games/wise: Added (Compare protein to DNA sequence).

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

17 files changed, 2781 insertions, 0 deletions

diff --git a/academic/wise/README b/academic/wise/README
new file mode 100644
index 0000000000000..6fe23af5ada4a
--- /dev/null
+++ b/academic/wise/README
@@ -0,0 +1,7 @@
+Wise compares a protein sequence to a genomic DNA sequence, allowing for
+introns and frameshifting errors.
+
+The Wise package is now a rather stately bioinformatics package that has
+been around for a while. Its key programs are genewise, a program for
+aligning proteins or protein HMMs to DNA, and dynamite a rather cranky
+"macro language" which automates the production of dynamic programming.
diff --git a/academic/wise/patches/01_welcome-csh.patch b/academic/wise/patches/01_welcome-csh.patch
new file mode 100644
index 0000000000000..3a9057e0629f1
--- /dev/null
+++ b/academic/wise/patches/01_welcome-csh.patch
@@ -0,0 +1,22 @@
+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/academic/wise/patches/02_isnumber.patch b/academic/wise/patches/02_isnumber.patch
new file mode 100644
index 0000000000000..a6ae90856d305
--- /dev/null
+++ b/academic/wise/patches/02_isnumber.patch
@@ -0,0 +1,14 @@
+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/academic/wise/patches/03_doc-nodycache.patch b/academic/wise/patches/03_doc-nodycache.patch
new file mode 100644
index 0000000000000..6fe7b1893c4be
--- /dev/null
+++ b/academic/wise/patches/03_doc-nodycache.patch
@@ -0,0 +1,15 @@
+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/academic/wise/patches/04_wise2-pdflatex-update.patch b/academic/wise/patches/04_wise2-pdflatex-update.patch
new file mode 100644
index 0000000000000..bbaf2861d7ebe
--- /dev/null
+++ b/academic/wise/patches/04_wise2-pdflatex-update.patch
@@ -0,0 +1,38 @@
+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/academic/wise/patches/05_glib2.patch b/academic/wise/patches/05_glib2.patch
new file mode 100644
index 0000000000000..908506524a7fc
--- /dev/null
+++ b/academic/wise/patches/05_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
+--- wise-2.4.1.orig/src/makefile
++++ wise-2.4.1/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
+--- wise-2.4.1.orig/src/snp/makefile
++++ wise-2.4.1/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
+--- wise-2.4.1.orig/src/corba/makefile
++++ wise-2.4.1/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) $?
+--- wise-2.4.1.orig/src/models/makefile
++++ wise-2.4.1/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)
+ 
+ 
+ #
+--- wise-2.4.1.orig/src/dnaindex/makefile
++++ wise-2.4.1/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 :
+--- wise-2.4.1.orig/src/dnaindex/assembly/makefile
++++ wise-2.4.1/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 :
+--- wise-2.4.1.orig/src/dynlibsrc/makefile
++++ wise-2.4.1/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) $?
+--- wise-2.4.1.orig/src/network/makefile
++++ wise-2.4.1/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 :
+--- wise-2.4.1.orig/src/other_programs/makefile
++++ wise-2.4.1/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
+--- wise-2.4.1.orig/src/base/makefile
++++ wise-2.4.1/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
+ 
+--- wise-2.4.1.orig/src/HMMer2/Makefile
++++ wise-2.4.1/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/academic/wise/patches/06_getline.patch b/academic/wise/patches/06_getline.patch
new file mode 100644
index 0000000000000..341cdae82e813
--- /dev/null
+++ b/academic/wise/patches/06_getline.patch
@@ -0,0 +1,305 @@
+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/academic/wise/patches/07_ld--as-needed.patch b/academic/wise/patches/07_ld--as-needed.patch
new file mode 100644
index 0000000000000..51ee254370770
--- /dev/null
+++ b/academic/wise/patches/07_ld--as-needed.patch
@@ -0,0 +1,52 @@
+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/academic/wise/patches/08_mayhem.patch b/academic/wise/patches/08_mayhem.patch
new file mode 100644
index 0000000000000..c54c7c66ab178
--- /dev/null
+++ b/academic/wise/patches/08_mayhem.patch
@@ -0,0 +1,103 @@
+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/academic/wise/patches/09_dnal-add-return-statement.patch b/academic/wise/patches/09_dnal-add-return-statement.patch
new file mode 100644
index 0000000000000..62931ed624023
--- /dev/null
+++ b/academic/wise/patches/09_dnal-add-return-statement.patch
@@ -0,0 +1,17 @@
+Author: Dejan Latinovic <Dejan.Latinovic@imgtec.com>
+Last-Update: Mon, 4 Aug 2014 17:10:38 +0000
+Bug-Debian: http://bugs.debian.org/751277
+Description: 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/academic/wise/patches/10_fix_path_to_data_files.patch b/academic/wise/patches/10_fix_path_to_data_files.patch
new file mode 100644
index 0000000000000..f437241cd1c39
--- /dev/null
+++ b/academic/wise/patches/10_fix_path_to_data_files.patch
@@ -0,0 +1,337 @@
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 04 Aug 2014 19:25:58 +0200
+Description: Brute force patch to fix the PATH to the data files to make the
+ tools finding the needed data for the test suite
+ .
+ In principle the PATH should be configurable and the test suite script even
+ contains a parameter (-cf) for this - but this seems to be ignored.
+ .
+ The correct way to deal with this would be a configuration option but I had
+ no intend to spend to much time into some software that was declared to be
+ orphaned (superseded by exonerate).  So this primitive patch works to run
+ the test suite successfully (which is not the case without the patch).
