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new package
Module Name: pkgsrc-wip
Committed By: zmsaif <zmsaif%nmsu.edu@localhost>
Pushed By: zmsaif
Date: Mon Jun 26 12:28:18 2017 -0600
Changeset: 3b86acd486bdb4021512153ce9ddf322090a8a42
Added Files:
wise3/DESCR
wise3/Makefile
wise3/PLIST
wise3/distinfo
wise3/patches/patch-corba_makefile
wise3/patches/patch-dnaindex_assembly_makefile
wise3/patches/patch-dnaindex_makefile
wise3/patches/patch-dynlibsrc_makefile
wise3/patches/patch-dynlibsrc_subseqhash.h
wise3/patches/patch-makefile
wise3/patches/patch-models_makefile
wise3/patches/patch-network_makefile
wise3/patches/patch-other__programs_makefile
wise3/patches/patch-snp_makefile
Log Message:
new package
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=3b86acd486bdb4021512153ce9ddf322090a8a42
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
wise3/DESCR | 0
wise3/Makefile | 40 +++++++
wise3/PLIST | 2 +
wise3/distinfo | 16 +++
wise3/patches/patch-corba_makefile | 27 +++++
wise3/patches/patch-dnaindex_assembly_makefile | 17 +++
wise3/patches/patch-dnaindex_makefile | 39 +++++++
wise3/patches/patch-dynlibsrc_makefile | 34 ++++++
wise3/patches/patch-dynlibsrc_subseqhash.h | 15 +++
wise3/patches/patch-makefile | 22 ++++
wise3/patches/patch-models_makefile | 138 +++++++++++++++++++++++++
wise3/patches/patch-network_makefile | 15 +++
wise3/patches/patch-other__programs_makefile | 15 +++
wise3/patches/patch-snp_makefile | 16 +++
14 files changed, 396 insertions(+)
diffs:
diff --git a/wise3/DESCR b/wise3/DESCR
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/wise3/Makefile b/wise3/Makefile
new file mode 100644
index 0000000000..bdd98d233a
--- /dev/null
+++ b/wise3/Makefile
@@ -0,0 +1,40 @@
+# $NetBSD$
+
+PKGNAME= wise-3
+DISTNAME= master
+CATEGORIES= biology
+MASTER_SITES= https://github.com/birney/wise3/archive/
+EXTRACT_SUFX= .zip
+
+MAINTAINER= INSERT_YOUR_MAIL_ADDRESS_HERE
+HOMEPAGE= http://github.com/birney/wise3/archive/
+COMMENT= TODO: Short description of the package
+#LICENSE= # TODO: (see mk/license.mk)
+
+.include "../../devel/glib/buildlink3.mk"
+.include "../../devel/glib2/buildlink3.mk"
+
+WRKSRC= ${WRKDIR}/wise3-master/src
+MAKE_FILE= makefile
+
+
+INSTALLATION_DIRS+= bin
+
+post-extract:
+ cd ${WRKSRC} && ${MAKE} clean
+ ${RM} -f ${WRKSRC}/models/porewise
+
+pre-build:
+ echo "XXX - the build will fail; that is ok; make install anyway"
+
+pre-install:
+ cd ${WRKSRC}/models && ${MAKE} porewise
+
+do-install:
+ ${INSTALL_PROGRAM} ${WRKSRC}/models/porewise ${DESTDIR}${PREFIX}/bin
+
+.include "../../mk/bsd.pkg.mk"
+
+xxx:
+ ${MAKE} clean-depends clean
+ ${MAKE}
diff --git a/wise3/PLIST b/wise3/PLIST
new file mode 100644
index 0000000000..05965e4636
--- /dev/null
+++ b/wise3/PLIST
@@ -0,0 +1,2 @@
+@comment $NetBSD$
+bin/porewise
diff --git a/wise3/distinfo b/wise3/distinfo
new file mode 100644
index 0000000000..56333ef883
--- /dev/null
+++ b/wise3/distinfo
@@ -0,0 +1,16 @@
+$NetBSD$
+
+SHA1 (master.zip) = 7a14d11aaf5117e7ee88fdd8630ff5e923e0af59
+RMD160 (master.zip) = 22d6e16dd5fa8bd7eaedb310c1d0f1fe84d6a3c4
+SHA512 (master.zip) = 40d2e5c41b3975eed13f27dc173505ed870756be751c862b03390d162334466447630c895cf1bfecaf9d47219c6004548efab1d77d011f8a29dd728511220877
+Size (master.zip) = 23258620 bytes
+SHA1 (patch-corba_makefile) = cb6b6477ebf2d415769d654c662b3b011de00c50
+SHA1 (patch-dnaindex_assembly_makefile) = 6a800b22cec96fc5f0a84bd234cff00ba61ab041
+SHA1 (patch-dnaindex_makefile) = b207b7892de1a0a1daaae1e19177d53b26754e85
+SHA1 (patch-dynlibsrc_makefile) = 2689b17b6bf6c4a8017e50c9c0a6aeaa34743331
+SHA1 (patch-dynlibsrc_subseqhash.h) = 17b704f3e7e889131f2260f4965d95570b027c33
+SHA1 (patch-makefile) = d3e3f04b8145d0303e3fe15ad8703b6f417b0031
+SHA1 (patch-models_makefile) = c9de700daf9b005477a54f93db73e7836e74a8a2
+SHA1 (patch-network_makefile) = 2677b51978f0a84fd7a2785b4444d76f1cacfb3c
+SHA1 (patch-other__programs_makefile) = d17504de849801e48d09d70543038ef5856cb5d4
+SHA1 (patch-snp_makefile) = 02a4401e3ac7a512fc423ddd05dcc7649b0bd9b4
diff --git a/wise3/patches/patch-corba_makefile b/wise3/patches/patch-corba_makefile
new file mode 100644
index 0000000000..d4a2e4ac0e
--- /dev/null
+++ b/wise3/patches/patch-corba_makefile
@@ -0,0 +1,27 @@
+$NetBSD$
+
+--- corba/makefile.orig 2014-06-19 15:10:23.000000000 +0000
++++ corba/makefile
+@@ -14,18 +14,18 @@ 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 `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 -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 -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 -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 -lm -lORBit -lIIOP -lORBitutil -lpthread
+
+ .c.o :
+ $(CC) $(CFLAGS) $(INCFLAGS) $?
