diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..075683e
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,2 @@
+wise2.2.0.tar.gz
+/wise2.4.1.tar.gz
diff --git a/dead.package b/dead.package
deleted file mode 100644
index 995362e..0000000
--- a/dead.package
+++ /dev/null
@@ -1 +0,0 @@
-Orphaned by upstream; no longer needed in Fedora
diff --git a/sources b/sources
new file mode 100644
index 0000000..08acc43
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+d70c404c1dc40ceef7718757b11bdaa0  wise2.4.1.tar.gz
diff --git a/wise2-build.patch b/wise2-build.patch
new file mode 100644
index 0000000..d30904b
--- /dev/null
+++ b/wise2-build.patch
@@ -0,0 +1,21 @@
+--- wise-2.4.0~/src/makefile	2007-07-15 23:39:24.000000000 +0200
++++ wise-2.4.0/src/makefile	2007-07-15 23:41:11.000000000 +0200
+@@ -109,7 +109,7 @@
+ bin : 
+ 	mkdir bin
+ 	cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin
+-	csh welcome.csh
++	./welcome.csh
+ 
+ libs : 
+ 	(cd base   ; $(MAKE) CC="$(CC)" CFLAGS="$(CFLAGS)" libwisebase.a )
+diff -urNad wise-2.4.0~/src/welcome.csh wise-2.4.0/src/welcome.csh
+--- wise-2.4.0~/src/welcome.csh	2007-07-15 23:39:24.000000000 +0200
++++ wise-2.4.0/src/welcome.csh	2007-07-15 23:40:46.000000000 +0200
+@@ -1,4 +1,4 @@
+-#!/bin/tcsh -f
++#!/bin/sh
+ 
+ echo ""
+ echo "Welcome to Wise2.4"
+
diff --git a/wise2-c99.patch b/wise2-c99.patch
new file mode 100644
index 0000000..4e2074f
--- /dev/null
+++ b/wise2-c99.patch
@@ -0,0 +1,29 @@
+No upstream bug tracking so tracked here:
+https://bugzilla.redhat.com/show_bug.cgi?id=2155977
+
+diff --git a/src/HMMer2/prior.c b/src/HMMer2/prior.c
+index a40eb9c..76517e2 100644
+--- a/src/HMMer2/prior.c
++++ b/src/HMMer2/prior.c
+@@ -4,6 +4,8 @@
+  * Support for Dirichlet prior data structure, p7prior_s.
+  */
+ 
++#include <string.h>
++
+ #include "config.h"
+ #include "structs.h"
+ #include "funcs.h" 
+diff --git a/src/external/mott/mott_api.c b/src/external/mott/mott_api.c
+index a42ab5b..4466095 100644
+--- a/src/external/mott/mott_api.c
++++ b/src/external/mott/mott_api.c
+@@ -1,6 +1,8 @@
+ #include<stdio.h>
+ #include<limits.h>
+ #include<math.h>
++#include<stdlib.h>
++#include<ctype.h>
+ #include"gapstat.h"
+ 
+ double default_lambda0, default_K0, default_Kplus, default_H, default_r, default_s, default_alpha;
diff --git a/wise2-getline.patch b/wise2-getline.patch
new file mode 100644
index 0000000..0e2fd1a
--- /dev/null
+++ b/wise2-getline.patch
@@ -0,0 +1,302 @@
+Index: wise-2.4.1/src/HMMer2/sqio.c
+===================================================================
+--- wise-2.4.1.orig/src/HMMer2/sqio.c	2009-10-31 20:10:25.000000000 +0000
++++ wise-2.4.1/src/HMMer2/sqio.c	2009-10-31 20:11:11.000000000 +0000
+@@ -213,7 +213,7 @@
+     }
+ }
+ 
+-/* Function: getline()
++/* Function: getline_()
+  * Date:     SRE, Tue Mar  3 08:30:01 1998 [St. Louis]
+  *
+  * Purpose:  read a line from a sequence file into V->sbuffer.
+@@ -229,7 +229,7 @@
+  * Returns:  (void)
+  */
+ static void 
+-getline(struct ReadSeqVars *V)
++getline_(struct ReadSeqVars *V)
+ {
+   char *cp;
+   
+@@ -299,7 +299,7 @@
+   V->seqlen = 0;
+   if (addfirst) addseq(V->sbuffer, V);
+   do {
+-    getline(V);
++    getline_(V);
+ 	/* feof() alone is a bug; files not necessarily \n terminated */
+     if (*(V->sbuffer) == '\0' && feof(V->f))
+       done = TRUE;
+@@ -327,7 +327,7 @@
+   char *sptr;
+ 				/* load first line of entry  */
+   while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+-    getline(V);
++    getline_(V);
+   if (feof(V->f)) return;
+ 
+   if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
+@@ -336,7 +336,7 @@
+       SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
+     }
+   do {
+-    getline(V);
++    getline_(V);
+     if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
+       SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
+     else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
+@@ -345,7 +345,7 @@
+ 	  SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
+       }
+   } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
+-  getline(V);			/* skip next line, coords */
++  getline_(V);			/* skip next line, coords */
+ 
+   readLoop(0, endPIR, V);
+ 
+@@ -359,7 +359,7 @@
+   /* get next line
+    */
+   while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+-    getline(V);
++    getline_(V);
+ }
+ 
+ 
+@@ -377,7 +377,7 @@
+   char *nm;
+ 				/* position past ';' comments */
+   do {
+-    getline(V);
++    getline_(V);
+   } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
+ 
+   if (!feof(V->f))
+@@ -389,7 +389,7 @@
+     }
+   
+   while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
+-    getline(V);
++    getline_(V);
+ }
+ 
+ static int 
+@@ -411,7 +411,7 @@
+ 	  if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
+ 	    SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
+ 	}
+-      getline(V);
++      getline_(V);
+     }
+ 
+   if (! feof(V->f))
+@@ -420,7 +420,7 @@
+   /* load next line
+    */
+   while ((!feof(V->f)) && (*V->sbuffer != ';')) 
+-    getline(V);
++    getline_(V);
+ }
+ 
+ 
+@@ -438,7 +438,7 @@
+   int   in_definition;
+ 
+   while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
+-    getline(V);
++    getline_(V);
+ 
+   if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
+     {
+@@ -449,7 +449,7 @@
+   in_definition = FALSE;
+   while (! feof(V->f))
+     {
+-      getline(V);
++      getline_(V);
+       if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
+ 	{
+ 	  if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
+@@ -482,11 +482,11 @@
+ 
+ 
+   while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
+-    getline(V);
++    getline_(V);
+ 				/* SRE: V->s now holds "//", so sequential
+ 				   reads are wedged: fixed Tue Jul 13 1993 */
+   while (!feof(V->f) && strstr(V->sbuffer, "LOCUS  ") != V->sbuffer)
+-    getline(V);
++    getline_(V);
+ }
+ 
+ static int
+@@ -515,7 +515,7 @@
+     Die("bogus GCGdata format? %s", V->sbuffer);
+ 
+ 				/* second line contains free text description */
+-  getline(V);
++  getline_(V);
+   SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
+ 
+   if (binary) {
+@@ -535,7 +535,7 @@
+   else readLoop(0, endGCGdata, V);
+   
+   while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+-    getline(V);
++    getline_(V);
+ }
+ 
+ static int
+@@ -555,12 +555,12 @@
+   if ((sptr = strtok(NULL, "\n")) != NULL)
+     SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
+ 				/* workaround for long NCBI NR lines */
+-  while (V->longline && ! feof(V->f)) getline(V);
++  while (V->longline && ! feof(V->f)) getline_(V);
+ 
+   readLoop(0, endPearson, V);
+ 
+   while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+-    getline(V);
++    getline_(V);
+ }
+ 
+ 
+@@ -587,7 +587,7 @@
+ 
+ 				/* make sure we have first line */
+   while (!feof(V->f) && strncmp(V->sbuffer, "ID  ", 4) != 0)
+-    getline(V);
++    getline_(V);
+ 
+   if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
+     {
+@@ -596,7 +596,7 @@