+
+--- a/src/models/estwise.c
++++ b/src/models/estwise.c
+@@ -484,8 +484,8 @@ boolean build_objects(void)
+ 
+ void build_defaults(void)
+ {
+-  codon_file = "codon.table";
+-  matrix_file = "BLOSUM62.bla";
++  codon_file = "/usr/share/wise/codon.table";
++  matrix_file = "/usr/share/wise/BLOSUM62.bla";
+   
+ 
+ 
+--- a/src/models/estwisedb.c
++++ b/src/models/estwisedb.c
+@@ -78,7 +78,7 @@ char * qend_str      = NULL;
+ int qend             = -1;
+ 
+ 
+-char * matrix_file      = "BLOSUM62.bla";
++char * matrix_file      = "/usr/share/wise/BLOSUM62.bla";
+ CompMat * mat           = NULL;
+ 
+ char * gap_str          = "12";
+@@ -849,8 +849,8 @@ void show_version(FILE * ofp)
+ 
+ void build_defaults(void)
+ {
+-  codon_file = "codon.table";
+-  matrix_file = "BLOSUM62.bla";
++  codon_file = "/usr/share/wise/codon.table";
++  matrix_file = "/usr/share/wise/BLOSUM62.bla";
+   
+ 
+ }
+--- a/src/models/pswdb.c
++++ b/src/models/pswdb.c
+@@ -40,7 +40,7 @@ int max_desc = 500;
+ 
+ char * querydb             = NULL;
+ char * targetdb            = NULL;
+-char * matrix_file      = "BLOSUM62.bla";
++char * matrix_file      = "/usr/share/wise/BLOSUM62.bla";
+ char * output_file 	= "-";
+ 
+ char * cutoff_str    = NULL;
+@@ -65,7 +65,7 @@ void show_help(FILE * ofp)
+    fprintf(ofp,"\npswdb <options> <query_db> <target_db>\nSeqs in fasta format\n"
+           "\t-g gap penalty (default 12)\n"
+           "\t-e ext penatly (default 2)\n"
+-          "\t-m comp matrix (default BLOSUM62.bla)\n"
++          "\t-m comp matrix (default /usr/share/wise/BLOSUM62.bla)\n"
+           "\t-abc use the abc model\n"
+           "\t-a   a penalty for above (default 120)\n"
+           "\t-b   b penalty for above (default 10)\n"
+@@ -397,7 +397,7 @@ int main(int argc,char *argv[])
+ 
+    matrix_file = strip_out_assigned_argument(&argc,argv,"m");
+    if( matrix_file == NULL)
+-      matrix_file = "BLOSUM62.bla";
++      matrix_file = "/usr/share/wise/BLOSUM62.bla";
+ 
+    /* database implementation stuff */
+    dbsi = new_DBSearchImpl_from_argv(&argc,argv);
+--- a/src/models/genewisedb.c
++++ b/src/models/genewisedb.c
+@@ -77,7 +77,7 @@ int qend             = -1;
+ char * gene_file        = NULL;
+ GeneFrequency21 * gf    = NULL;
+ 
+-char * matrix_file      = "BLOSUM62.bla";
++char * matrix_file      = "/usr/share/wise/BLOSUM62.bla";
+ CompMat * mat           = NULL;
+ 
+ char * gap_str          = "12";
+@@ -1015,9 +1015,9 @@ void show_version(FILE * ofp)
+ 
+ void build_defaults(void)
+ {
+-  gene_file = "human.gf";
+-  codon_file = "codon.table";
+-  matrix_file = "BLOSUM62.bla";
++  gene_file = "/usr/share/wise/human.gf";
++  codon_file = "/usr/share/wise/codon.table";
++  matrix_file = "/usr/share/wise/BLOSUM62.bla";
+   
+ 
+ }
+--- a/src/models/genewise.c
++++ b/src/models/genewise.c
+@@ -749,10 +749,10 @@ boolean build_objects(void)
+ 
+ void build_defaults(void)
+ {
+-  gene_file = "human.gf";
+-  new_gene_file = "gene.stat";
+-  codon_file = "codon.table";
+-  matrix_file = "BLOSUM62.bla";
++  gene_file = "/usr/share/wise/human.gf";
++  new_gene_file = "/usr/share/wise/gene.stat";
++  codon_file = "/usr/share/wise/codon.table";
++  matrix_file = "/usr/share/wise/BLOSUM62.bla";
+   
+ 
+ }
+--- a/src/models/scanwisep.c
++++ b/src/models/scanwisep.c
+@@ -157,7 +157,7 @@ ScanWiseHSPImpl * new_ScanWiseHSPImpl_fr
+   out->use_multiscan = FALSE;
+   out->ior_file = NULL;
+   out->direct_sequence = NULL;
+-  out->matrix_file = "BLOSUM62.bla";
++  out->matrix_file = "/usr/share/wise/BLOSUM62.bla";
+   out->step = 32;
+   out->host = "localhost";
+   out->port = 4050;
+@@ -546,7 +546,7 @@ int main(int argc,char ** argv)
+ 
+   /* ugly, but we don't want to bounce matrices around the network... */
+ 
+-  mat = read_Blast_file_CompMat("BLOSUM62.bla");
++  mat = read_Blast_file_CompMat("/usr/share/wise/BLOSUM62.bla");
+   
+   erroroff(REPORT);
+ 
+--- a/src/models/psw.c
++++ b/src/models/psw.c
+@@ -24,7 +24,7 @@ void show_help(FILE * ofp)
+ 	  "\tOPTIONS\n"
+ 	  "\t-g gap penalty (default 12)\n"
+ 	  "\t-e ext penatly (default 2)\n"
+-	  "\t-m comp matrix (default BLOSUM62.bla)\n"
++	  "\t-m comp matrix (default /usr/share/wise/BLOSUM62.bla)\n"
+ 	  "\t-abc use the abc model\n"
+ 	  "\t-a   a penalty for above (default 120)\n"
+ 	  "\t-b   b penalty for above (default 10)\n"
+@@ -126,7 +126,7 @@ int main(int argc,char ** argv)
+   
+   comp_file = strip_out_assigned_argument(&argc,argv,"m");
+   if( comp_file == NULL)
+-    comp_file = "BLOSUM62.bla";
++    comp_file = "/usr/share/wise/BLOSUM62.bla";
+ 
+   if( (temp = strip_out_assigned_argument(&argc,argv,"dpenv")) != NULL ) {
+     dpenv = read_DPEnvelope_file(temp);
+--- a/src/test/basic_cdna.out
++++ b/src/test/basic_cdna.out
+@@ -3,13 +3,13 @@ This program is freely distributed under
+ Copyright (c) GRL limited: portions of the code are from separate copyrights
+ 
+ Query protein:    roa1_drome
+-Comp Matrix:      BLOSUM62.bla
++Comp Matrix:      /usr/share/wise/BLOSUM62.bla
+ Gap open:         12
+ Gap extension:    2
+ Start/End         default
+ Target Sequence   HSHNCPA1
+ Strand:           both
+-Codon Table:      codon.table
++Codon Table:      /usr/share/wise/codon.table
+ Subs error:       1e-05
+ Indel error:      1e-05
+ Algorithm         333
+--- a/src/test/basic_genomic.out
++++ b/src/test/basic_genomic.out
+@@ -3,17 +3,17 @@ This program is freely distributed under
+ Copyright (c) GRL limited: portions of the code are from separate copyright
+ 
+ Query protein:       roa1_drome
+-Comp Matrix:         BLOSUM62.bla
++Comp Matrix:         /usr/share/wise/BLOSUM62.bla
+ Gap open:            12
+ Gap extension:       2
+ Start/End            default
+ Target Sequence      HSHNCPA1
+ Strand:              forward
+ Start/End (protein)  default
+-Gene Parameter file: gene.stat
++Gene Parameter file: /usr/share/wise/gene.stat
+ Splice site model:   GT/AG only
+ GT/AG bits penalty   -9.96
+-Codon Table:         codon.table
++Codon Table:         /usr/share/wise/codon.table
+ Subs error:          1e-06
+ Indel error:         1e-06
+ Null model           syn
+--- a/src/test/pswdb.out
++++ b/src/test/pswdb.out
+@@ -12,7 +12,7 @@ Gap open:       12
+ Gap extension:  2
+ Query info from:     road.pep
+ Database info from:  pep.fa
+-Comp Matrix:         BLOSUM62.bla
++Comp Matrix:         /usr/share/wise/BLOSUM62.bla
