Thanks again to Yavor Doganov <yavor@gnu.org> for another very helpful hint

 fi

 # 5. Checks for libraries

@@ -731,6 +731,29 @@ AC_CONFIG_FILES([easel/testsuite/Makefil

 AC_CONFIG_FILES([easel/Makefile])

 AC_CONFIG_FILES([easel/documentation/Makefile])

+

+AH_TOP([

+/* RAMLIMIT (in MB) defines how much memory we're

+ * allowed to expend on alignment algorithms without

+ * switching to more efficient memory forms - e.g.

+ * in smallcyk.c

+ */

+#ifndef RAMLIMIT

+#define RAMLIMIT 0

+#endif

+

+/* SRE_CONLEVEL will prob move to squid somewhere.

+ *  Set to 1 to activate contract checking, during debugging.

+ */

+#define SRE_CONLEVEL 1

+#if (SRE_CONLEVEL >= 1)

+#include <assert.h>

+#endif

+

+#define CMSEQDBENV       "BLASTDB"

+#define CMDBENV          "RFAMDB"

+])

+

 ################################################################

 # 13. AC_OUTPUT

 ################################################################