sci-biology/wise: drop package

present in ::gentoo

Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Aisha Tammy <gentoo@aisha.cc>

15 files changed, 0 insertions, 1433 deletions

diff --git a/sci-biology/wise/Manifest b/sci-biology/wise/Manifest
deleted file mode 100644
index e0adc951a..000000000
--- a/sci-biology/wise/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST wise2.4.1.tar.gz 3193910 BLAKE2B 45e33b1a4c8ffcb73ad1d2c50be4baeb3a0958a94c2c057db163b33ae33edd5e7159d7fd818725fd13c9ccb2440f61a747e2535b68e0eb25bc09c907d0b4da4d SHA512 aca14bf4fb1ab6070847cfd857d5b3c518695a020fc85b67e1f34b69b5cdb7b28b68c5779eca9af84679d56ca98f7caf1f8c2596ff02b5dd304cd9235aeb2f61
diff --git a/sci-biology/wise/files/01_welcome-csh.patch b/sci-biology/wise/files/01_welcome-csh.patch
deleted file mode 100644
index 3a9057e06..000000000
--- a/sci-biology/wise/files/01_welcome-csh.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-Author: Philipp Benner <mail@philipp-benner.de>
-Description: Avoid dependency from csh
-
---- wise-2.4.1.orig/src/makefile
-+++ wise-2.4.1/src/makefile
-@@ -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 )
---- wise-2.4.1.orig/src/welcome.csh
-+++ wise-2.4.1/src/welcome.csh
-@@ -1,4 +1,4 @@
--#!/bin/tcsh -f
-+#!/bin/sh
- 
- echo ""
- echo "Welcome to Wise2.4"
diff --git a/sci-biology/wise/files/02_isnumber.patch b/sci-biology/wise/files/02_isnumber.patch
deleted file mode 100644
index a6ae90856..000000000
--- a/sci-biology/wise/files/02_isnumber.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Author: Philipp Benner <mail@philipp-benner.de>
-Description: Replace isnumber() (which does not exist on linux) by isdigit().
-
---- wise-2.4.1.orig/src/models/phasemodel.c
-+++ wise-2.4.1/src/models/phasemodel.c
-@@ -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/sci-biology/wise/files/03_doc-nodycache.patch b/sci-biology/wise/files/03_doc-nodycache.patch
deleted file mode 100644
index 6fe7b1893..000000000
--- a/sci-biology/wise/files/03_doc-nodycache.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-Author Philipp Benner <mail@philipp-benner.de>
-Description: Documentation bugfix.
-
---- wise-2.4.1.orig/docs/wise2.tex
-+++ wise-2.4.1/docs/wise2.tex
-@@ -1617,7 +1617,8 @@
- \item[-hithelp]   more detailed help on hitlist formats
- \item[-dymem]      memory style [default/linear/explicit]
- \item[-kbyte]       memory amount to use [4000]
--\item[-\[no\]dycache] implicitly cache dy matrix usage (default yes)
-+\item[-dycache] implicitly cache dy matrix usage (default)
-+\item[-nodycache] do not implicitly cache dy matrix usage
- \item[-dydebug]     drop into dynamite dp matrix debugger
- \item[-paldebug]    print PackAln after debugger run if used
- \item[-help]      show help options
diff --git a/sci-biology/wise/files/04_wise2-pdflatex-update.patch b/sci-biology/wise/files/04_wise2-pdflatex-update.patch
deleted file mode 100644
index bbaf2861d..000000000
--- a/sci-biology/wise/files/04_wise2-pdflatex-update.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-Author Philipp Benner <mail@philipp-benner.de>
-Description: Make wise2.tex pdflatex compatible.
