annotate tool_dependencies.xml @ 16:7719329e5b98 draft

Depend on iuc versions of libraries

<?xml version="1.0"?>
<tool_dependency>
  <package name="openssl" version="1.0.1g">
    <repository changeset_revision="3b19041c651c" name="package_openssl_1_0" owner="iuc" 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="ad3c23208758" 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="3b19041c651c" name="package_openssl_1_0" owner="iuc" 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="ad3c23208758" 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, 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
          # whitespace-safe either it doesn't really matter (currently).
          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

      The Python programming language version 3.

      http://www.python.org


      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. 

      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;!-- other install time dependencies --&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
	# Create virtual environment MY_TOOL_venv
	pyvenv MY_TOOL_venv
	# install python packages
	MY_TOOL_venv/bin/pip3 install {{NEEDED_PYTHON_PACKAGES}}
      &lt;/action&gt;

      &lt;action type="set_environment"&gt;
        &lt;!-- Remove any incoming PYTHONPATH elements from Galaxy's own python 2 environment,
	     but include an existing install time PYTHONPATH (e.g. from other python3 virtual
	     environments in the dependency hierarchy. --&gt;
	&lt;environment_variable name="PYTHONPATH" action="set_to"&gt;$INSTALL_DIR/MY_TOOL_venv/lib/python3.4/site-packages:$ENV[PYTHONPATH]&lt;/environment_variable&gt;
	&lt;!-- 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 --&gt;
	&lt;environment_variable name="PATH" action="prepend_to"&gt;$INSTALL_DIR/MY_TOOL_venv/bin&lt;/environment_variable&gt;
	&lt;!-- Clear incoming PYTHONHOME just like the venv's 'activate' command does --&gt;
	&lt;environment_variable name="PYTHONHOME" action="set_to"&gt;&lt;/environment_variable&gt;
	&lt;!-- To find shared libraries for python built-in modules such as libssl or libsqlite3
	     we need to re-export LD_LIBRARY_PATH --&gt;
	&lt;environment_variable name="LD_LIBRARY_PATH" action="prepend_to"&gt;$ENV[LD_LIBRARY_PATH]&lt;/environment_variable&gt;
      &lt;/action&gt;

    </readme>

  </package>
</tool_dependency>