+ [Warning: Can't fit histogram to a db smaller than 1,000]
+ 
+ 
+--- a/src/models/genestats.c
++++ b/src/models/genestats.c
+@@ -22,7 +22,7 @@ void show_help_GeneModelParam(FILE * ofp
+   fprintf(ofp,"  -splice_score_offset    [%.1f]  score offset for splice sites\n",DEFAULT_SPLICE_OFFSET_SCORE);
+   fprintf(ofp,"  -[no]splice_gtag        make just gtag splice sites (default is gtag, ie no model)\n");  
+   fprintf(ofp,"  -splice_gtag_prob       [0.001] probability for gt/ag \n");
+-  fprintf(ofp,"  -genestats              [gene.stat]\n");
++  fprintf(ofp,"  -genestats              [/usr/share/wise/gene.stat]\n");
+ 
+ }
+ 
+@@ -270,7 +270,7 @@ GeneModelParam * std_GeneModelParam(void
+   out->min_collar   = -5.0;
+   out->max_collar   = +5.0;
+   out->score_offset = DEFAULT_SPLICE_OFFSET_SCORE;
+-  out->gene_stats_file = stringalloc("gene.stat");
++  out->gene_stats_file = stringalloc("/usr/share/wise/gene.stat");
+   out->use_gtag_splice = TRUE;
+ 
+   out->prob_for_gtag = 0.001;
+--- a/src/models/genestats.dy
++++ b/src/models/genestats.dy
+@@ -103,7 +103,7 @@ void show_help_GeneModelParam(FILE * ofp
+   fprintf(ofp,"  -splice_score_offset    [%.1f]  score offset for splice sites\n",DEFAULT_SPLICE_OFFSET_SCORE);
+   fprintf(ofp,"  -[no]splice_gtag        make just gtag splice sites (default is gtag, ie no model)\n");  
+   fprintf(ofp,"  -splice_gtag_prob       [0.001] probability for gt/ag \n");
+-  fprintf(ofp,"  -genestats              [gene.stat]\n");
++  fprintf(ofp,"  -genestats              [/usr/share/wise/gene.stat]\n");
+ 
+ }
+ 
+@@ -290,7 +290,7 @@ GeneModelParam * std_GeneModelParam(void
+   out->min_collar   = -5.0;
+   out->max_collar   = +5.0;
+   out->score_offset = DEFAULT_SPLICE_OFFSET_SCORE;
+-  out->gene_stats_file = stringalloc("gene.stat");
++  out->gene_stats_file = stringalloc("/usr/share/wise/gene.stat");
+   out->use_gtag_splice = TRUE;
+ 
+   out->prob_for_gtag = 0.001;
+--- a/src/models/testgenestat.c
++++ b/src/models/testgenestat.c
+@@ -23,7 +23,7 @@ int main(int argc,char ** argv)
+ 
+   seq = read_fasta_file_Sequence("../../test_data/human.genomic");
+   
+-  ifp = openfile("gene.stat","r");
++  ifp = openfile("/usr/share/wise/gene.stat","r");
+   
+   st = read_GeneStats(ifp); 
+   
+--- a/src/test/hmm_genomic.out
++++ b/src/test/hmm_genomic.out
+@@ -7,10 +7,10 @@ Start/End            local
+ Target Sequence      HSHNCPA1
+ Strand:              forward
+ Start/End (protein)  local
+-Gene Parameter file: gene.stat
++Gene Parameter file: /usr/share/wise/gene.stat
+ Splice site model:   GT/AG only
+ GT/AG bits penalty   -9.96
+-Codon Table:         codon.table
++Codon Table:         /usr/share/wise/codon.table
+ Subs error:          1e-06
+ Indel error:         1e-06
+ Null model           syn
+--- a/src/test/hmm_cdna.out
++++ b/src/test/hmm_cdna.out
+@@ -6,7 +6,7 @@ Query model:      unnamed
+ Start/End         default
+ Target Sequence   HSHNCPA1
+ Strand:           both
+-Codon Table:      codon.table
++Codon Table:      /usr/share/wise/codon.table
+ Subs error:       1e-05
+ Indel error:      1e-05
+ Algorithm         333L
+--- a/src/test/genewise-db.out
++++ b/src/test/genewise-db.out
+@@ -12,8 +12,8 @@ Search mode:           Single protein vs
+ Protein info from:     rrm.HMM
+ Dna info from:         dna.db
+ Start/End (protein)    global
+-Gene Paras:            human.gf
+-Codon Table:           codon.table
++Gene Paras:            /usr/share/wise/human.gf
++Codon Table:           /usr/share/wise/codon.table
+ Subs error:            1e-05
+ Indel error:           1e-05
+ Model splice?          model
+--- a/src/test/genewise-db-lite.out
++++ b/src/test/genewise-db-lite.out
+@@ -12,8 +12,8 @@ Search mode:           Single protein vs
+ Protein info from:     rrm.HMM
+ Dna info from:         dna.db
+ Start/End (protein)    global
+-Gene Paras:            human.gf
+-Codon Table:           codon.table
++Gene Paras:            /usr/share/wise/human.gf
++Codon Table:           /usr/share/wise/codon.table
+ Subs error:            1e-05
+ Indel error:           1e-05
+ Model splice?          model
+--- a/src/test/estwise-db.out
++++ b/src/test/estwise-db.out
+@@ -13,7 +13,7 @@ Search mode:           Single protein vs
+ Protein info from:     rrm.HMM
+ Dna info from:         dna.db
+ Start/End              local
+-Codon Table:           codon.table
++Codon Table:           /usr/share/wise/codon.table
+ Subs error:            0.01
+ Indel error:           0.01
+ Null model:            synchronous
+--- a/src/test/genewisedb-pfam.out
++++ b/src/test/genewisedb-pfam.out
+@@ -12,8 +12,8 @@ Search mode:           Single genomic vs
+ Protein info from:     rrm.HMM
+ Dna info from:         short.dna
+ Start/End (protein)    default
+-Gene Paras:            human.gf
+-Codon Table:           codon.table
++Gene Paras:            /usr/share/wise/human.gf
++Codon Table:           /usr/share/wise/codon.table
+ Subs error:            1e-05
+ Indel error:           1e-05
+ Model splice?          model
diff --git a/academic/wise/patches/11_consistent_manual_dates.patch b/academic/wise/patches/11_consistent_manual_dates.patch
new file mode 100644
index 0000000000000..eaea1eec9012c
--- /dev/null
+++ b/academic/wise/patches/11_consistent_manual_dates.patch
@@ -0,0 +1,53 @@
+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/academic/wise/patches/cross.patch b/academic/wise/patches/cross.patch
new file mode 100644
index 0000000000000..f6da1363d080c
--- /dev/null
+++ b/academic/wise/patches/cross.patch
@@ -0,0 +1,266 @@
+Date: Sat, 18 Apr 2020 11:59:09 +0200
+From: Helmut Grohne <helmut@subdivi.de>
+Bug-Debian: https://bugs.debian.org/958094
+Description: Do not hard code the build architecture pkg-config
+
+--- a/src/corba/makefile
++++ b/src/corba/makefile
+@@ -1,9 +1,10 @@
+ 
+ 
+ CC = cc
++PKG_CONFIG ?= pkg-config
+ INCFLAGS = -I../base/ -I../dynlibsrc
+ #gCFLAGS = -Wall -g -pedantic -c  -DUNIX -I../base/
+-#CFLAGS +=  -c  -DUNIX  -I../base/ `pkg-config --cflags glib-2.0` -I/usr/local/include/orbit-1.0/
++#CFLAGS +=  -c  -DUNIX  -I../base/ `$(PKG_CONFIG) --cflags glib-2.0` -I/usr/local/include/orbit-1.0/
+ CFLAGS  += $(CPPFLAGS) -pthread -c  -DUNIX  -I../base/ -I../dynlibsrc `orbit-config --cflags client`
+ LDFLAGS += -L../base/ -lm -lpthread
+ AR_OPTIONS = ru
+@@ -14,18 +15,18 @@ hspscan_corba.c : hspscan_corba.idl
