenal python 2 environment
          unset PYTHONPATH
          unset PYTHONHOME

          ./configure --prefix="$INSTALL_DIR" --with-ensurepip --enable-loadable-sqlite-extensions \
          &amp;&amp; make \
          &amp;&amp; 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>
          <!-- empty PYTHONPATH, otherwise we will get Galaxy's Python 2 libraries in the Python 3 path -->
          <environment_variable action="set_to" name="PYTHONPATH" />
          <environment_variable action="set_to" name="PYTHONHOME">$INSTALL_DIR</environment_variable>
          <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable>
        </action>
      </actions>
    </install>

    <readme>
    Python 3.4.1

    This build of python is configured with --enable-loadable-sqlite-extensions and a --prefix, any other settings are default. This build does not include modules for lzma, Tkinter and dbm, but does include ssl, gdbm and sqlite. Adding the missing modules should not be very difficult but requires wrapping the external sources that these modules require inside galaxy. 

    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:

      &lt;action type="set_environment_for_install"&gt;
        &lt;repository name="python3" owner="jankanis"&gt;
          &lt;package name="python3" version="3.4.1" /&gt;
        &lt;/repository&gt;
      &lt;/action&gt;
      &lt;action type="shell_command"&gt;
        # 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
        pyvenv {{\$MY_PACKAGE_NAME}}
        . {{\$MY_PACKAGE_NAME}}/bin/activate
        pip3 install {{\$PYTHON-PACKAGE}}
      &lt;/action&gt;
      &lt;action type="set_environment"&gt;
        &lt;environment_variable name="PYTHONPATH" action="prepend_to"&gt;\$INSTALL_DIR/lib/python3.4/site-packages&lt;/environment_variable&gt;
      &lt;/action&gt;

    </readme>
    
  </package>
</tool_dependency>