+     }
+ 
+   do {
+-    getline(V);
++    getline_(V);
+     if (!feof(V->f) && strstr(V->sbuffer, "AC  ") == V->sbuffer)
+       {
+ 	if ((sptr = strtok(V->sbuffer+5, ";  \t\n")) != NULL)
+@@ -620,7 +620,7 @@
+ 
+ 				/* load next record's ID line */
+   while (!feof(V->f) && strncmp(V->sbuffer, "ID  ", 4) != 0)
+-    getline(V);
++    getline_(V);
+ }
+ 
+ 
+@@ -636,7 +636,7 @@
+ {
+   char *sptr;
+ 
+-  getline(V);  /*s == "seqLen seqid string..."*/
++  getline_(V);  /*s == "seqLen seqid string..."*/
+ 
+   if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
+     SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -647,7 +647,7 @@
+   readLoop(0, endZuker, V);
+ 
+   while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
+-    getline(V);
++    getline_(V);
+ }
+ 
+ static void 
+@@ -669,7 +669,7 @@
+ 
+   do {
+     done = feof(V->f);
+-    getline(V);
++    getline_(V);
+     if (! done) addseq(V->sbuffer, V);
+   } while (!done);
+ }
+@@ -681,7 +681,7 @@
+   char *sptr;
+   int   dostruc = FALSE;
+ 
+-  while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
++  while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline_(V);
+ 
+   if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
+     SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -689,7 +689,7 @@
+   /*CONSTCOND*/
+   while (1)
+     {
+-      getline(V);
++      getline_(V);
+       if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
+ 
+       if (strncmp(V->sbuffer, "SRC ", 4) == 0)
+@@ -721,14 +721,14 @@
+   while (1)
+     {
+ 				/* sequence line */
+-      getline(V);
++      getline_(V);
+       if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) 
+ 	break;
+       addseq(V->sbuffer, V);
+ 				/* structure line */
+       if (dostruc)
+ 	{
+-	  getline(V);
++	  getline_(V);
+ 	  if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
+ 	  addstruc(V->sbuffer, V);
+ 	}
+@@ -736,7 +736,7 @@
+ 
+ 
+   while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
+-    getline(V);
++    getline_(V);
+ }
+ 
+ 
+@@ -816,7 +816,7 @@
+ 
+   /* Load the first line.
+    */
+-  getline(dbfp);
++  getline_(dbfp);
+ 
+   return dbfp;
+ }
+@@ -833,7 +833,7 @@
+     Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
+ 
+   fseek(sqfp->f, offset, SEEK_SET);
+-  getline(sqfp);
++  getline_(sqfp);
+ }
+ 
+ 
+@@ -853,7 +853,7 @@
+   if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
+   else {
+     rewind(sqfp->f);
+-    getline(sqfp);
++    getline_(sqfp);
+   }
+ }
+ 
+@@ -949,7 +949,7 @@
+       do {			/* skip leading comments on GCG file */
+ 	gotuw = (strstr(V->sbuffer,"..") != NULL);
+ 	if (gotuw) readUWGCG(V);
+-	getline(V);
++	getline_(V);
+       } while (! feof(V->f));
+       break;
+ 
diff --git a/wise2-glib2.patch b/wise2-glib2.patch
new file mode 100644
index 0000000..8c8a448
--- /dev/null
+++ b/wise2-glib2.patch
@@ -0,0 +1,703 @@
+Author: Barry deFreese <bdefreese@debian.org>
+Description: To build wise2 with the Glib version 2.0 instead of 1.2.
+Forwarded: birney@sanger.ac.uk
+--- a/src/makefile
++++ b/src/makefile
+@@ -31,13 +31,13 @@
+ 
+ 
+ # Intel icc flags
+-# CFLAGS = -c  -O3 -axWK -ipo `glib-config --cflags`
++# CFLAGS += -c  -axWK -ipo `pkg-config --cflags glib-2.0`
+ 
+ # alpha flags (-pthread)
+-# CFLAGS = -c -O3 -pthread `glib-config --cflags`
++# CFLAGS += -c -pthread `pkg-config --cflags glib-2.0`
+ 
+ # normal linux/bsd/mac flags
+-CFLAGS = -c -O3  `glib-config --cflags`
++CFLAGS += $(CPPFLAGS) -c  `pkg-config --cflags glib-2.0`
+ 
+ 
+ EXTRALIBS = -lm
+--- a/src/snp/makefile
++++ b/src/snp/makefile
+@@ -5,9 +5,9 @@
+ CC = cc
+ #CFLAGS = -c -O2  -pg -I../base/ -I../dynlibsrc/
+ #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE  -DUNIX  -I../base/ -I../dynlibsrc/ -I.
+-CFLAGS = -c -g3 -O2  -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags`
++CFLAGS += $(CPPFLAGS) -c -g3  -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0`
+ 
+-LFLAGS =  -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm
++LDFLAGS +=  -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lpthread -lm
+ AR_OPTIONS = ru
+ 
+ RANLIB_NEEDED = 0
+@@ -16,7 +16,7 @@
+ 	$(CC) $(CFLAGS) $(INCFLAGS) $?
+ 
+ test_est : test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o 
+-	$(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS)
++	$(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LDFLAGS)
+ 
+ INCFLAGS = -I../base/ -I../dynlibsrc/
+ DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn
+--- a/src/corba/makefile
++++ b/src/corba/makefile
+@@ -3,9 +3,9 @@
+ CC = cc
+ INCFLAGS = -I../base/ -I../dynlibsrc
+ #gCFLAGS = -Wall -g -pedantic -c  -DUNIX -I../base/
+-#CFLAGS =  -O2 -c  -DUNIX  -I../base/ `glib-config --cflags` -I/usr/local/include/orbit-1.0/
+-CFLAGS =  -pthread -c  -DUNIX  -I../base/ -I../dynlibsrc `orbit-config --cflags client`
+-LFLAGS =   -L../base/ -lm -lpthread
++#CFLAGS +=  -c  -DUNIX  -I../base/ `pkg-config --cflags glib-2.0` -I/usr/local/include/orbit-1.0/
++CFLAGS  += $(CPPFLAGS) -pthread -c  -DUNIX  -I../base/ -I../dynlibsrc `orbit-config --cflags client`
++LDFLAGS += -L../base/ -lm -lpthread
+ AR_OPTIONS = ru
+ 
+ 
+@@ -14,18 +14,18 @@
+ 	orbit-idl hspscan_corba.idl
+ 
+ test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o 
+-	cc -g -o test_server  test_server.o hspscan_server_impl.o  hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o  corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o   ../dynlibsrc/libdyna_glib.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
++	cc -g -o test_server  test_server.o hspscan_server_impl.o  hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o  corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o   ../dynlibsrc/libdyna_glib.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
+ 
+ scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o 
+-	cc -o scanwise_protein_index  scanwise_protein_index.o hspscan_server_impl.o  hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o  corba_singleton.o  ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
++	cc -o scanwise_protein_index  scanwise_protein_index.o hspscan_server_impl.o  hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o  corba_singleton.o  ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
+ 
+ 
+ test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o 
+-	cc -g -o test_client  test_client.o  hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
++	cc -g -o test_client  test_client.o  hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
+ 
+ 
+ test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o 
+-	cc -g -o test_wrapper test_wrapper.o  hspscan_corba-common.o hspscan_corba-stubs.o   corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a  `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
++	cc -g -o test_wrapper test_wrapper.o  hspscan_corba-common.o hspscan_corba-stubs.o   corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a  `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
+ 
+ .c.o :
+ 	$(CC) $(CFLAGS) $(INCFLAGS) $?