+ 	orbit-idl hspscan_corba.idl
+ 
+ test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o 
+-	cc -g -o test_server  test_server.o hspscan_server_impl.o  hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o  corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o   ../dynlibsrc/libdyna_glib.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
++	cc -g -o test_server  test_server.o hspscan_server_impl.o  hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o  corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o   ../dynlibsrc/libdyna_glib.a `$(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 `pkg-config --libs glib-2.0` -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 `$(PKG_CONFIG) --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
+ 
+ 
+ test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o 
+-	cc -g -o test_client  test_client.o  hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread
++	cc -g -o test_client  test_client.o  hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `$(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  `pkg-config --libs glib-2.0` -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/dnaindex/assembly/makefile
++++ b/src/dnaindex/assembly/makefile
+@@ -26,10 +26,11 @@ arraymatcher : arraymatcher.o assemblygr
+ 
+ 
+ CC = cc
+-CFLAGS += $(CPPFLAGS) -Wall -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config --cflags glib-2.0`
++PKG_CONFIG ?= pkg-config
++CFLAGS += $(CPPFLAGS) -Wall -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `$(PKG_CONFIG) --cflags glib-2.0`
+ 
+ 
+-LDFLAGS +=  -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm
++LDFLAGS +=  -g -L../../base/ -L../../dynlibsrc/ -lpthread `$(PKG_CONFIG) --libs glib-2.0` -lm
+ 
+ 
+ .c.o :
+--- a/src/dnaindex/makefile
++++ b/src/dnaindex/makefile
+@@ -27,14 +27,14 @@ all: $(ASSEMBLY_OBJ)
+ 
+ 
+ kwise : kwise.o $(ASSEMBLY_OBJ)
+-	$(CC) -o kwise kwise.o $(ASSEMBLY_OBJ)  -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0`
++	$(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 $(LDFLAGS) `pkg-config --libs glib-2.0`
++	$(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 $(LDFLAGS) `pkg-config --libs glib-2.0`
++	$(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 $(LDFLAGS)
+@@ -70,10 +70,11 @@ show_euler : show_euler.o eulerindex.o s
+ 	$(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS)
+ 
+ CC = cc
+-CFLAGS += $(CPPFLAGS) -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0`
++PKG_CONFIG ?= pkg-config
++CFLAGS += $(CPPFLAGS) -pthread -c  -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `$(PKG_CONFIG) --cflags glib-2.0`
+ 
+ 
+-LDFLAGS +=  -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -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
+@@ -82,11 +82,12 @@ DYNHELPEROBJ = packaln.o \
+ 
+ 
+ CC = cc
++PKG_CONFIG ?= pkg-config
+ INCFLAGS = -I../base/
+ #CFLAGS = -Wall -g -pedantic -c  -DUNIX -I../base/
+-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 += $(CPPFLAGS) -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -c  -DUNIX -I../base/ `$(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/
+ LDFLAGS +=  -g -L../base/ -lm 
+ AR_OPTIONS = ru
+@@ -148,13 +149,13 @@ test_shadowindex : test_shadowindex.o sh
+ 	$(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) $(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  
++	$(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) $(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`
++	$(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) $(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`
++	$(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
+--- a/src/makefile
++++ b/src/makefile
+@@ -23,6 +23,7 @@
+ # Most likely you have a non ANSI C compiler
+ # CC =  /opt/intel_cc_80/bin/icc
+ CC = cc
++PKG_CONFIG ?= pkg-config
+ 
+ # These are the CFLAGS to use. These days Wise2 is inherently
+ # pthreaded, and everything is compiled with threads. However
+@@ -31,13 +32,13 @@ CC = cc
+ 
+ 
+ # Intel icc flags
+-# CFLAGS += -c  -axWK -ipo `pkg-config --cflags glib-2.0`
++# CFLAGS += -c  -axWK -ipo `$(PKG_CONFIG) --cflags glib-2.0`
+ 
+ # alpha flags (-pthread)
+-# CFLAGS += -c -pthread `pkg-config --cflags glib-2.0`
++# CFLAGS += -c -pthread `$(PKG_CONFIG) --cflags glib-2.0`
+ 
+ # normal linux/bsd/mac flags
+-CFLAGS += $(CPPFLAGS) -c  `pkg-config --cflags glib-2.0`
++CFLAGS += $(CPPFLAGS) -c  `$(PKG_CONFIG) --cflags glib-2.0`
+ 
+ 
+ EXTRALIBS = -lm
+--- a/src/models/makefile
++++ b/src/models/makefile
+@@ -192,10 +192,10 @@ psw : psw.o seqaligndisplay.o proteinsw.
+ 	$(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 `pkg-config --cflags glib-2.0` $?
++	$(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `$(PKG_CONFIG) --cflags glib-2.0` $?
+ 
+ hsp2aln_sw.o : hsp2aln_sw.c
+-	$(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $?
++	$(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 
+@@ -226,25 +226,25 @@ scanwisep_compress : scanwisep_compress.
+ 
+ 
+ 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   $(LDFLAGS)  -L../external/mott -lmott -ldyna_glib -ldyna  -lwisebase  $(EXTRALIBS) `pkg-config --libs glib-2.0` -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 $(LDFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config --libs glib-2.0` -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) `pkg-config --cflags glib-2.0` $?
++	$(CC) $(CFLAGS) $(INCFLAGS) `$(PKG_CONFIG) --cflags glib-2.0` $?
+ 
+ promoterwise.o : promoterwise.c  
+-	$(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $?
++	$(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 $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config --libs glib-2.0` -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 $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config --libs glib-2.0` -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 $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  $(EXTRALIBS) `pkg-config --libs glib-2.0` -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 $(LDFLAGS) -ldyna_glib -ldyna -lwisebase  -lpthread
+@@ -343,13 +343,14 @@ HMMER_DEFINE =
+ 
+ 
+ CC = cc
++PKG_CONFIG ?= pkg-config
+ #CFLAGS = -c -O2  -pg -I../base/ -I../dynlibsrc/
+ #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE  -DUNIX  -I../base/ -I../dynlibsrc/ -I.
