# HG changeset patch
# User jankanis
# Date 1401095464 14400
# Node ID 4091cf3b81e5ff1a86c791f507f95249d2943492
# Parent  bad79cc1a7b101f90862c581749320d90b959169
Uploaded

diff -r bad79cc1a7b1 -r 4091cf3b81e5 tool_dependencies.xml
--- a/tool_dependencies.xml	Sat May 24 18:38:31 2014 -0400
+++ b/tool_dependencies.xml	Mon May 26 05:11:04 2014 -0400
@@ -31,17 +31,31 @@
         </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
-          export CPPFLAGS="$CPPFLAGS -I$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=$INSTALL_DIR --with-ensurepip --enable-loadable-sqlite-extensions \
-	  &amp;&amp; make \
-	  &amp;&amp; make install
-	</action>
+          # The python build system doesn't check CPATH / C(PLUS)_INCLUDE_PATH which is set by the depended-upon
+          # tool definitions for these sources, but it does check CPPFLAGS / LDFLAGS
+          # Currently not whitespace-safe, but galaxy itself isn't whitespace-safe either so it doesn't matter (yet)
+          oldifs="$IFS"
+          IFS=:
+          for p in $CPLUS_INCLUDE_PATH
+          do
+              CPPFLAGS="$CPPFLAGS -I$p"
+          done
+          for p in $LD_LIBRARY_PATH
+          do
+              LDFLAGS="$LDFLAGS -L$p/lib"
+          done
+          IFS="$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>