+--- a/src/models/makefile
++++ b/src/models/makefile
+@@ -62,46 +62,46 @@
+ #	$(CC) $(CFLAGS) -I../HMMer2/ $(INCFLAGS) wise2xhmmer2.c
+ 
+ testgenestat : testgenestat.o genestats.o pwmdna.o 
+-	$(CC) -o testgenestat testgenestat.o genestats.o pwmdna.o -ldyna -lwisebase $(LFLAGS) 
++	$(CC) -o testgenestat testgenestat.o genestats.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) 
+ 
+ test_aligng : test_aligng.o aligngenemodel.o pwmdna.o 
+-	$(CC) -o test_aligng test_aligng.o aligngenemodel.o pwmdna.o  -ldyna -lwisebase $(LFLAGS) 
++	$(CC) -o test_aligng test_aligng.o aligngenemodel.o pwmdna.o  -ldyna -lwisebase $(LDFLAGS) 
+ 
+ makepwm : makepwm.o pwmdna.o 
+-	$(CC) -o makepwm makepwm.o pwmdna.o -ldyna -lwisebase $(LFLAGS) 
++	$(CC) -o makepwm makepwm.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) 
+ 
+ testwise2xhmmer2.o : testwise2xhmmer2.c
+ 	$(CC) $(CFLAGS) -I../HMMer2/ $(INCFLAGS) testwise2xhmmer2.c
+ 
+ testwise2xhmmer2 : testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o 
+-	$(CC) -o testwise2xhmmer2 wise2xhmmer2.o testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o -ldyna -lwisebase -lhmmer $(LFLAGS) 
++	$(CC) -o testwise2xhmmer2 wise2xhmmer2.o testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o -ldyna -lwisebase -lhmmer $(LDFLAGS) 
+ 
+ plan7test.o : plan7test.c
+ 	$(CC) $(CFLAGS) -I../HMMer2/ plan7test.c
+ 
+ plan7test : plan7test.o plan7.o wise2xhmmer2.o threestatemodel.o threestatedb.o  pfamhmmer1db.o
+-	$(CC) -o plan7test plan7test.o plan7.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o -ldyna -lwisebase -lhmmer $(LFLAGS) 
++	$(CC) -o plan7test plan7test.o plan7.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o -ldyna -lwisebase -lhmmer $(LDFLAGS) 
+ 
+ seqstat : seqstat.o
+-	$(CC) -o seqstat seqstat.o -ldyna -lwisebase $(LFLAGS)
++	$(CC) -o seqstat seqstat.o -ldyna -lwisebase $(LDFLAGS)
+ 
+ mutatedna : mutatedna.o
+-	$(CC) -o mutatedna mutatedna.o -ldyna -lwisebase $(LFLAGS) 
++	$(CC) -o mutatedna mutatedna.o -ldyna -lwisebase $(LDFLAGS) 
+ 
+ revcomp : revcomp.o
+-	$(CC) -o revcomp revcomp.o -ldyna -lwisebase $(LFLAGS) 
++	$(CC) -o revcomp revcomp.o -ldyna -lwisebase $(LDFLAGS) 
+ 
+ stupid_motif_scan : stupid_motif_scan.o
+-	$(CC) -o stupid_motif_scan stupid_motif_scan.o -ldyna -lwisebase $(LFLAGS) 
++	$(CC) -o stupid_motif_scan stupid_motif_scan.o -ldyna -lwisebase $(LDFLAGS) 
+ 
+ seqtrunc : seqtrunc.o
+-	$(CC) -o seqtrunc seqtrunc.o -ldyna -lwisebase $(LFLAGS) 
++	$(CC) -o seqtrunc seqtrunc.o -ldyna -lwisebase $(LDFLAGS) 
+ 
+ seqlist : seqlist.o
+-	$(CC) -o seqlist seqlist.o -ldyna -lwisebase $(LFLAGS) 
++	$(CC) -o seqlist seqlist.o -ldyna -lwisebase $(LDFLAGS) 
+ 
+ testpwm : testpwm.o pwmdna.o
+-	$(CC) -o testpwm testpwm.o pwmdna.o -ldyna -lwisebase $(LFLAGS)  -lefence
++	$(CC) -o testpwm testpwm.o pwmdna.o -ldyna -lwisebase $(LDFLAGS)  -lefence
+ 
+ 
+ threestate : $(MODELOBJ)
+@@ -111,29 +111,29 @@
+ pwise : $(MODELOBJ) threestatemat.o threestatedisplay.o
+ 
+ test : test.o proteinsw.o protprotdis.o
+-	$(CC) -o test test.o proteinsw.o protprotdis.o  -ldyna_glib -ldyna -lwisebase ../dynlibsrc/matrix.o $(LFLAGS)
++	$(CC) -o test test.o proteinsw.o protprotdis.o  -ldyna_glib -ldyna -lwisebase ../dynlibsrc/matrix.o $(LDFLAGS)
+ 
+ testanc : testanc.o proteinsw.o abc.o pba.o sw_wrap.o
+-	$(CC) -o testanc testanc.o proteinsw.o abc.o pba.o sw_wrap.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -o testanc testanc.o proteinsw.o abc.o pba.o sw_wrap.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ test_tf : test_transfactor.o transfactor.o pwmdna.o
+-	$(CC) -o test_tf test_transfactor.o transfactor.o pwmdna.o $(LFLAGS) -ldyna -lwisebase 
++	$(CC) -o test_tf test_transfactor.o transfactor.o pwmdna.o $(LDFLAGS) -ldyna -lwisebase 
+ 
+ motifwise : motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o 
+-	$(CC) -o motifwise motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase 
++	$(CC) -o motifwise motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase 
+ 
+ motifcluster : motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o 
+-	$(CC) -o motifcluster motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase 
++	$(CC) -o motifcluster motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase 
+ 
+ motifdiff : motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o 
+-	$(CC) -o motifdiff motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase 
++	$(CC) -o motifdiff motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase 
+ 
+ 
+ cdtest : cdtest.o cdna2genomic.o d2d_display.o
+-	$(CC) -o cdtest cdtest.o cdna2genomic.o d2d_display.o  -ldyna_glib -ldyna -lwisebase $(LFLAGS)
++	$(CC) -o cdtest cdtest.o cdna2genomic.o d2d_display.o  -ldyna_glib -ldyna -lwisebase $(LDFLAGS)
+ 
+ prob2bits : prob2bits.o
+-	$(CC) -o prob2bits  $(LFLAGS) -ldyna_glib -ldyna -lwisebase 
++	$(CC) -o prob2bits  $(LDFLAGS) -ldyna_glib -ldyna -lwisebase 
+ 
+ quick :
+ 	cc -O -c -I../dynlibsrc/ -I../base/ genewise6.c
+@@ -180,161 +180,161 @@
+ 	$(CC) $(CFLAGS) fivestarscan.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I.
+ 
+ oldpostwise : oldpostwise.o $(NEWG) 
+-	$(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  
++	$(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  
+ 
+ testdna : testdna.o dnaalign.o seqaligndisplay.o 
+-	$(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ dnal : dnal.o dnaalign.o seqaligndisplay.o 
+-	$(CC) -o dnal dnal.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -o dnal dnal.o dnaalign.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ psw : psw.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o
+-	$(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o   $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o   $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ scanwisep.o : scanwisep.c
+-	$(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $?
++	$(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config --cflags glib-2.0` $?
+ 
+ hsp2aln_sw.o : hsp2aln_sw.c
+-	$(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
++	$(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $?