+-CFLAGS += -c -g3  -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0`
+-#CFLAGS += -c  -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0`
++CFLAGS += -c -g3  -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `$(PKG_CONFIG) --cflags glib-2.0`
++#CFLAGS += -c  -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `$(PKG_CONFIG) --cflags glib-2.0`
+ #LDFLAGS =  -L../base/ -L../dynlibsrc/ -L../HMMer2/  
+ 
+-LDFLAGS +=  -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config --libs glib-2.0`
++LDFLAGS +=  -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `$(PKG_CONFIG) --libs glib-2.0`
+ AR_OPTIONS = ru
+ 
+ RANLIB_NEEDED = 0
+--- a/src/network/makefile
++++ b/src/network/makefile
+@@ -2,9 +2,10 @@
+ .SUFFIXES :  .dy
+ 
+ CC = cc
++PKG_CONFIG ?= pkg-config
+ INCFLAGS = -I../base/  -I../socket -I../dynlibsrc -I../dnaindex
+-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`
++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
+--- a/src/other_programs/makefile
++++ b/src/other_programs/makefile
+@@ -3,8 +3,9 @@
+ .SUFFIXES :  .dy
+ 
+ CC = cc
+-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`
++PKG_CONFIG ?= pkg-config
++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/snp/makefile
++++ b/src/snp/makefile
+@@ -3,11 +3,12 @@
+ 
+ 
+ CC = cc
++PKG_CONFIG ?= pkg-config
+ #CFLAGS = -c -O2  -pg -I../base/ -I../dynlibsrc/
+ #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE  -DUNIX  -I../base/ -I../dynlibsrc/ -I.
+-CFLAGS += $(CPPFLAGS) -c -g3  -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0`
++CFLAGS += $(CPPFLAGS) -c -g3  -DUNIX  -I../base/ -I../dynlibsrc/ -I. -pthread `$(PKG_CONFIG) --cflags glib-2.0`
+ 
+-LDFLAGS +=  -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lpthread -lm
++LDFLAGS +=  -g -L../base/ -L../dynlibsrc/ -lpthread `$(PKG_CONFIG) --libs glib-2.0` -lpthread -lm
+ AR_OPTIONS = ru
+ 
+ RANLIB_NEEDED = 0
diff --git a/academic/wise/patches/spelling.patch b/academic/wise/patches/spelling.patch
new file mode 100644
index 0000000000000..cb46f070ce9a3
--- /dev/null
+++ b/academic/wise/patches/spelling.patch
@@ -0,0 +1,702 @@
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Fri, 22 Sep 2017 09:18:47 +0200
+Description: Fix spelling issues
+
+--- a/src/dynlibsrc/hscore.c
++++ b/src/dynlibsrc/hscore.c
+@@ -413,7 +413,7 @@ DataScore * new_DataScore_from_storage(H
+   if( hs->st_len == 0 ) {
+     new = new_DataScoreStorage();
+     if( new == NULL ) {
+-      warn("could not make inital data score storage!");
++      warn("could not make initial data score storage!");
+       return NULL;
+     }
+     add_st_Hscore(hs,new);
+--- a/src/dynlibsrc/hscore.dy
++++ b/src/dynlibsrc/hscore.dy
+@@ -422,7 +422,7 @@ DataScore * new_DataScore_from_storage(H
+   if( hs->st_len == 0 ) {
+     new = new_DataScoreStorage();
+     if( new == NULL ) {
+-      warn("could not make inital data score storage!");
++      warn("could not make initial data score storage!");
+       return NULL;
+     }
+     add_st_Hscore(hs,new);
+--- a/docs/dynamite.tex
++++ b/docs/dynamite.tex
+@@ -2839,7 +2839,7 @@ needs at least one offset to be non zero
+ Once all the semantics of the Dynamite blueprint is ok, the compiler then turns its
+ attention to the calc lines. This is like a mini-parser operating inside the dynamite
+ parser, but unlike the dynamite parser, this once was written in yacc/lex and is
+-a more vanilla parser enviroment.
++a more vanilla parser environment.
+ 
+ \subsubsection{Parser Syntax error on calc line}
+ 
+--- a/docs/wise2.tex
++++ b/docs/wise2.tex
+@@ -121,7 +121,7 @@ Warning Error
+         Could not read a GeneFrequency file in human.gf
+ ...
+ \end{verbatim}
+-This means that the enviroment variable WISECONFIGDIR has not been
++This means that the environment variable WISECONFIGDIR has not been
+ set up correctly. You need to find where the distribution was downloaded
+ to (a directory called something like wise2.1.16b) and inside that
+ directory should be the configuration directory wisecfg. You need to
+@@ -427,7 +427,7 @@ sequence flag) as well. An example run w
+ \begin{verbatim}
+ genewisedb -pfam Pfam -dnas myseq.fa
+ \end{verbatim}
+-If you have set up the HMMER package to work with Pfam using the enviroment
++If you have set up the HMMER package to work with Pfam using the environment
+ variable HMMERDB, Wise2 will also pick that up as well.
+ 
+ 
+@@ -675,7 +675,7 @@ mathematically it is almost that easy: t
+ of the probability.
+ 
+ Perhaps a better known example is the relationship between the old
+-profile technology, as developped by Gribskov and Gibson along with
++profile technology, as developed by Gribskov and Gibson along with
+ others, and its probabilistic partner, profile Hidden Markov Models
+ (profile HMMs).  In terms of the actual algorithm these two methods
+ are very similar: it is simply that the profile HMM has a strong
+@@ -1639,7 +1639,7 @@ Of course there are many options to chan
+ \subsection{dba - Dna Block Aligner}
+ \label{sec:dba}
+ 
+-dba - standing for Dna Block Aligner, was developped by Niclas Jareborg,
++dba - standing for Dna Block Aligner, was developed by Niclas Jareborg,
+ Richard Durbin and Ewan Birney for characterising shared regulatory regions
+ of genomic DNA, either in upstream regions or introns of genes
+ 
+--- a/src/base/wisefile.c
++++ b/src/base/wisefile.c
+@@ -329,7 +329,7 @@ FILE * openfile(const char * filename,co
+  *
+  *
+  *
+- * Arg:         envname [READ ] enviroment variable to read from [NullString]
++ * Arg:         envname [READ ] environment variable to read from [NullString]
+  * Arg:        filename [UNKN ] Undocumented argument [char *]
+  * Arg:            name [READ ] filename to open [NullString]
+  * Arg:             env [UNKN ] Undocumented argument [char *]
+@@ -344,17 +344,17 @@ FILE * envopenfile(char * filename,char
+   char path [512];
+ 
+   if( filename == NULL || env == NULL ) {
+-    warn("Passed a NULL filename or enviroment name into Envfile. Should trap this elsewhere");
++    warn("Passed a NULL filename or environment name into Envfile. Should trap this elsewhere");
+     return NULL;
+   }
+ 
+   if( (envp = getenv(env)) == NULL ) {
+-    /* fail gracefully - somebody might query a number of enviroment variables */
++    /* fail gracefully - somebody might query a number of environment variables */
+     return NULL;
+   }
+ 
+   if( strlen(filename) + strlen(envp) < 490 ) {
+-    warn("Really long filename/enviroment variables [%s] [%s] Can't cope!",filename,envp);
++    warn("Really long filename/environment variables [%s] [%s] Can't cope!",filename,envp);
+     return NULL;
+   }
+   sprintf(path,"%s/%s",filename,envp);
+--- a/src/base/wisefile.dy
++++ b/src/base/wisefile.dy
+@@ -302,7 +302,7 @@ in HMMer2. You call it as
+ 
+ %arg
+ name r filename to open
+-envname r enviroment variable to read from
++envname r environment variable to read from
+ return a valid file pointer or NULL
+ %%
+ FILE * envopenfile(char * filename,char * env)
+@@ -311,17 +311,17 @@ FILE * envopenfile(char * filename,char
+   char path [512];
+ 
+   if( filename == NULL || env == NULL ) {
+-    warn("Passed a NULL filename or enviroment name into Envfile. Should trap this elsewhere");
++    warn("Passed a NULL filename or environment name into Envfile. Should trap this elsewhere");
+     return NULL;
+   }
+ 
+   if( (envp = getenv(env)) == NULL ) {
+-    /* fail gracefully - somebody might query a number of enviroment variables */
++    /* fail gracefully - somebody might query a number of environment variables */
+     return NULL;
+   }
+ 
+   if( strlen(filename) + strlen(envp) < 490 ) {
+-    warn("Really long filename/enviroment variables [%s] [%s] Can't cope!",filename,envp);
++    warn("Really long filename/environment variables [%s] [%s] Can't cope!",filename,envp);
+     return NULL;
+   }
+   sprintf(path,"%s/%s",filename,envp);
+--- a/src/base/wisefile.h
++++ b/src/base/wisefile.h
+@@ -143,7 +143,7 @@ FILE * Wise2_openfile(const char * filen
+  *
+  *
+  *
+- * Arg:         envname [READ ] enviroment variable to read from [NullString]
++ * Arg:         envname [READ ] environment variable to read from [NullString]
+  * Arg:        filename [UNKN ] Undocumented argument [char *]
+  * Arg:            name [READ ] filename to open [NullString]
+  * Arg:             env [UNKN ] Undocumented argument [char *]
+--- a/LICENSE
++++ b/LICENSE
+@@ -19,7 +19,7 @@ an acknowledgement of the authorship nee
+ 
+ The HMMer2 libaries (Sean Eddy's HMM package) and the models directory
+ (The algorithms for the Wise2 package, and final executable programs)
+-are both distributed under a Gnu General Public License (GPL). This
++are both distributed under a GNU General Public License (GPL). This
+ means that the entire package as it is distributed with these portions
+ in is also licensed under GPL, due to the 'infectious' nature of the
+ GPL.