-
---- wise-2.4.1.orig/docs/wise2.tex
-+++ wise-2.4.1/docs/wise2.tex
-@@ -1,6 +1,7 @@
- 
- \documentclass{article}
--\usepackage{epsfig}
-+%\usepackage{epsfig}
-+\usepackage{graphicx}
- 
- \begin{document}
- \newcommand{\programtext}[1]{{\tt #1}}
-@@ -707,8 +708,9 @@
- \begin{figure}
- \begin{center}
- \leavevmode  
--\epsfxsize 300pt
--\epsfbox{genewise21.eps}
-+%\epsfxsize 300pt
-+%\epsfbox{genewise21.eps}
-+%\includegraphics[scale=0.75]{genewise21.pdf}
- \newline     
- \caption{GeneWise21:93 Algorithm. The dark circles represent states, and the
- arrows between them transitions. Black transitions are standard
-@@ -898,8 +900,9 @@
- \begin{figure}
- \begin{center}
- \leavevmode  
--\epsfxsize 300pt
--\epsfbox{genewise6.eps}
-+%\epsfxsize 300pt
-+%\epsfbox{genewise6.eps}
-+%\includegraphics[scale=0.75]{genewise6.pdf}
- \newline     
- \caption{GeneWise6:23}
- \label{Figure:genewise623}
diff --git a/sci-biology/wise/files/06_getline.patch b/sci-biology/wise/files/06_getline.patch
deleted file mode 100644
index 341cdae82..000000000
--- a/sci-biology/wise/files/06_getline.patch
+++ /dev/null
@@ -1,305 +0,0 @@
-Author: Philipp Benner <philipp@debian.org>
-Last-Update: Sat, 31 Oct 2009 21:25:52 +0000
-Bug-Debian: http://bugs.debian.org/552821
-Description: Fixed conflicting definitions of getline().
-
---- wise-2.4.1.orig/src/HMMer2/sqio.c
-+++ wise-2.4.1/src/HMMer2/sqio.c
-@@ -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/sci-biology/wise/files/07_ld--as-needed.patch b/sci-biology/wise/files/07_ld--as-needed.patch
deleted file mode 100644
index 51ee25437..000000000
--- a/sci-biology/wise/files/07_ld--as-needed.patch
+++ /dev/null
@@ -1,52 +0,0 @@
-Description: Fix FTBFS with ld --as-needed.
-Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/wise/+bug/832935
-
---- wise-2.4.1.orig/src/models/makefile
-+++ wise-2.4.1/src/models/makefile
-@@ -215,7 +215,7 @@
- 	$(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 @@
- 	$(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 @@
- 
- 
- 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 @@
- 	$(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/sci-biology/wise/files/08_mayhem.patch b/sci-biology/wise/files/08_mayhem.patch
deleted file mode 100644
index c54c7c66a..000000000
--- a/sci-biology/wise/files/08_mayhem.patch
+++ /dev/null
@@ -1,103 +0,0 @@
-Author: Philipp Benner <philipp@debian.org>
-Last-Update: Sun, 07 Jul 2013 13:33:01 +0200
-Description: Fix run time errors detected by Mayhem
-
---- wise-2.4.1.orig/src/models/dbac.c
-+++ wise-2.4.1/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);  
---- wise-2.4.1.orig/src/models/estwise.c
-+++ wise-2.4.1/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;
- 
---- wise-2.4.1.orig/src/models/genewise.c
-+++ wise-2.4.1/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 ) {
---- wise-2.4.1.orig/src/models/estwisedb.c
-+++ wise-2.4.1/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;
- 
---- wise-2.4.1.orig/src/models/promoterwise.c
-+++ wise-2.4.1/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/sci-biology/wise/files/09_dnal-add-return-statement.patch b/sci-biology/wise/files/09_dnal-add-return-statement.patch
deleted file mode 100644
index 237e59688..000000000
--- a/sci-biology/wise/files/09_dnal-add-return-statement.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-Author: Dejan Latinovic <Dejan.Latinovic@imgtec.com>
-Last-Update: Mon, 4 Aug 2014 17:10:38 +0000
-Bug-Debian: http://bugs.debian.org/751277
-Desription: Make sure dnal has a valid return value
- This affects a bug reported against python-biopython.