+ 
+ scanwisep_mysql.o : scanwisep.c
+ 	$(CC)  $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c 
+ 
+ scanwisep_mysql : scanwisep_mysql.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
+-	$(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../mysql/protein_index/mysql_protein_index.o  $(LFLAGS) -L../external/mott -L/usr/local/mysql/lib -ldyna_glib -ldyna ott -lwisebase -lmysqlclient -lm $(EXTRALIBS) -lpthread -lZ
++	$(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../mysql/protein_index/mysql_protein_index.o  $(LDFLAGS) -L../external/mott -L/usr/local/mysql/lib -ldyna_glib -ldyna ott -lwisebase -lmysqlclient -lm $(EXTRALIBS) $(LDFLAGS) -lpthread -lZ
+ 
+ 
+ scanwisep_corba.o : scanwisep.c
+ 	$(CC)  $(CFLAGS) -DSCAN_CORBA -I../corba -I../external/mott `orbit-config --cflags server` scanwisep.c 
+ 
+ scanwisep_corba : scanwisep_corba.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
+-	$(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   ../corba/hspscan_corba-common.o ../corba/hspscan_corba-stubs.o   ../corba/corba_singleton.o ../corba/hspscan_corba_wrapper.o $(LFLAGS) -L../external/mott -ldyna_glib -ldyna -lmott -lwisebase  $(EXTRALIBS) `orbit-config --libs server` -lpthread 
++	$(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   ../corba/hspscan_corba-common.o ../corba/hspscan_corba-stubs.o   ../corba/corba_singleton.o ../corba/hspscan_corba_wrapper.o $(LDFLAGS) -L../external/mott -ldyna_glib -ldyna -lmott -lwisebase  $(EXTRALIBS) `orbit-config --libs server` -lpthread 
+ 
+ 
+ scanwisep_wiseserver.o : scanwisep.c
+ 	$(CC)  $(CFLAGS) $(INCFLAGS)  -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c 
+ 
+ scanwise : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
+-	$(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   ../network/net_hspscan.o ../network/client_multihspscan.o  $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase  $(EXTRALIBS) -lpthread 
++	$(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   ../network/net_hspscan.o ../network/client_multihspscan.o  $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase  $(EXTRALIBS) -lpthread 
+ 
+ scanwisep_compress.o : scanwisep.c
+ 	$(CC)  $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c 
+ 
+ scanwisep_compress : scanwisep_compress.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
+-	$(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   ../dnaindex/compressed_protein_index.o ../dnaindex/singleseqspace.o  ../dnaindex/kmer_direct.o  ../dnaindex/kmer_index_interface.o  $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase  $(EXTRALIBS) -lpthread 
++	$(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   ../dnaindex/compressed_protein_index.o ../dnaindex/singleseqspace.o  ../dnaindex/kmer_direct.o  ../dnaindex/kmer_index_interface.o  $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase  $(EXTRALIBS) -lpthread 
+ 
+ 
+ 
+ scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
+-	$(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   $(LFLAGS)  -L../external/mott -lmott -ldyna_glib -ldyna  -lwisebase  $(EXTRALIBS) `glib-config --libs` -lpthread
++	$(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   $(LDFLAGS)  -L../external/mott -lmott -ldyna_glib -ldyna  -lwisebase  $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread
+ 
+ test_gwhsp : test_gwhsp.o genewisehsp.o
+-	$(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `glib-config --libs` -lpthread
++	$(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LDFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread
+ 
+ localcishit.o : localcishit.c
+-	$(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
++	$(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $?
+ 
+ promoterwise.o : promoterwise.c  
+-	$(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
++	$(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $?
+ 
+ promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o
+-	$(CC) -g -o promoterwise promoterwise.o localdba.o  localcishit.o localcispara.o dbadisplay.o  motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o  pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `glib-config --libs` -lpthread
++	$(CC) -g -o promoterwise promoterwise.o localdba.o  localcishit.o localcispara.o dbadisplay.o  motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o  pairwiseshortdna.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread
+ 
+ test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o
+-	$(CC) -o test_deng test_deng.o  localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `glib-config --libs` -lpthread
++	$(CC) -o test_deng test_deng.o  localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread
+ 
+ promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o
+-	$(CC) -o promotercluster promotercluster.o  localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `glib-config --libs` -lpthread
++	$(CC) -o promotercluster promotercluster.o  localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread
+ 
+ dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o 
+-	$(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o  seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  -lpthread
++	$(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o  seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  -lpthread
+ 
+ pswdb : pswdb.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o 
+-	$(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ efpswdb : pswdb.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o 
+-	$(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  -lefence $(EXTRALIBS)
++	$(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  -lefence $(EXTRALIBS)
+ 
+ dba : dbac.o dba.o slimdba.o bigdba.o dbadisplay.o
+-	$(CC) -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ lba : lba.o largeblockdp.o seqaligndisplay.o 
+-	$(CC) -o lba lba.o largeblockdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -o lba lba.o largeblockdp.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ 
+ fastdba : fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o
+-	$(CC) -o fastdba fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -o fastdba fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ evopairwise : evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o 
+-	$(CC) -o evopairwise evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o  wise2xhmmer2.o seqaligndisplay.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -o evopairwise evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o  wise2xhmmer2.o seqaligndisplay.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ test_threestatehsp : test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o threestatehsp.o 
+-	$(CC) -o test_threestatehsp test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o  seqaligndisplay.o threestatehsp.o  wise2xhmmer2.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -o test_threestatehsp test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o  seqaligndisplay.o threestatehsp.o  wise2xhmmer2.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ makerandomdb : makerandomdb.o 
+-	$(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -o makerandomdb makerandomdb.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ genewise : genewise.o $(NEWG) 
+-	$(CC) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ cdnawise : cdnawise.o $(NEWG) cdnawise10.o 
+-	$(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ fivestar : fivestar.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o
+-	$(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o  threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o  threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ 
+ fivestarsearch : fivestarsearch.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o
+-	$(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o  threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o  threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ fivestarscan : fivestarscan.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o
+-	$(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o  threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o  threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ 
+ editdist : editdist.o editdistdp.o standardout.o seqaligndisplay.o 
+-	$(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase 
++	$(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase 
+ 
+ 
+ efgw   : genewise.o $(NEWG) 
+-	$(CC) -g -o genewise genewise.o  $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) -lefence
++	$(CC) -g -o genewise genewise.o  $(NEWG)  $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) -lefence
+ 
+ 
+ genewisedb : genewisedb.o $(NEWG) 
+-	$(CC) -g -o genewisedb genewisedb.o  $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) 
++	$(CC) -g -o genewisedb genewisedb.o  $(NEWG)  $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) 
+ 
+ estwisedb : estwisedb.o $(NEWG) 
+-	$(CC) -g -o estwisedb estwisedb.o $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -g -o estwisedb estwisedb.o $(NEWG)  $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ edb : estwisedb.o $(NEWG) 
+-	$(CC) -g -o estwisedb estwisedb.o $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) -lefence
++	$(CC) -g -o estwisedb estwisedb.o $(NEWG)  $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) -lefence
+ 
+ estwise : estwise.o $(NEWG) 
+-	$(CC) -g -o estwise estwise.o  $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -g -o estwise estwise.o  $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ 
+ amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o 
+-	$(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ genomewise : genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneutil.o geneoutput.o
+-	$(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ sywise : sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o geneutil.o standardout.o
+-	$(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o  standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o  standardout.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ alignwise : alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o
+-	$(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ test_splice : test_splice.o  aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o
+-	$(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o
+-	$(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ pseudowise : pseudowise.o pseudowise7.o $(NEWG) 
+-	$(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o
+-	$(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ 
+ HMMER_LIBS = ../HMMer2/
+@@ -345,11 +345,11 @@
+ CC = cc
+ #CFLAGS = -c -O2  -pg -I../base/ -I../dynlibsrc/
+ #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE  -DUNIX  -I../base/ -I../dynlibsrc/ -I.