+--- a/docs/wise3arch.tex
++++ b/docs/wise3arch.tex
+@@ -49,7 +49,7 @@ clear up a considerable amount of confus
+ 
+ \subsection{Committment to open source, freely available code}
+ 
+-The Wise2 package has been licensed under the Gnu Public License since
++The Wise2 package has been licensed under the GNU General Public License since
+ its inception.  In addition, parts of the package has even less
+ restrictive Licenses. I have a strong committment to keep Wise a
+ freely available, open source package. The aim of the open
+--- a/src/corba/scanwise_protein_index.c
++++ b/src/corba/scanwise_protein_index.c
+@@ -19,7 +19,7 @@ char * program_name = "scanwise_protein_
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/dnaindex/assembly/badkmer.c
++++ b/src/dnaindex/assembly/badkmer.c
+@@ -25,7 +25,7 @@ void show_help(FILE * ofp)
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EBI 2003\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/dnaindex/assembly/pathwise.c
++++ b/src/dnaindex/assembly/pathwise.c
+@@ -40,7 +40,7 @@ void show_help(FILE * ofp)
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EBI 2003\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/dnaindex/bigseqwise.c
++++ b/src/dnaindex/bigseqwise.c
+@@ -10,7 +10,7 @@ char * program_name = "bigseqwise";
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/dnaindex/findbad_kmer.c
++++ b/src/dnaindex/findbad_kmer.c
+@@ -13,7 +13,7 @@ char * program_name = "findbad_kmer";
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/dnaindex/kwise.c
++++ b/src/dnaindex/kwise.c
+@@ -15,7 +15,7 @@ char * program_name = "kwise";
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/alignwise.c
++++ b/src/models/alignwise.c
+@@ -61,7 +61,7 @@ void show_Gene_debug(AlnBlock * alb,Sequ
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/amplimer_resolver.c
++++ b/src/models/amplimer_resolver.c
+@@ -10,7 +10,7 @@ char * program_name = "amplimer_resolver
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/cdnawise.c
++++ b/src/models/cdnawise.c
+@@ -15,7 +15,7 @@ void show_version(FILE * ofp)
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+ 
+ 
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL (2001) and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/clonewise.c
++++ b/src/models/clonewise.c
+@@ -25,7 +25,7 @@ int mismatch_score   = -1;
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/dbac.c
++++ b/src/models/dbac.c
+@@ -363,7 +363,7 @@ void show_version(FILE * ofp)
+   fprintf(ofp,"  Released %s\n",RELEASE_DAY);  
+   fprintf(ofp,"  Compiled %s\n",COMPILE_DATE);  
+   fprintf(ofp,"dba was written by Niclas Jareborg, Ewan Birney and Richard Durbin\n");  
+-  fprintf(ofp,"Copyright (c) 1998,1999,2000,2001 GRL ltd. It is distributed under a Gnu Public License\n");  
++  fprintf(ofp,"Copyright (c) 1998,1999,2000,2001 GRL ltd. It is distributed under a GNU General Public License\n");  
+   fprintf(ofp,"See GNULICENSE in source directory for more information\n");  
+ }  
+ 
+--- a/src/models/dnal.c
++++ b/src/models/dnal.c
+@@ -104,7 +104,7 @@ void show_short_help(FILE * ofp)
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/dnawise.c
++++ b/src/models/dnawise.c
+@@ -8,7 +8,7 @@ char * program_name = "dnawise";
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/editdist.c
++++ b/src/models/editdist.c
+@@ -8,7 +8,7 @@ char * program_name = "editdist";
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/estwise.c
++++ b/src/models/estwise.c
+@@ -557,7 +557,7 @@ void show_help(FILE * ofp)
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/estwisedb.c
++++ b/src/models/estwisedb.c
+@@ -807,7 +807,7 @@ boolean show_header(FILE * ofp)
+   fprintf(ofp,"-------------------------------------------------------------\n");
+   fprintf(ofp,"Wise2 - database searching mode\n");
+   fprintf(ofp,"Program: %s version: %s released: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY);
+-  fprintf(ofp,"This program is freely distributed under a Gnu Public License.\n");
++  fprintf(ofp,"This program is freely distributed under a GNU General Public License.\n");
+   fprintf(ofp,"   See -version for more info on copyright\n");
+   fprintf(ofp,"Bugs and credits to Ewan Birney <birney@sanger.ac.uk>\n");
+   fprintf(ofp,"-------------------------------------------------------------\n\n");
+@@ -836,7 +836,7 @@ boolean show_header(FILE * ofp)
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/evopairwise.c
++++ b/src/models/evopairwise.c
+@@ -15,7 +15,7 @@ char * program_name = "evopairwise";
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/fivestar.c
++++ b/src/models/fivestar.c
+@@ -14,7 +14,7 @@ char * program_name = "fivestar";
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/fivestarscan.c
++++ b/src/models/fivestarscan.c
+@@ -14,7 +14,7 @@ char * program_name = "fivestarscan";
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/fivestarsearch.c
++++ b/src/models/fivestarsearch.c
+@@ -12,7 +12,7 @@ char * program_name = "fivestarsearch";
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/genewise.c
++++ b/src/models/genewise.c
+@@ -858,7 +858,7 @@ void show_help(FILE * ofp)
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/genewisedb.c
++++ b/src/models/genewisedb.c
+@@ -505,7 +505,7 @@ boolean show_header(FILE * ofp)
+ {
+   fprintf(ofp,"Wise2 - database searching mode\n");
+   fprintf(ofp,"Program: %s version: %s released: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY);
+-  fprintf(ofp,"This program is freely distributed under a Gnu Public License.\n");
++  fprintf(ofp,"This program is freely distributed under a GNU General Public License.\n");
+   fprintf(ofp,"   See -version for more info on copyright\n");
+   fprintf(ofp,"Bugs and credits to Ewan Birney <birney@sanger.ac.uk>\n");
+   fprintf(ofp,"-----------------------------------------------------\n\n");
+@@ -1003,7 +1003,7 @@ void show_help(FILE * ofp)
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/genomewise.c
++++ b/src/models/genomewise.c
+@@ -16,7 +16,7 @@ void show_utr_exon_genomewise(AlnBlock *
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/lba.c
++++ b/src/models/lba.c
+@@ -8,7 +8,7 @@ char * program_name = "lba";