-
---- wise-2.4.1.orig/src/models/dnal.c
-+++ wise-2.4.1/src/models/dnal.c
-@@ -75,6 +75,8 @@
- 
-   if( show_alb == TRUE )
-     dump_ascii_AlnBlock(alb,stdout);
-+
-+  return 0;
- }
- 
- 
diff --git a/sci-biology/wise/files/11_consistent_manual_dates.patch b/sci-biology/wise/files/11_consistent_manual_dates.patch
deleted file mode 100644
index eaea1eec9..000000000
--- a/sci-biology/wise/files/11_consistent_manual_dates.patch
+++ /dev/null
@@ -1,53 +0,0 @@
-Description: Use fixed dates for manuals.
- These make the build reproducible. I have picked the file modificatin dates of
- the corresponding source .tex files.
-Author: Sascha Steinbiss <sascha@steinbiss.name>
---- a/docs/dynamite.tex
-+++ b/docs/dynamite.tex
-@@ -1,4 +1,5 @@
- \documentstyle{article}
-+\pdftrailerid{}
- \begin{document}
- 
- \newcommand{\programtext}[1]{{\tt #1}}
-@@ -10,6 +11,7 @@
- Hinxton, Cambridge CB10 1SA,\\
- England.\\
- Email: birney@sanger.ac.uk}
-+\date{18/6/2001}
- 
- \maketitle
-  
---- a/docs/wise2.tex
-+++ b/docs/wise2.tex
-@@ -1,5 +1,6 @@
- 
- \documentclass{article}
-+\pdftrailerid{}
- %\usepackage{epsfig}
- \usepackage{graphicx}
- 
-@@ -13,6 +14,7 @@
- Hinxton, Cambridge CB10 1SD,\\
- England.\\
- Email: birney@ebi.ac.uk}
-+\date{18/6/2001}
- 
- \maketitle
-  
---- a/docs/wise2api.tex
-+++ b/docs/wise2api.tex
-@@ -1,4 +1,5 @@
- \documentstyle{article}
-+\pdftrailerid{}
- \begin{document}
- 
- \newcommand{\programtext}[1]{{\tt #1}}
-@@ -10,6 +11,7 @@
- Hinxton, Cambridge CB10 1SA,\\
- England.\\
- Email: birney@sanger.ac.uk}
-+\date{18/6/2001}
- 
- \maketitle
-  
diff --git a/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch b/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch
deleted file mode 100644
index 1ec433f19..000000000
--- a/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch
+++ /dev/null
@@ -1,301 +0,0 @@
-diff -ur wise2.2.0.orig/src/HMMer2/sqio.c wise2.2.0/src/HMMer2/sqio.c
---- wise2.2.0.orig/src/HMMer2/sqio.c	2001-06-18 16:59:51.000000000 +0300
-+++ wise2.2.0/src/HMMer2/sqio.c	2009-08-05 22:39:04.000000000 +0300
-@@ -213,7 +213,7 @@
-     }
- }
- 
--/* Function: getline()
-+/* Function: get_line()
-  * 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)
-+get_line(struct ReadSeqVars *V)
- {
-   char *cp;
-   
-@@ -299,7 +299,7 @@
-   V->seqlen = 0;
-   if (addfirst) addseq(V->sbuffer, V);
-   do {
--    getline(V);
-+    get_line(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);
-+    get_line(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);
-+    get_line(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 */
-+  get_line(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);
-+    get_line(V);
- }
- 
- 
-@@ -377,7 +377,7 @@
-   char *nm;
- 				/* position past ';' comments */
-   do {
--    getline(V);
-+    get_line(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);
-+    get_line(V);
- }
- 
- static int 
-@@ -411,7 +411,7 @@
- 	  if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
- 	    SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
- 	}
--      getline(V);
-+      get_line(V);
-     }
- 
-   if (! feof(V->f))
-@@ -420,7 +420,7 @@
-   /* load next line
-    */
-   while ((!feof(V->f)) && (*V->sbuffer != ';')) 
--    getline(V);
-+    get_line(V);
- }
- 
- 
-@@ -438,7 +438,7 @@
-   int   in_definition;
- 
-   while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
--    getline(V);
-+    get_line(V);
- 
-   if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
-     {
-@@ -449,7 +449,7 @@
-   in_definition = FALSE;
-   while (! feof(V->f))
-     {
--      getline(V);
-+      get_line(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);
-+    get_line(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);
-+    get_line(V);
- }
- 
- static int
-@@ -515,7 +515,7 @@
