annotate tool_dependencies.xml @ 5:fb4d95141633 draft

update dependency to latest openssl that builds shared libraries

<?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="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" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
            <package name="openssl" version="1.0.1g" />
          </repository>
        </action>
        <!--
         Python3 config doesn't search for some optional dependencies
         in non-standard locations. Patch config.py to also look at
         the repositories we just installed above
         -->
        <action type="shell_command">
          patch &lt;&lt; EOF
--- a/setup.py
+++ b/setup.py
@@ -750,10 +750,14 @@
         exts.append( Extension('_socket', ['socketmodule.c'],
                                depends = ['socketmodule.h']) )
         # Detect SSL support for the socket module (via _ssl)
+        CUSTOM_OPENSSL = os.environ.get('OPENSSL_ROOT_DIR')
         search_for_ssl_incs_in = [
                               '/usr/local/ssl/include',
                               '/usr/contrib/ssl/include/'
                              ]
+        if CUSTOM_OPENSSL:
+            search_for_ssl_incs_in.append(os.path.join(CUSTOM_OPENSSL, 'include'))
+        
         ssl_incs = find_file('openssl/ssl.h', inc_dirs,
                              search_for_ssl_incs_in
                              )
@@ -762,10 +766,12 @@
                                ['/usr/kerberos/include'])
             if krb5_h:
                 ssl_incs += krb5_h
-        ssl_libs = find_library_file(self.compiler, 'ssl',lib_dirs,
-                                     ['/usr/local/ssl/lib',
-                                      '/usr/contrib/ssl/lib/'
-                                     ] )
+
+        search_for_ssl_libs_in = ['/usr/local/ssl/lib',
+                                  '/usr/contrib/ssl/lib/']
+        if CUSTOM_OPENSSL:
+            search_for_ssl_libs_in.append(os.path.join(CUSTOM_OPENSSL, 'lib'))
+        ssl_libs = find_library_file(self.compiler, 'ssl', lib_dirs, search_for_ssl_libs_in)
 
         if (ssl_incs is not None and
             ssl_libs is not None):
EOF
        </action>
        <action type="autoconf">--prefix=$INSTALL_DIR --with-ensurepip</action>
        <action type="set_environment">
          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</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. Configured with the default settings, using --prefix=$INSTALL_DIR.

      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>