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/motifcluster.c
++++ b/src/models/motifcluster.c
+@@ -8,7 +8,7 @@ char * program_name = "motifcluster";
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/motifdiff.c
++++ b/src/models/motifdiff.c
+@@ -8,7 +8,7 @@ char * program_name = "motifdiff";
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/motifwise.c
++++ b/src/models/motifwise.c
+@@ -8,7 +8,7 @@ char * program_name = "motifwise";
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/oldpostwise.c
++++ b/src/models/oldpostwise.c
+@@ -375,7 +375,7 @@ void show_help(char * help_arg)
+ void show_version(void)
+ {
+   fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(stdout,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(stdout,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(stdout,"The source code is copyright (c) GRL 1998 and others\n");
+   fprintf(stdout,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(stdout,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/promotercluster.c
++++ b/src/models/promotercluster.c
+@@ -7,7 +7,7 @@ char * program_name = "promotercluster";
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/promoterwise.c
++++ b/src/models/promoterwise.c
+@@ -15,7 +15,7 @@ char * program_name = "promoterwise";
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/pseudowise.c
++++ b/src/models/pseudowise.c
+@@ -13,7 +13,7 @@ char * program_name = "pseudowise";
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/psw.c
++++ b/src/models/psw.c
+@@ -259,7 +259,7 @@ int main(int argc,char ** argv)
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/pswdb.c
++++ b/src/models/pswdb.c
+@@ -95,7 +95,7 @@ void show_help(FILE * ofp)
+ void show_version(void)
+ {
+   fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(stdout,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(stdout,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(stdout,"The source code is copyright (c) EMBL 1998 and others\n");
+   fprintf(stdout,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(stdout,"For more information read the GNULICENSE file in the distribution\n\n");
+@@ -347,7 +347,7 @@ boolean show_header(FILE * ofp)
+   fprintf(ofp,"-------------------------------------------------------------\n");
+   fprintf(ofp,"Wise2 - Protein vs. Protein\n");
+   fprintf(ofp,"Program: %s version: %s released: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY);
+-  fprintf(ofp,"This program is freely distributed under a Gnu Public License.\n");
++  fprintf(ofp,"This program is freely distributed under a GNU General Public License.\n");
+   fprintf(ofp,"   See -version for more info on copyright\n");
+   fprintf(ofp,"Bugs and credits to: Richard Copley <copley@embl-heidelberg.de>\n"); 
+   fprintf(ofp,"                     Ewan Birney <birney@sanger.ac.uk>\n");
+--- a/src/models/scanwisep.c
++++ b/src/models/scanwisep.c
+@@ -421,7 +421,7 @@ HitList * HitList_from_HSP_HSP2HitListIm
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/statwise.c
++++ b/src/models/statwise.c
+@@ -11,7 +11,7 @@ char * codon_table = "codon.table";
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/models/sywise.c
++++ b/src/models/sywise.c
+@@ -12,7 +12,7 @@ char * codon_table = "codon.table";
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/network/wise_proteinindex_server.c
++++ b/src/network/wise_proteinindex_server.c
+@@ -26,7 +26,7 @@ char * program_name = "scanwise_server";
+ void show_version(FILE * ofp)
+ {
+   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
+-  fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n");
++  fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n");
+   fprintf(ofp,"The source code is copyright (c) EMBL and others\n");
+   fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n");
+   fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n");
+--- a/src/test/estwise-db.out
++++ b/src/test/estwise-db.out
+@@ -1,7 +1,7 @@
+ -------------------------------------------------------------
+ Wise2 - database searching mode
+ Program: estwisedb version: $Name: wise2-4-1 $ released: unreleased
+-This program is freely distributed under a Gnu Public License.
++This program is freely distributed under a GNU General Public License.
+    See -version for more info on copyright
+ Bugs and credits to Ewan Birney <birney@sanger.ac.uk>
+ -------------------------------------------------------------
+--- a/src/test/genewise-db-lite.out
++++ b/src/test/genewise-db-lite.out
+@@ -1,6 +1,6 @@
+ Wise2 - database searching mode
+ Program: genewisedb version: $Name: wise2-4-1 $ released: unreleased
+-This program is freely distributed under a Gnu Public License.
++This program is freely distributed under a GNU General Public License.
+    See -version for more info on copyright
+ Bugs and credits to Ewan Birney <birney@sanger.ac.uk>
+ -----------------------------------------------------
+--- a/src/test/genewise-db.out
++++ b/src/test/genewise-db.out
+@@ -1,6 +1,6 @@
+ Wise2 - database searching mode
+ Program: genewisedb version: $Name: wise2-4-1 $ released: unreleased
+-This program is freely distributed under a Gnu Public License.
++This program is freely distributed under a GNU General Public License.
+    See -version for more info on copyright
+ Bugs and credits to Ewan Birney <birney@sanger.ac.uk>
+ -----------------------------------------------------
+--- a/src/test/genewisedb-pfam.out
++++ b/src/test/genewisedb-pfam.out
+@@ -1,6 +1,6 @@
+ Wise2 - database searching mode
+ Program: genewisedb version: $Name: wise2-4-1 $ released: unreleased
+-This program is freely distributed under a Gnu Public License.
++This program is freely distributed under a GNU General Public License.
+    See -version for more info on copyright
+ Bugs and credits to Ewan Birney <birney@sanger.ac.uk>
+ -----------------------------------------------------
+--- a/src/test/pswdb.out
++++ b/src/test/pswdb.out
+@@ -1,7 +1,7 @@
+ -------------------------------------------------------------
+ Wise2 - Protein vs. Protein
+ Program: pswdb version: $Name: wise2-4-1 $ released: unreleased
+-This program is freely distributed under a Gnu Public License.
++This program is freely distributed under a GNU General Public License.