-     Die("bogus GCGdata format? %s", V->sbuffer);
- 
- 				/* second line contains free text description */
--  getline(V);
-+  get_line(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);
-+    get_line(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)) get_line(V);
- 
-   readLoop(0, endPearson, V);
- 
-   while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
--    getline(V);
-+    get_line(V);
- }
- 
- 
-@@ -587,7 +587,7 @@
- 
- 				/* make sure we have first line */
-   while (!feof(V->f) && strncmp(V->sbuffer, "ID  ", 4) != 0)
--    getline(V);
-+    get_line(V);
- 
-   if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
-     {
-@@ -596,7 +596,7 @@
-     }
- 
-   do {
--    getline(V);
-+    get_line(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);
-+    get_line(V);
- }
- 
- 
-@@ -636,7 +636,7 @@
- {
-   char *sptr;
- 
--  getline(V);  /*s == "seqLen seqid string..."*/
-+  get_line(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);
-+    get_line(V);
- }
- 
- static void 
-@@ -669,7 +669,7 @@
- 
-   do {
-     done = feof(V->f);
--    getline(V);
-+    get_line(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) get_line(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);
-+      get_line(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);
-+      get_line(V);
-       if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) 
- 	break;
-       addseq(V->sbuffer, V);
- 				/* structure line */
-       if (dostruc)
- 	{
--	  getline(V);
-+	  get_line(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);
-+    get_line(V);
- }
- 
- 
-@@ -816,7 +816,7 @@
- 
-   /* Load the first line.
-    */
--  getline(dbfp);
-+  get_line(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);
-+  get_line(sqfp);
- }
- 
- 
-@@ -853,7 +853,7 @@
-   if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
-   else {
-     rewind(sqfp->f);
--    getline(sqfp);
-+    get_line(sqfp);
-   }
- }
- 
-@@ -949,7 +949,7 @@
-       do {			/* skip leading comments on GCG file */
- 	gotuw = (strstr(V->sbuffer,"..") != NULL);
- 	if (gotuw) readUWGCG(V);
--	getline(V);
-+	get_line(V);
-       } while (! feof(V->f));
-       break;
- 
diff --git a/sci-biology/wise/files/wise-2.4.1-cflags.patch b/sci-biology/wise/files/wise-2.4.1-cflags.patch
deleted file mode 100644
index 705ada853..000000000
--- a/sci-biology/wise/files/wise-2.4.1-cflags.patch
+++ /dev/null
@@ -1,407 +0,0 @@
---- wise2.4.1/src/makefile.old	2017-01-10 15:22:43.545646202 +0000
-+++ wise2.4.1/src/makefile	2017-01-10 15:23:58.484888011 +0000
-@@ -22,7 +22,7 @@
- # Change the cc line to gcc if you get compiler errors
- # Most likely you have a non ANSI C compiler
- # CC =  /opt/intel_cc_80/bin/icc
--CC = cc
-+CC += gcc
- 
- # These are the CFLAGS to use. These days Wise2 is inherently
- # pthreaded, and everything is compiled with threads. However
-@@ -31,13 +31,13 @@
- 
- 
- # Intel icc flags
--# CFLAGS = -c  -O3 -axWK -ipo `glib-config --cflags`
-+# CFLAGS = -c  -O3 -axWK -ipo `pkg-config glib-2.0 --cflags`
- 
- # alpha flags (-pthread)
--# CFLAGS = -c -O3 -pthread `glib-config --cflags`
-+# CFLAGS = -c -O3 -pthread `pkg-config glib-2.0 --cflags`
- 
- # normal linux/bsd/mac flags
--CFLAGS = -c -O3  `glib-config --cflags`
-+CFLAGS += -c `pkg-config glib-2.0 --cflags`
- 
- 
- EXTRALIBS = -lm
---- wise2.4.1/src/base/makefile.old	2017-01-10 15:11:43.396368920 +0000
-+++ wise2.4.1/src/base/makefile	2017-01-10 15:12:30.590885552 +0000
-@@ -20,8 +20,8 @@
- 
- 
- #CFLAGS = -c  -g -DUNIX -DWISE_MEMORY_WATCH
--CFLAGS = -c  -O2 -DUNIX -pthread
--LFLAGS =  -g  -lm 
-+CFLAGS += -c  -DUNIX -pthread
-+LFLAGS =  -lm 
- DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D
- AR_OPTIONS = ru
- 
---- wise2.4.1/src/corba/makefile.old	2017-01-10 15:12:43.086757650 +0000