+-CFLAGS = -c -g3 -O2  -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags`
+-#CFLAGS = -c  -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags`
+-#LFLAGS =  -L../base/ -L../dynlibsrc/ -L../HMMer2/  
++CFLAGS += -c -g3  -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0`
++#CFLAGS += -c  -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0`
++#LDFLAGS =  -L../base/ -L../dynlibsrc/ -L../HMMer2/  
+ 
+-LFLAGS =  -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs`
++LDFLAGS +=  -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config --libs glib-2.0`
+ AR_OPTIONS = ru
+ 
+ RANLIB_NEEDED = 0
+@@ -360,7 +360,7 @@
+ 
+ 
+ #test : test.o libwisedb.a 
+-#	$(CC) -o test  test.o libwisedb.a  -lprob -ldyn  -lwisebase $(LFLAGS)
++#	$(CC) -o test  test.o libwisedb.a  -lprob -ldyn  -lwisebase $(LDFLAGS)
+ 
+ 
+ #
+--- a/src/dnaindex/makefile
++++ b/src/dnaindex/makefile
+@@ -27,53 +27,53 @@
+ 
+ 
+ kwise : kwise.o $(ASSEMBLY_OBJ)
+-	$(CC) -o kwise kwise.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
++	$(CC) -o kwise kwise.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0`
+ 
+ arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ) 
+-	$(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
++	$(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0`
+ 
+ 
+ findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ)
+-	$(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
++	$(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0`
+ 
+ make_shotgun : make_shotgun.o shotgun.o
+-	$(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS)
++	$(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LDFLAGS)
+ 
+ test_dnanumber : test_dnanumber.o dnanumber.o
+-	$(CC) -o test_dnanumber test_dnanumber.o dnanumber.o -ldyna -lwisebase $(LFLAGS)
++	$(CC) -o test_dnanumber test_dnanumber.o dnanumber.o -ldyna -lwisebase $(LDFLAGS)
+ 
+ test_linkindex : test_linkindex.o linkindex.o dnanumber.o
+-	$(CC) -o test_linkindex test_linkindex.o linkindex.o dnanumber.o -ldyna -lwisebase $(LFLAGS)
++	$(CC) -o test_linkindex test_linkindex.o linkindex.o dnanumber.o -ldyna -lwisebase $(LDFLAGS)
+ 
+ test_forwardindex : test_forwardindex.o forwardindex.o 
+-	$(CC) -o test_forwardindex test_forwardindex.o forwardindex.o -ldyna -lwisebase $(LFLAGS)
++	$(CC) -o test_forwardindex test_forwardindex.o forwardindex.o -ldyna -lwisebase $(LDFLAGS)
+ 
+ test_euler : test_euler.o eulerindex.o singleseqspace.o
+-	$(CC) -o test_euler test_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS)
++	$(CC) -o test_euler test_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS)
+ 
+ test_kmer : test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o  kmer_assembly_untangler.o kmer_assembly_contig.o kmer_assembly_error.o assembly.o 
+-	$(CC) -o test_kmer  test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o  largeseqreader.o kmer_assembly_untangler.o   kmer_assembly_error.o kmer_assembly_contig.o assembly.o  -ldyna -lwisebase $(LFLAGS)
++	$(CC) -o test_kmer  test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o  largeseqreader.o kmer_assembly_untangler.o   kmer_assembly_error.o kmer_assembly_contig.o assembly.o  -ldyna -lwisebase $(LDFLAGS)
+ 
+ kmer_stat : kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o 
+-	$(CC) -o kmer_stat kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o  largeseqreader.o -ldyna -lwisebase $(LFLAGS)
++	$(CC) -o kmer_stat kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o  largeseqreader.o -ldyna -lwisebase $(LDFLAGS)
+ 
+ test_compara : test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o
+-	$(CC) -o test_compara test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LFLAGS)
++	$(CC) -o test_compara test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LDFLAGS)
+ 
+ bigseqwise : bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o
+-	$(CC) -o bigseqwise bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LFLAGS)
++	$(CC) -o bigseqwise bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LDFLAGS)
+ 
+ 
+ 
+ 
+ show_euler : show_euler.o eulerindex.o singleseqspace.o
+-	$(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS)
++	$(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS)
+ 
+ CC = cc
+-CFLAGS = -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags`
++CFLAGS += $(CPPFLAGS) -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0`
+ 
+ 
+-LFLAGS =  -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm
++LDFLAGS +=  -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm
+ 
+ 
+ .c.o :
+--- a/src/dnaindex/assembly/makefile
++++ b/src/dnaindex/assembly/makefile
+@@ -3,33 +3,33 @@
+ .SUFFIXES :  .dy
+ 
+ test_basegraph : test_basegraph.o basegraph.o
+-	$(CC) -o test_basegraph test_basegraph.o basegraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o $(LFLAGS) -ldyna -lwisebase
++	$(CC) -o test_basegraph test_basegraph.o basegraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o $(LDFLAGS) -ldyna -lwisebase
+ 
+ test_assemblygraph : test_assemblygraph.o assemblygraph.o assemblystats.o basegraph.o
+-	$(CC) -o test_assemblygraph test_assemblygraph.o  assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase
++	$(CC) -o test_assemblygraph test_assemblygraph.o  assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase
+ 
+ 
+ test_graphtangle : test_graphtangle.o assemblygraph.o assemblystats.o basegraph.o graphtangle.o assemblypath.o 
+-	$(CC) -o test_graphtangle test_graphtangle.o  assemblystats.o basegraph.o assemblygraph.o graphtangle.o assemblypath.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../kmer_hash.o $(LFLAGS) -ldyna -lwisebase
++	$(CC) -o test_graphtangle test_graphtangle.o  assemblystats.o basegraph.o assemblygraph.o graphtangle.o assemblypath.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../kmer_hash.o $(LDFLAGS) -ldyna -lwisebase
+ 
+ 
+ pathwise : pathwise.o supertangle.o assemblygraph.o assemblystats.o basegraph.o graphtangle.o assemblypath.o grapherror.o graphmanager.o depthmanager.o 
+-	$(CC) -o pathwise pathwise.o  supertangle.o depthmanager.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o graphtangle.o assemblypath.o grapherror.o graphmanager.o  ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../assembly_sanger_project.o $(LFLAGS) -ldyna -lwisebase