+    See -version for more info on copyright
+ Bugs and credits to: Richard Copley <copley@embl-heidelberg.de>
+                      Ewan Birney <birney@sanger.ac.uk>
+--- a/src/models/genefrequency.c
++++ b/src/models/genefrequency.c
+@@ -636,7 +636,7 @@ double double_from_line(char * buffer)
+   ret = strtod(runner,&end);
+ 
+   if( end == runner || isalnum((int)*end) ) {
+-    warn("Bad conversion of string [%s] to double [%f] occured",runner,ret);
++    warn("Bad conversion of string [%s] to double [%f] occurred",runner,ret);
+   }
+ 
+   return ret;
+--- a/src/models/genefrequency.dy
++++ b/src/models/genefrequency.dy
+@@ -597,7 +597,7 @@ double double_from_line(char * buffer)
+   ret = strtod(runner,&end);
+ 
+   if( end == runner || isalnum((int)*end) ) {
+-    warn("Bad conversion of string [%s] to double [%f] occured",runner,ret);
++    warn("Bad conversion of string [%s] to double [%f] occurred",runner,ret);
+   }
+ 
+   return ret;
+--- a/src/models/seqerror.dy
++++ b/src/models/seqerror.dy
+@@ -42,7 +42,7 @@ Sequence * seq
+ SequenceErrorSet * ses
+ %info
+ This holds a sequence and what
+-errors have occured in it.
++errors have occurred in it.
+ %%
+ 
+ 
+--- a/src/models/seqerror.h
++++ b/src/models/seqerror.h
+@@ -72,7 +72,7 @@ typedef struct Wise2_SequenceErrorSet Wi
+ /* Object ErrorSequence
+  *
+  * Descrip: This holds a sequence and what
+- *        errors have occured in it.
++ *        errors have occurred in it.
+  *
+  *
+  */
diff --git a/academic/wise/slack-desc b/academic/wise/slack-desc
new file mode 100644
index 0000000000000..c99b9025f0093
--- /dev/null
+++ b/academic/wise/slack-desc
@@ -0,0 +1,19 @@
+# HOW TO EDIT THIS FILE:
+# The "handy ruler" below makes it easier to edit a package description.
+# Line up the first '|' above the ':' following the base package name, and
+# the '|' on the right side marks the last column you can put a character in.
+# You must make exactly 11 lines for the formatting to be correct.  It's also
+# customary to leave one space after the ':' except on otherwise blank lines.
+
+    |-----handy-ruler------------------------------------------------------|
+wise: wise (Compare protein to DNA sequence)
+wise:
+wise: Wise compares a protein sequence to a genomic DNA sequence,
+wise: allowing for introns and frameshifting errors.
+wise:
+wise: https://www.ebi.ac.uk/~birney/wise2/
+wise: https://www.ebi.ac.uk/Tools/psa/genewise/
+wise:
+wise:
+wise:
+wise:
diff --git a/academic/wise/wise.SlackBuild b/academic/wise/wise.SlackBuild
new file mode 100644
index 0000000000000..c4c9dc56c96fa
--- /dev/null
+++ b/academic/wise/wise.SlackBuild
@@ -0,0 +1,118 @@
+#!/bin/bash
+
+# Slackware build script for <wise>
+
+# Copyright 2023 Petar Petrov, slackalaxy@gmail.com
+# All rights reserved.
+#
+# Redistribution and use of this script, with or without modification, is
+# permitted provided that the following conditions are met:
+#
+# 1. Redistributions of this script must retain the above copyright
+#    notice, this list of conditions and the following disclaimer.
+#
+#  THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED
+#  WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+#  MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO
+#  EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+#  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+#  PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+#  OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+#  WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+#  OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+#  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+cd $(dirname $0) ; CWD=$(pwd)
+
+PRGNAM=wise
+VERSION=${VERSION:-2.4.1}
+BUILD=${BUILD:-1}
+TAG=${TAG:-_SBo}
+PKGTYPE=${PKGTYPE:-tgz}
+
+if [ -z "$ARCH" ]; then
+  case "$( uname -m )" in
+    i?86) ARCH=i586 ;;
+    arm*) ARCH=arm ;;
+       *) ARCH=$( uname -m ) ;;
+  esac
+fi
+
+if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then
+  echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE"
+  exit 0
+fi
+
+TMP=${TMP:-/tmp/SBo}
+PKG=$TMP/package-$PRGNAM
+OUTPUT=${OUTPUT:-/tmp}
+
+if [ "$ARCH" = "i586" ]; then
+  SLKCFLAGS="-O2 -march=i586 -mtune=i686"
+elif [ "$ARCH" = "i686" ]; then
+  SLKCFLAGS="-O2 -march=i686 -mtune=i686"
+elif [ "$ARCH" = "x86_64" ]; then
+  SLKCFLAGS="-O2 -fPIC"
+else
+  SLKCFLAGS="-O2"
+fi
+
+set -e
+
+rm -rf $PKG
+mkdir -p $TMP $PKG $OUTPUT
+cd $TMP
+rm -rf $PRGNAM-$VERSION
+tar xvf $CWD/${PRGNAM}_${VERSION}.orig.tar.gz
+cd $PRGNAM-$VERSION
+chown -R root:root .
+find -L . \
+ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
+  -o -perm 511 \) -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
+  -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
+
+patch -p1 -i $CWD/patches/01_welcome-csh.patch
+patch -p1 -i $CWD/patches/02_isnumber.patch
+patch -p1 -i $CWD/patches/03_doc-nodycache.patch
+patch -p1 -i $CWD/patches/04_wise2-pdflatex-update.patch
+patch -p1 -i $CWD/patches/05_glib2.patch
+patch -p1 -i $CWD/patches/06_getline.patch
+patch -p1 -i $CWD/patches/07_ld--as-needed.patch
+patch -p1 -i $CWD/patches/08_mayhem.patch
+patch -p1 -i $CWD/patches/09_dnal-add-return-statement.patch
+patch -p1 -i $CWD/patches/10_fix_path_to_data_files.patch
+patch -p1 -i $CWD/patches/11_consistent_manual_dates.patch
+patch -p1 -i $CWD/patches/spelling.patch
+patch -p1 -i $CWD/patches/cross.patch
+
+cd src
+CFLAGS="$SLKCFLAGS" \
+CXXFLAGS="$SLKCFLAGS" \
+make all
+
+mkdir -p $PKG/usr/bin
+mkdir -p $PKG/usr/share/$PRGNAM
+
+cd bin
+for i in * ; do
+	install -m 755 $i $PKG/usr/bin/$i
+done
+	
+cd ../..
+cp -a test_data wisecfg/* $PKG/usr/share/$PRGNAM
+
+find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
+  | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
+
+mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION
+cp -a \
+  LICENSE README docs/{*.tex,*.eps,papers} \
+  $PKG/usr/doc/$PRGNAM-$VERSION
+cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild
+
+mkdir -p $PKG/install
+cat $CWD/slack-desc > $PKG/install/slack-desc
+
+cd $PKG
+/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE
diff --git a/academic/wise/wise.info b/academic/wise/wise.info
new file mode 100644
index 0000000000000..1aafd927eeefb
--- /dev/null
+++ b/academic/wise/wise.info
@@ -0,0 +1,10 @@
+PRGNAM="wise"
+VERSION="2.4.1"
+HOMEPAGE="https://www.ebi.ac.uk/Tools/psa/genewise/"
+DOWNLOAD="http://deb.debian.org/debian/pool/main/w/wise/wise_2.4.1.orig.tar.gz"
+MD5SUM="9e90132c19a653831ce63b5af7f08302"
+DOWNLOAD_x86_64=""
+MD5SUM_x86_64=""
+REQUIRES=""
+MAINTAINER="Petar Petrov"
+EMAIL="slackalaxy@gmail.com"