-+++ wise2.4.1/src/corba/makefile	2017-01-10 15:17:24.179888689 +0000
-@@ -1,10 +1,10 @@
- 
- 
--CC = cc
-+CC += gcc
- 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`
-+#CFLAGS =  -O2 -c  -DUNIX  -I../base/ `pkg-config glib-2.0 --cflags` -I/usr/local/include/orbit-1.0/
-+CFLAGS +=  -pthread -c  -DUNIX  -I../base/ -I../dynlibsrc `pkg-config ORBit-2.0 --cflags`
- LFLAGS =   -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) $(CFLAGS) $(LDFLAGS) -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 glib-2.0 --libs` -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) $(CFLAGS) $(LDFLAGS) -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 glib-2.0 --libs` -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) $(CFLAGS) $(LDFLAGS) -o test_client  test_client.o  hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -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) $(CFLAGS) $(LDFLAGS) -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 glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
- 
- .c.o :
- 	$(CC) $(CFLAGS) $(INCFLAGS) $?
---- wise2.4.1/src/dnaindex/assembly/makefile.old	2017-01-10 15:17:42.238704557 +0000
-+++ wise2.4.1/src/dnaindex/assembly/makefile	2017-01-10 15:19:04.599866950 +0000
-@@ -25,11 +25,11 @@
- 
- 
- 
--CC = cc
--CFLAGS = -Wall -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags`
-+CC += gcc
-+CFLAGS += -Wall -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config glib-2.0 --cflags`
- 
- 
--LFLAGS =  -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm
-+LFLAGS =  -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm
- 
- 
- .c.o :
---- wise2.4.1/src/dnaindex/makefile.old	2017-01-10 15:19:16.053750635 +0000
-+++ wise2.4.1/src/dnaindex/makefile	2017-01-10 15:19:50.679398862 +0000
-@@ -27,14 +27,14 @@
- 
- 
- 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 $(LFLAGS) `pkg-config glib-2.0 --libs`
- 
- 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 $(LFLAGS) `pkg-config glib-2.0 --libs`
- 
- 
- 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 $(LFLAGS) `pkg-config glib-2.0 --libs`
- 
- make_shotgun : make_shotgun.o shotgun.o
- 	$(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS)
-@@ -69,11 +69,11 @@
- show_euler : show_euler.o eulerindex.o singleseqspace.o
- 	$(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS)
- 
--CC = cc
--CFLAGS = -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags`
-+CC += gcc
-+CFLAGS += -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags`
- 
- 
--LFLAGS =  -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm
-+LFLAGS =  -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm
- 
- 
- .c.o :
---- wise2.4.1/src/dynlibsrc/makefile.old	2017-01-10 15:20:08.159221406 +0000
-+++ wise2.4.1/src/dynlibsrc/makefile	2017-01-10 15:21:22.739464830 +0000
-@@ -81,12 +81,12 @@
- 
- 
- 
--CC = cc
-+CC += gcc
- 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 +=  -pthread -DCOMPILE_VERBOSITY -DPTHREAD -c -DUNIX -I../base/ `pkg-config glib-2.0 --cflags`
-+#CFLAGS =  -Wall -g3 -pg -DPTHREAD -O2  -c  -DUNIX -I../base/ `pkg-config glib-2.0 --cflags`
-+#CFLAGS =   -O2 -c -pthread  -DUNIX  -I../base/ `pkg-config glib-2.0 --cflags`
- #CFLAGS =   -O -c -DUNIX -DNOERROR -I../base/
- LFLAGS =  -g -L../base/ -lm 
- AR_OPTIONS = ru
-@@ -148,13 +148,13 @@
- 	$(CC) -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) -o test_seqhash `pkg-config glib-2.0 --libs` 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) -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o  ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs`
- 
- 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) -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o  ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs`
- 
- 
- testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o