++	$(CC) -o pathwise pathwise.o  supertangle.o depthmanager.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o graphtangle.o assemblypath.o grapherror.o graphmanager.o  ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../assembly_sanger_project.o $(LDFLAGS) -ldyna -lwisebase
+ 
+ 
+ badkmer : badkmer.o assemblygraph.o assemblystats.o basegraph.o
+-	$(CC) -o badkmer badkmer.o  assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase
++	$(CC) -o badkmer badkmer.o  assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase
+ 
+ arraymatcher : arraymatcher.o assemblygraph.o assemblystats.o basegraph.o
+-	$(CC) -o arraymatcher arraymatcher.o  assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase
++	$(CC) -o arraymatcher arraymatcher.o  assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase
+ 
+ 
+ 
+ CC = cc
+-CFLAGS = -Wall -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags`
++CFLAGS += $(CPPFLAGS) -Wall -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config --cflags glib-2.0`
+ 
+ 
+-LFLAGS =  -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm
++LDFLAGS +=  -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm
+ 
+ 
+ .c.o :
+--- a/src/dynlibsrc/makefile
++++ b/src/dynlibsrc/makefile
+@@ -84,11 +84,11 @@
+ CC = cc
+ INCFLAGS = -I../base/
+ #CFLAGS = -Wall -g -pedantic -c  -DUNIX -I../base/
+-CFLAGS =  -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -O2 -c  -DUNIX -I../base/ `glib-config --cflags`
+-#CFLAGS =  -Wall -g3 -pg -DPTHREAD -O2  -c  -DUNIX -I../base/ `glib-config --cflags`
+-#CFLAGS =   -O2 -c -pthread  -DUNIX  -I../base/ `glib-config --cflags`
++CFLAGS += $(CPPFLAGS) -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -c  -DUNIX -I../base/ `pkg-config --cflags glib-2.0`
++#CFLAGS +=  -Wall -g3 -pg -DPTHREAD  -c  -DUNIX -I../base/ `pkg-config --cflags glib-2.0`
++#CFLAGS +=   -c -pthread  -DUNIX  -I../base/ `pkg-config --cflags glib-2.0`
+ #CFLAGS =   -O -c -DUNIX -DNOERROR -I../base/
+-LFLAGS =  -g -L../base/ -lm 
++LDFLAGS +=  -g -L../base/ -lm 
+ AR_OPTIONS = ru
+ 
+ RANLIB_NEEDED = 0
+@@ -133,47 +133,47 @@
+ #
+ 
+ test_genomic : genomic.o test_genomic.o sequence.o codon.o
+-	$(CC) -o test_genomic test_genomic.o genomic.o sequence.o codon.o ../base/libwisebase.a -lm
++	$(CC) $(LDFLAGS)-o test_genomic test_genomic.o genomic.o sequence.o codon.o ../base/libwisebase.a -lm
+ 
+ test_tree : tree.o test_tree.o
+-	$(CC) -o test_tree test_tree.o tree.o libdyna.a ../base/libwisebase.a -lm
++	$(CC) $(LDFLAGS) -o test_tree test_tree.o tree.o libdyna.a ../base/libwisebase.a -lm
+ 
+ test_intallocator : intallocator.o test_intallocator.o 
+-	$(CC) -o test_intallocator intallocator.o test_intallocator.o  ../base/libwisebase.a -lm
++	$(CC) $(LDFLAGS) -o test_intallocator intallocator.o test_intallocator.o  ../base/libwisebase.a -lm
+ 
+ test_psi : test_psi.o proteinstreamedindex.o 
+-	$(CC) -o test_psi test_psi.o  proteinstreamedindex.o ./libdyna.a ../base/libwisebase.a -lm
++	$(CC) $(LDFLAGS) -o test_psi test_psi.o  proteinstreamedindex.o ./libdyna.a ../base/libwisebase.a -lm
+ 
+ test_shadowindex : test_shadowindex.o shadowseqindex.o shadowseq.o libdyna.a
+-	$(CC) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm
++	$(CC) $(LDFLAGS) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm
+ 
+ test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a
+-	$(CC) -g -o test_seqhash `glib-config --libs` test_seqhash.o subseqhash.o hsp.o  hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm  
++	$(CC) $(LDFLAGS) -g -o test_seqhash `pkg-config --libs glib-2.0` test_seqhash.o subseqhash.o hsp.o  hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm  
+ 
+ test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o 
+-	$(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o  ../base/libwisebase.a -lm `glib-config --libs`
++	$(CC) $(LDFLAGS) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o  ../base/libwisebase.a -lm `pkg-config --libs glib-2.0`
+ 
+ test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o 
+-	$(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o  ../base/libwisebase.a -lm `glib-config --libs`
++	$(CC) $(LDFLAGS) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o  ../base/libwisebase.a -lm `pkg-config --libs glib-2.0`
+ 
+ 
+ testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o
+-	$(CC) -o testgendb probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm
++	$(CC) $(LDFLAGS) -o testgendb probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm
+ 
+ testseqalign : seqalign.o testseqalign.o sequence.o codon.o
+-	$(CC) -o testseqalign testseqalign.o seqalign.o sequence.o codon.o ../base/libwisebase.a -lm
++	$(CC) $(LDFLAGS) -o testseqalign testseqalign.o seqalign.o sequence.o codon.o ../base/libwisebase.a -lm
+ 
+ testanc : libdyna.a
+-	$(CC) -o testanc ../models/testanc.o ../models/proteinsw.o ../models/abc.o ../models/pba.o ../models/sw_wrap.o libdyna.a ../base/libwisebase.a -lm
++	$(CC) $(LDFLAGS) -o testanc ../models/testanc.o ../models/proteinsw.o ../models/abc.o ../models/pba.o ../models/sw_wrap.o libdyna.a ../base/libwisebase.a -lm
+ 
+ testdb : testdb.o sequencedb.o sequence.o codon.o probability.o
+-	$(CC) -o testdb testdb.o sequencedb.o sequence.o codon.o probability.o ../base/libwisebase.a -lm
++	$(CC) $(LDFLAGS) -o testdb testdb.o sequencedb.o sequence.o codon.o probability.o ../base/libwisebase.a -lm
+ 
+ testpdb : testpdb.o protein.o proteindb.o complexevalset.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o histogram.o 
+-	$(CC) -o testpdb testpdb.o protein.o proteindb.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o complexevalset.o histogram.o ../base/libwisebase.a -lm
++	$(CC) $(LDFLAGS) -o testpdb testpdb.o protein.o proteindb.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o complexevalset.o histogram.o ../base/libwisebase.a -lm
+ 
+ testpb : testpairbase.o pairbase.o pairbaseseq.o sequence.o seqalign.o codon.o probability.o complexsequence.o complexevalset.o
+-	$(CC) -g -o testpb testpairbase.o pairbase.o pairbaseseq.o sequence.o codon.o seqalign.o probability.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm
++	$(CC) $(LDFLAGS) -g -o testpb testpairbase.o pairbase.o pairbaseseq.o sequence.o codon.o seqalign.o probability.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm
+ 
+ .c.o :
+ 	$(CC) $(CFLAGS) $(INCFLAGS) $?
