# HG changeset patch
# User jankanis
# Date 1400968444 14400
# Node ID d3ea5f1b4d794134471b1a0abaf77daeb55d8990
# Parent  a468d4d76af311154bcce4093bef172609aa609d
Another attempt at getting the environment settings right.

diff -r a468d4d76af3 -r d3ea5f1b4d79 tool_dependencies.xml
--- a/tool_dependencies.xml	Sat May 24 13:41:15 2014 -0400
+++ b/tool_dependencies.xml	Sat May 24 17:54:04 2014 -0400
@@ -17,6 +17,7 @@
     <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" />
@@ -29,15 +30,20 @@
           </repository>
         </action>
 
-	<action type="set_environment">
-	  <environment_variable action="set_to" name="CFLAGS">$CFLAGS -I$SQLITE_ROOT_DIR/lib -I$GDBM_ROOT_PATH/lib -I$OPENSSL_ROOT_DIR/lib</environment_variable>
-	  <environment_variable action="set_to" name="CPPFLAGS">$CPPFLAGS -I$SQLITE_ROOT_DIR/lib -I$GDBM_ROOT_PATH/lib -I$OPENSSL_ROOT_DIR/lib</environment_variable>
-	  <environment_variable action="set_to" name="LDFLAGS">$LDFLAGS -L$SQLITE_ROOT_DIR/include -L$GDBM_ROOT_PATH/include -L$OPENSSL_ROOT_DIR/include</environment_variable>
+        <action type="shell_command">
+	  # The python build system doesn't check C_INCLUDE_PATH which is set by the depended-upon tool 
+	  # definitions for these sources, but it does check CFLAGS. 
+          export CFLAGS="$CFLAGS -I$SQLITE_ROOT_DIR/lib -I$GDBM_ROOT_PATH/lib -I$OPENSSL_ROOT_DIR/lib"
+	  export LDFLAGS="$LDFLAGS -L$SQLITE_ROOT_DIR/include -L$GDBM_ROOT_PATH/include -L$OPENSSL_ROOT_DIR/include"
+	  # 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 instal
 	</action>
+	<action type="make_install" />
 
-	<!-- We need a shell command here because the variables set above are not passed to type="autotool" commands -->
-        <action type="shell_command">bash &lt;/dev/tty &gt;/dev/tty 2&gt;&amp;1 &amp;&amp; ./configure --prefix=$INSTALL_DIR --with-ensurepip --enable-loadable-sqlite-extensions</action>
-	<action type="make_install" />
         <action type="set_environment">
           <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
           <!-- empty PYTHONPATH, otherwise we will get Galaxy's Python 2 libraries in the Python 3 path -->