---- wise2.4.1/src/external/mott/makefile.old	2017-01-10 15:21:45.914229629 +0000
-+++ wise2.4.1/src/external/mott/makefile	2017-01-10 15:22:13.528950163 +0000
-@@ -14,10 +14,10 @@
- wise2_mott_bridge.o : wise2_mott_bridge.c
- 	$(CC) $(CFLAGS) -I../../dynlibsrc -I../../base wise2_mott_bridge.c
- 
--CC = cc
-+CC += gcc
- 
--CFLAGS =  -Wall -g3 -DPTHREAD -O2 -c 
--LFLAGS =  -g -L../base/ -lm 
-+CFLAGS =  -DPTHREAD -c 
-+LFLAGS =  -L../base/ -lm 
- AR_OPTIONS = ru
- 
- 
---- wise2.4.1/src/models/makefile.old	2017-01-10 15:24:11.908752314 +0000
-+++ wise2.4.1/src/models/makefile	2017-01-10 15:34:14.159658724 +0000
-@@ -50,6 +50,8 @@
- 	proteinsw.o \
- 	estquick3.o 
- 
-+EXTRALIBS += `pkg-config glib-2.0 --libs`
-+
- all : dnal psw pswdb dba estwise genewise genewisedb estwisedb genomewise sywise pseudowise promoterwise scanwise libmodel.a
- 
- libmodel.a : $(NEWG) 
-@@ -180,7 +182,7 @@
- 	$(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) $(LDFLAGS) -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -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)
-@@ -192,10 +194,10 @@
- 	$(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o   $(LFLAGS) -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 glib-2.0 --cflags` $?
- 
- hsp2aln_sw.o : hsp2aln_sw.c
--	$(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
-+	$(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
- 
- 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 
-@@ -212,10 +214,10 @@
- 
- 
- scanwisep_wiseserver.o : scanwisep.c
--	$(CC)  $(CFLAGS) $(INCFLAGS)  -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c 
-+	$(CC)  $(CFLAGS) $(INCFLAGS)  -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c `pkg-config glib-2.0 --libs`
- 
- 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  $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase  $(EXTRALIBS) -lpthread `pkg-config glib-2.0 --libs`
- 
- scanwisep_compress.o : scanwisep.c
- 	$(CC)  $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c 
-@@ -226,25 +228,25 @@
- 
- 
- 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   $(LFLAGS)  -L../external/mott -lmott -ldyna_glib -ldyna  -lwisebase  $(EXTRALIBS) `pkg-config glib-2.0 --libs` -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 $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
- 
- localcishit.o : localcishit.c
--	$(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
-+	$(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
- 
- promoterwise.o : promoterwise.c  
--	$(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
-+	$(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
- 
- 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 $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config glib-2.0 --libs` -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 $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config glib-2.0 --libs` -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 $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config glib-2.0 --libs` -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
-@@ -275,35 +277,35 @@
- 	$(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -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) $(LDFLAGS) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config glib-2.0 --libs`
- 
- cdnawise : cdnawise.o $(NEWG) cdnawise10.o 
--	$(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -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) $(LDFLAGS) -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)
- 
- 
- 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) $(LDFLAGS) -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)
- 
- 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) $(LDFLAGS) -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)
- 
- 