+--- a/src/network/makefile
++++ b/src/network/makefile
+@@ -3,8 +3,8 @@
+ 
+ CC = cc
+ INCFLAGS = -I../base/  -I../socket -I../dynlibsrc -I../dnaindex
+-CFLAGS =    -O2  -c -pthread  -DUNIX  -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `glib-config --cflags`
+-LFLAGS =  -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `glib-config --libs`
++CFLAGS += $(CPPFLAGS)  -c -pthread  -DUNIX  -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config --cflags glib-2.0`
++LDFLAGS +=  -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0`
+ AR_OPTIONS = ru
+ 
+ RANLIB_NEEDED = 0
+@@ -13,7 +13,7 @@
+ 
+ 
+ scanwise_server : wise_proteinindex_server.o net_hspscan.o ../dynlibsrc/libdyna.a ../dynlibsrc/libdyna_glib.a ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o 
+-	$(CC) -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o  -ldyna_glib -ldyna -lwisesocket -lwisebase $(LFLAGS) -lpthread 
++	$(CC) -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o  -ldyna_glib -ldyna -lwisesocket -lwisebase $(LDFLAGS) -lpthread 
+ 
+ 
+ .c.o :
+--- a/src/other_programs/makefile
++++ b/src/other_programs/makefile
+@@ -3,8 +3,8 @@
+ .SUFFIXES :  .dy
+ 
+ CC = cc
+-CFLAGS =   -O2 -g3 -c -pthread  -DUNIX  -I../base/ -I../dynlibsrc `glib-config --cflags`
+-LFLAGS =  -g -L../base/ -L../dynlibsrc  -lm `glib-config --libs`
++CFLAGS += $(CPPFLAGS) -g3 -c -pthread  -DUNIX  -I../base/ -I../dynlibsrc `pkg-config --cflags glib-2.0`
++LDFLAGS += -g -L../base/ -L../dynlibsrc  -lm `pkg-config --libs glib-2.0`
+ AR_OPTIONS = ru
+ 
+ RANLIB_NEEDED = 0
+--- a/src/base/makefile
++++ b/src/base/makefile
+@@ -19,9 +19,9 @@
+ 
+ 
+ 
+-#CFLAGS = -c  -g -DUNIX -DWISE_MEMORY_WATCH
+-CFLAGS = -c  -O2 -DUNIX -pthread
+-LFLAGS =  -g  -lm 
++#CFLAGS += -c  -g -DUNIX -DWISE_MEMORY_WATCH
++CFLAGS += $(CPPFLAGS) -c -DUNIX -pthread
++LDFLAGS += -g -lm 
+ DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D
+ AR_OPTIONS = ru
+ 
+--- a/src/HMMer2/Makefile
++++ b/src/HMMer2/Makefile
+@@ -13,7 +13,7 @@
+ ## your compiler and compiler flags
+ #
+ CC     = cc
+-CFLAGS = -g 
++CFLAGS += $(CPPFLAGS) -g 
+ 
+ ## machine specific definitions
+ #
+@@ -75,25 +75,25 @@
+ all: 	$(PROGS)
+ 
+ hmmalign: $(OBJ) hmmalign.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o $@ hmmalign.o $(OBJ) $(LIBS) 
++	$(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmalign.o $(OBJ) $(LIBS) 
+ 
+ hmmbuild: $(OBJ) hmmbuild.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o $@ hmmbuild.o $(OBJ) $(LIBS) 
++	$(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmbuild.o $(OBJ) $(LIBS) 
+ 
+ hmmcalibrate: $(OBJ) hmmcalibrate.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o $@ hmmcalibrate.o $(OBJ) $(LIBS) 
++	$(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmcalibrate.o $(OBJ) $(LIBS) 
+ 
+ hmmconvert: $(OBJ) hmmconvert.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o $@ hmmconvert.o $(OBJ) $(LIBS) 
++	$(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmconvert.o $(OBJ) $(LIBS) 
+ 
+ hmmemit: $(OBJ) hmmemit.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o $@ hmmemit.o $(OBJ) $(LIBS) 
++	$(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmemit.o $(OBJ) $(LIBS) 
+ 
+ hmmpfam: $(OBJ) hmmpfam.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o $@ hmmpfam.o $(OBJ) $(LIBS) 
++	$(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmpfam.o $(OBJ) $(LIBS) 
+ 
+ hmmsearch: $(OBJ) hmmsearch.o
+-	$(CC) $(CFLAGS) $(MDEFS) -o $@ hmmsearch.o $(OBJ) $(LIBS) 
++	$(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmsearch.o $(OBJ) $(LIBS) 
+ 
+ #######
+ ## Target used in making Shiva test suite
diff --git a/wise2-isnumber.patch b/wise2-isnumber.patch
new file mode 100755
index 0000000..c678582
--- /dev/null
+++ b/wise2-isnumber.patch
@@ -0,0 +1,18 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 02_isnumber.dpatch by Philipp Benner <mail@philipp-benner.de>
+##
+## DP: Replace isnumber() (which does not exist on linux) by isdigit().
+
+@DPATCH@
+diff -urNad wise-2.4.0~/src/models/phasemodel.c wise-2.4.0/src/models/phasemodel.c
+--- wise-2.4.0~/src/models/phasemodel.c	2007-07-01 22:44:39.000000000 +0200
++++ wise-2.4.0/src/models/phasemodel.c	2007-07-16 00:24:16.000000000 +0200
+@@ -20,7 +20,7 @@
+     if( line[0] == '#' ) {
+       continue;
+     }
+-    if( !isnumber(line[0]) ) {
++    if( !isdigit(line[0]) ) {
+       warn("Bad looking line in intron file, %s",line);
+       continue;
+     }
diff --git a/wise2-ld--as-needed.patch b/wise2-ld--as-needed.patch
new file mode 100644
index 0000000..b8db369
--- /dev/null
+++ b/wise2-ld--as-needed.patch
@@ -0,0 +1,54 @@
+Description: Fix FTBFS with ld --as-needed.
+Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/wise/+bug/832935
+
+diff --git a/src/models/makefile b/src/models/makefile
+index 1766fee..e4634b5 100644
+--- a/src/models/makefile
++++ b/src/models/makefile
+@@ -215,7 +215,7 @@ scanwisep_wiseserver.o : scanwisep.c
+ 	$(CC)  $(CFLAGS) $(INCFLAGS)  -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c 
+ 
+ scanwise : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
+-	$(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   ../network/net_hspscan.o ../network/client_multihspscan.o  $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase  $(EXTRALIBS) -lpthread 
++	$(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   ../network/net_hspscan.o ../network/client_multihspscan.o  $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase  $(EXTRALIBS) -lpthread $(LDFLAGS)
+ 
+ scanwisep_compress.o : scanwisep.c
+ 	$(CC)  $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c 
+@@ -275,7 +275,7 @@ makerandomdb : makerandomdb.o
+ 	$(CC) -o makerandomdb makerandomdb.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ genewise : genewise.o $(NEWG) 
+-	$(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) $(LDFLAGS)
+ 
+ cdnawise : cdnawise.o $(NEWG) cdnawise10.o 
+ 	$(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+@@ -300,16 +300,16 @@ efgw   : genewise.o $(NEWG)
+ 
+ 
+ genewisedb : genewisedb.o $(NEWG) 
+-	$(CC) -g -o genewisedb genewisedb.o  $(NEWG)  $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) 
++	$(CC) -g -o genewisedb genewisedb.o  $(NEWG)  $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)  $(LDFLAGS)
+ 
+ estwisedb : estwisedb.o $(NEWG) 
+-	$(CC) -g -o estwisedb estwisedb.o $(NEWG)  $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -g -o estwisedb estwisedb.o $(NEWG)  $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) $(LDFLAGS)
+ 
+ edb : estwisedb.o $(NEWG) 
+ 	$(CC) -g -o estwisedb estwisedb.o $(NEWG)  $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) -lefence
+ 
+ estwise : estwise.o $(NEWG) 
+-	$(CC) -g -o estwise estwise.o  $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -g -o estwise estwise.o  $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) $(LDFLAGS)
+ 
+ 
+ amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o 
+@@ -331,7 +331,7 @@ statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o
+ 	$(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
+ 