- 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) $(LDFLAGS) -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase 
- 
- 
- efgw   : genewise.o $(NEWG) 
--	$(CC) -g -o genewise genewise.o  $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) -lefence
-+	$(CC) $(LDFLAGS) -o genewise genewise.o  $(NEWG)  $(LFLAGS) -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) $(LDFLAGS) -o genewisedb genewisedb.o  $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config glib-2.0 --libs`
- 
- estwisedb : estwisedb.o $(NEWG) 
--	$(CC) -g -o estwisedb estwisedb.o $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
-+	$(CC) $(LDFLAGS) -o estwisedb estwisedb.o $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config glib-2.0 --libs`
- 
- edb : estwisedb.o $(NEWG) 
- 	$(CC) -g -o estwisedb estwisedb.o $(NEWG)  $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) -lefence
-@@ -313,28 +315,28 @@
- 
- 
- 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) $(LDFLAGS) -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -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) $(LDFLAGS) -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -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) $(LDFLAGS) -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o  standardout.o geneutil.o $(LFLAGS) -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) $(LDFLAGS) -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -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) $(LDFLAGS) -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -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) $(LDFLAGS) -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -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) $(LDFLAGS) -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config glib-2.0 --libs`
- 
- 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) $(LDFLAGS) -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS)
- 
- 
- HMMER_LIBS = ../HMMer2/
-@@ -342,14 +344,14 @@
- HMMER_DEFINE = 
- 
- 
--CC = cc
-+CC += gcc
- #CFLAGS = -c -O2  -pg -I../base/ -I../dynlibsrc/
- #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE  -DUNIX  -I../base/ -I../dynlibsrc/ -I.
--CFLAGS = -c -g3 -O2  -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags`
--#CFLAGS = -c  -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags`
-+CFLAGS = -c -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0 --cflags`
-+#CFLAGS = -c  -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags`
- #LFLAGS =  -L../base/ -L../dynlibsrc/ -L../HMMer2/  
- 
--LFLAGS =  -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs`
-+LFLAGS =  -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config glib-2.0 --libs`
- AR_OPTIONS = ru
- 
- RANLIB_NEEDED = 0
---- wise2.4.1/src/network/makefile.old	2017-01-10 15:34:31.649482055 +0000
-+++ wise2.4.1/src/network/makefile	2017-01-10 15:35:11.545079297 +0000
-@@ -1,10 +1,10 @@
- 
- .SUFFIXES :  .dy
- 
--CC = cc
-+CC += gcc
- 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 += -c -pthread  -DUNIX  -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config glib-2.0 --cflags`
-+LFLAGS =  -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config glib-2.0 --libs`
- AR_OPTIONS = ru
- 
- RANLIB_NEEDED = 0
---- wise2.4.1/src/snp/makefile.old	2017-01-10 15:35:18.714006953 +0000
-+++ wise2.4.1/src/snp/makefile	2017-01-10 15:36:14.330445965 +0000
-@@ -2,12 +2,12 @@
- .SUFFIXES :  .dy
- 
- 
--CC = cc
-+CC += gcc
- #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 -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0 --cflags`
- 
--LFLAGS =  -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm
-+LFLAGS =  -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -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) $(LDFLAGS) -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 $(LFLAGS)
- 
- INCFLAGS = -I../base/ -I../dynlibsrc/
- DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn
diff --git a/sci-biology/wise/files/wise-env b/sci-biology/wise/files/wise-env
deleted file mode 100644
index 3f781c808..000000000
--- a/sci-biology/wise/files/wise-env
+++ /dev/null
@@ -1 +0,0 @@
-WISECONFIGDIR="/usr/share/wise/wisecfg"
diff --git a/sci-biology/wise/metadata.xml b/sci-biology/wise/metadata.xml
deleted file mode 100644
index 8417d1580..000000000
--- a/sci-biology/wise/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-biology/wise/wise-2.4.1.ebuild b/sci-biology/wise/wise-2.4.1.ebuild
deleted file mode 100644
index 4ea9cb90a..000000000
--- a/sci-biology/wise/wise-2.4.1.ebuild
+++ /dev/null
@@ -1,96 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs versionator
-
-DESCRIPTION="Genewise, promoterwise: align protein HMMs to DNA for CDS predictions"
-HOMEPAGE="http://www.ebi.ac.uk/~birney/wise2"
-SRC_URI="http://www.ebi.ac.uk/~birney/${PN}2/${PN}$(delete_version_separator 3).tar.gz"
-#SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${PN}$(delete_version_separator 3).tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc static-libs"
-
-RDEPEND="sci-biology/hmmer:2"
-DEPEND="
-	${RDEPEND}
-	dev-lang/perl
-	virtual/latex-base
-	dev-libs/glib"
-
-S="${WORKDIR}"/${PN}$(delete_version_separator 3)
-
-src_prepare() {
-	epatch "${FILESDIR}"/wise-2.2.0-glibc-2.10.patch
-	epatch "${FILESDIR}"/wise-2.4.1-cflags.patch
-	epatch "${FILESDIR}"/01_welcome-csh.patch
-	epatch "${FILESDIR}"/02_isnumber.patch
-	epatch "${FILESDIR}"/03_doc-nodycache.patch
-	epatch "${FILESDIR}"/04_wise2-pdflatex-update.patch
-	# the two below are already in wise-2.2.0-glibc-2.10.patch wise-2.4.1-cflags.patch
-	#epatch "${FILESDIR}"/06_getline.patch
-	#epatch "${FILESDIR}"/07_ld--as-needed.patch
-	epatch "${FILESDIR}"/08_mayhem.patch
-	epatch "${FILESDIR}"/09_dnal-add-return-statement.patch
-	epatch "${FILESDIR}"/11_consistent_manual_dates.patch
-#	cd "${S}"/docs || die
-#	cat "${S}"/src/models/*.tex "${S}"/src/dynlibsrc/*.tex | perl gettex.pl > temp.tex || die
-#	cat wise2api.tex temp.tex apiend.tex > api.tex || die
-#	epatch "${FILESDIR}"/${PN}-api.tex.patch
-	#
-	# eventually, zap bundled but modified version of hmmer-2?
-	# This is not recommended, because sean and I diverged a while back on indexing
-	# strategies. At some point I will need to port the later HMMer into Wise2.
-	# rm -rf src/HMMer2 || die "Cannot zap bundled hmmer-2 sources"
-	# sed -e "s#HMMER_INCLUDE = ../HMMer2/#HMMER_INCLUDE = ${EPREFIX}/usr/include/hmmer2#" -i src/makefile || die
-	# sed -e "s#HMMER_LIBS.* = ../HMMer2/#HMMER_LIBS = ${EPREFIX}/usr/$(get_libdir)"#" -i src/makefile || die
-	# TODO: change eventual callers of the hmmer-2 binaries?
-	# ./test_data/*.{HMM,hmm}
-	# ./src/test/*.{HMM,hmm}
-	# ./src/perl/makelib.pl
-	#for e in hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmpfam hmmsearch; do \
-	#	# append '2' to the filename in "$e"
-	#done
-}
-
-src_compile() {
-	emake \
-		-C src \
-		CC="$(tc-getCC)" \
-		all
-	if use doc; then
-		cd "${S}"/docs || die
-		for i in api appendix dynamite wise2 wise3arch; do
-			latex ${i} || die
-			latex ${i} || die
-			dvips ${i}.dvi -o || die
-		done
-	fi
-}
-
-src_test() {
-	cd "${S}"/src || die
-	WISECONFIGDIR="${S}/wisecfg" emake test
-}
-
-src_install() {
-	dobin "${S}"/src/bin/* "${S}"/src/dynlibsrc/testgendb
-	use static-libs && \
-		dolib.a \
-			"${S}"/src/base/libwisebase.a \
-			"${S}"/src/dynlibsrc/libdyna.a \
-			"${S}"/src/models/libmodel.a
-
-	insinto /usr/share/${PN}
-	doins -r "${S}"/wisecfg
-
-	if use doc; then
-		insinto /usr/share/doc/${PF}
-		doins "${S}"/docs/*.ps
-	fi
-	newenvd "${FILESDIR}"/${PN}-env 24wise || die "Failed to install env file"
-}