+ pseudowise : pseudowise.o pseudowise7.o $(NEWG) 
+-	$(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
++	$(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) $(LDFLAGS)
+ 
+ clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o
+ 	$(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
diff --git a/wise2-mayhem.patch b/wise2-mayhem.patch
new file mode 100644
index 0000000..f4b7724
--- /dev/null
+++ b/wise2-mayhem.patch
@@ -0,0 +1,99 @@
+--- a/src/models/dbac.c
++++ b/src/models/dbac.c
+@@ -535,8 +535,12 @@
+    *  
+    */  
+   
+-  one = read_fasta_file_Sequence(*argv++);  
+-  two = read_fasta_file_Sequence(*argv++);  
++  if( (one = read_fasta_file_Sequence(*argv++)) == NULL ) {
++    fatal("Unable to read the sequence in file");
++  }
++  if( (two = read_fasta_file_Sequence(*argv++)) == NULL ) {
++    fatal("Unable to read the sequence in file");
++  }
+   
+   uppercase_Sequence(one);  
+   uppercase_Sequence(two);  
+--- a/src/models/estwise.c
++++ b/src/models/estwise.c
+@@ -313,7 +313,7 @@
+     }
+   }
+ 
+-  if( reverse == TRUE ) {
++  if( cdna && reverse == TRUE ) {
+     if( tstart > tend ) {
+       warn("You have already reversed the DNA by using %d - %d truncation. Re-reversing",tstart,tend);
+     }
+@@ -323,7 +323,7 @@
+     cdna = cdna_temp;
+   }
+ 
+-  if( target_abs == TRUE ) {
++  if( cdna && target_abs == TRUE ) {
+     cdna->baseseq->offset = 1;
+     cdna->baseseq->end  = strlen(cdna->baseseq->seq);
+   }
+@@ -472,8 +472,11 @@
+   }
+ 
+   cp = flat_cDNAParser(indel_error);
+-  cm = flat_CodonMapper(ct);
+-  sprinkle_errors_over_CodonMapper(cm,subs_error);
++
++  if( ct ) {
++    cm = flat_CodonMapper(ct);
++    sprinkle_errors_over_CodonMapper(cm,subs_error);
++  }
+ 
+   return ret;
+ 
+--- a/src/models/genewise.c
++++ b/src/models/genewise.c
+@@ -550,8 +550,10 @@
+       ret =  FALSE;
+     }
+ 
+-    gen->baseseq->offset = 1;
+-    gen->baseseq->end  = strlen(gen->baseseq->seq);
++    if ( gen ) {
++      gen->baseseq->offset = 1;
++      gen->baseseq->end  = strlen(gen->baseseq->seq);
++    }
+   }
+ 
+   if( alg_str != NULL ) {
+--- a/src/models/estwisedb.c
++++ b/src/models/estwisedb.c
+@@ -688,8 +688,11 @@
+ 
+ 
+   cps = flat_cDNAParser(indel_error);
+-  cm = flat_CodonMapper(ct);
+-  sprinkle_errors_over_CodonMapper(cm,subs_error);
++
++  if( ct ) {
++    cm = flat_CodonMapper(ct);
++    sprinkle_errors_over_CodonMapper(cm,subs_error);
++  }
+ 
+   return ret;
+ 
+--- a/src/models/promoterwise.c
++++ b/src/models/promoterwise.c
+@@ -147,8 +147,12 @@
+ 
+   lchs = standard_LocalCisHitScore(NMaskType_VARIABLE);
+ 
+-  query = read_fasta_file_Sequence(argv[1]);
+-  target = read_fasta_file_Sequence(argv[2]);
++  if( (query = read_fasta_file_Sequence(argv[1])) == NULL ) {
++    fatal("Unable to read the sequence in query file");
++  }
++  if( (target = read_fasta_file_Sequence(argv[2])) == NULL ) {
++    fatal("Unable to read the sequence in target file");
++  }
+ 
+   for(i=0;i<query->len;i++) {
+     query->seq[i] = toupper(query->seq[i]);
diff --git a/wise2.spec b/wise2.spec
new file mode 100644
index 0000000..846e652
--- /dev/null
+++ b/wise2.spec
@@ -0,0 +1,137 @@
+%define _lto_cflags %{nil}
+
+Name:           wise2
+Version:        2.4.1
+Release:        %autorelease
+Summary:        Tools for comparison of bio-polymers
+
+## Everything is licensed under a BSD-style license except for
+## the HMMer2 libraries and models directory which are GPLv2+
+## see LICENSE files for details. 
+License:        BSD-3-Clause AND GPL-2.0-or-later
+URL:            http://www.ebi.ac.uk/~birney/%{name}/
+Source0:        http://www.ebi.ac.uk/~birney/%{name}/wise%{version}.tar.gz
+
+## Patches from Debian package. Thanks to Philipp Benner
+Patch0:         %{name}-build.patch
+Patch1:         %{name}-isnumber.patch
+Patch2:         %{name}-glib2.patch
+Patch3:         %{name}-getline.patch
+Patch4:         %{name}-ld--as-needed.patch
+Patch5:         %{name}-mayhem.patch
+Patch6:         %{name}-c99.patch
+
+BuildRequires:  make
+BuildRequires:  glib2-devel
+BuildRequires:  gcc
+BuildRequires:  perl
+BuildRequires:  strace
+
+%description
+Wise2 is a package focused on comparisons of bio-polymers, commonly DNA
+sequence and protein sequence.  A strength of Wise2 is the
+comparison of DNA sequence at the level of its protein
+translation. This comparison allows the simultaneous prediction of
+gene structure with homology based alignment.
+
+
+%package doc
+Summary:    Wise2 documentation
+BuildArch:  noarch
+
+%description doc
+Wise2, Wise2api and Dynamite documentation files.
+
+
+%package examples
+Summary:    Wise2 examples
+Requires:   %{name}%{?_isa} = %{version}-%{release}
+
+%description examples
+Here are some examples that you might want to try out.  The
+Wise2 executables of course should be installed before.
+
+%prep
+%autosetup -p1 -n wise%{version}
+
+# Remove spurious-executable-perm
+chmod a-x src/external/mott/mott_api.c
+chmod a-x src/external/mott/mott_api.h
+chmod a-x src/external/mott/gaplib.c
+chmod a-x src/external/mott/gapstat.h
+
+## fix interpreter in examples
+sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' docs/gettex.pl
+## fix perms 
+chmod -x test_data/rrm.HMM
+
+## pull out licenses
+for i in base dynlibsrc dyc
+do
+    cp src/$i/LICENSE LICENSE.$i
+done
+cp src/models/GNULICENSE LICENSE.GPL
+
+%build
+## removed "{?_smp_mflags}", does not support parallel build
+export LDFLAGS="%{__global_ldflags}"
+make -C src CC=gcc \
+ CFLAGS=" -c %{build_cflags} -pthread -D_GNU_SOURCE %(pkg-config --cflags glib-2.0) -D_POSIX_C_SOURCE=200112L" all
+
+%install
+pushd src/bin
+mkdir -p $RPM_BUILD_ROOT%{_bindir}
+for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb
+do
+    install -pm 755 $i $RPM_BUILD_ROOT%{_bindir} 
+done
+popd
+
+# install architecture-independent data and config files
+mkdir -p $RPM_BUILD_ROOT%{_datadir}/wise2
+pushd wisecfg
+install -pm 644 * $RPM_BUILD_ROOT%{_datadir}/wise2
+popd
+
+# install architecture-independent files to run example tests
+mkdir -p $RPM_BUILD_ROOT%{_datadir}/wise2/examples
+pushd test_data
+install -pm 644 * $RPM_BUILD_ROOT%{_datadir}/wise2/examples
+popd
+
+# install scripts to automatically set the WISECONFIGDIR environment variable
+mkdir -p $RPM_BUILD_ROOT%{_sysconfdir}/profile.d
+echo "export WISECONFIGDIR=%{_datadir}/wise2/" > $RPM_BUILD_ROOT%{_sysconfdir}/profile.d/wise2.sh
+echo "setenv WISECONFIGDIR %{_datadir}/wise2/" > $RPM_BUILD_ROOT%{_sysconfdir}/profile.d/wise2.csh
+
+%check
+export WISECONFIGDIR=$PWD/wisecfg
+make -C src test
+
+%files
+%doc README
+%license LICENSE LICENSE.base LICENSE.dynlibsrc LICENSE.dyc LICENSE.GPL
+%{_bindir}/genewisedb
+%{_bindir}/estwisedb
+%{_bindir}/genewise
+%{_bindir}/estwise
+%{_bindir}/scanwise
+%{_bindir}/promoterwise
+%{_bindir}/pswdb
+%{_bindir}/dba
+%{_bindir}/psw
+%{_bindir}/scanwise_server
+%{_bindir}/dnal
+%{_datadir}/wise2/
+%config(noreplace) %{_sysconfdir}/profile.d/*
+
+%files doc
+%license LICENSE
+%doc docs
+
+%files examples
+%doc test_data/README
+%{_datadir}/wise2/examples/
+
+%changelog
+%autochangelog