diff --git a/wise3/patches/patch-dnaindex_assembly_makefile b/wise3/patches/patch-dnaindex_assembly_makefile
new file mode 100644
index 0000000000..bff27b0f66
--- /dev/null
+++ b/wise3/patches/patch-dnaindex_assembly_makefile
@@ -0,0 +1,17 @@
+$NetBSD$
+
+--- dnaindex/assembly/makefile.orig 2014-06-19 15:10:23.000000000 +0000
++++ dnaindex/assembly/makefile
+@@ -26,10 +26,10 @@ arraymatcher : arraymatcher.o assemblygr
+
+
+ CC = cc
+-CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags`
++CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/
+
+
+-LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm
++LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread -lm
+
+
+ .c.o :
diff --git a/wise3/patches/patch-dnaindex_makefile b/wise3/patches/patch-dnaindex_makefile
new file mode 100644
index 0000000000..753e6996fb
--- /dev/null
+++ b/wise3/patches/patch-dnaindex_makefile
@@ -0,0 +1,39 @@
+$NetBSD$
+
+--- dnaindex/makefile.orig 2014-06-19 15:10:23.000000000 +0000
++++ dnaindex/makefile
+@@ -26,17 +26,17 @@ ASSEMBLY_OBJ = kmer_assembly.o \
+ all: $(ASSEMBLY_OBJ)
+
+ find_single_kmers : find_single_kmers.o dnamapping.o
+- $(CC) -o find_single_kmers find_single_kmers.o dnamapping.o -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
++ $(CC) -o find_single_kmers find_single_kmers.o dnamapping.o -ldyna -lwisebase $(LFLAGS)
+
+ kwise : kwise.o $(ASSEMBLY_OBJ)
+- $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
++ $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS)
+
+ arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ)
+- $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
++ $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS)
+
+
+ findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ)
+- $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
++ $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS)
+
+ make_shotgun : make_shotgun.o shotgun.o
+ $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS)
+@@ -72,10 +72,10 @@ show_euler : show_euler.o eulerindex.o s
+ $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS)
+
+ CC = cc
+-CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags`
++CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/
+
+
+-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm
++LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread -lm
+
+
+ .c.o :
diff --git a/wise3/patches/patch-dynlibsrc_makefile b/wise3/patches/patch-dynlibsrc_makefile
new file mode 100644
index 0000000000..7ff52babaf
--- /dev/null
+++ b/wise3/patches/patch-dynlibsrc_makefile
@@ -0,0 +1,34 @@
+$NetBSD$
+
+--- dynlibsrc/makefile.orig 2014-06-19 15:10:23.000000000 +0000
++++ dynlibsrc/makefile
+@@ -85,9 +85,9 @@ DYNHELPEROBJ = packaln.o \
+ 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 = -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -O2 -c -DUNIX -I../base/
++#CFLAGS = -Wall -g3 -pg -DPTHREAD -O2 -c -DUNIX -I../base/
++#CFLAGS = -O2 -c -pthread -DUNIX -I../base/
+ #CFLAGS = -O -c -DUNIX -DNOERROR -I../base/
+ LFLAGS = -g -L../base/ -lm
+ AR_OPTIONS = ru
+@@ -149,13 +149,13 @@ test_shadowindex : test_shadowindex.o sh
+ $(CC) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm
+
+ test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a
+- $(CC) -g -o test_seqhash `glib-config --libs` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm
++ $(CC) -g -o test_seqhash 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) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm
+
+ 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`
++ $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm
+
+
+ testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o
diff --git a/wise3/patches/patch-dynlibsrc_subseqhash.h b/wise3/patches/patch-dynlibsrc_subseqhash.h
new file mode 100644
index 0000000000..61a8e4ac9b
--- /dev/null
+++ b/wise3/patches/patch-dynlibsrc_subseqhash.h
@@ -0,0 +1,15 @@
+$NetBSD$
+
+--- dynlibsrc/subseqhash.h.orig 2014-06-19 15:10:23.000000000 +0000
++++ dynlibsrc/subseqhash.h
+@@ -6,8 +6,8 @@ extern "C" {
+ #include "sequence.h"
+ #include "seqlookup.h"
+ #include "linkedlist_lookpos.h"
+-#include "glib.h"
+-
++#include "/home/zmsaif/pkg-2017Q1/include/glib/glib-1.2/glib.h"
++#include "/home/zmsaif/pkg-2017Q1/include/glib/glib-2.0/glib.h"
+ #include "wisebase.h"
+
+
diff --git a/wise3/patches/patch-makefile b/wise3/patches/patch-makefile
new file mode 100644
index 0000000000..0be95823c8
--- /dev/null
+++ b/wise3/patches/patch-makefile
@@ -0,0 +1,22 @@
+$NetBSD$
+
+--- makefile.orig 2014-06-19 15:10:23.000000000 +0000
++++ makefile
+@@ -22,7 +22,7 @@
+ # Change the cc line to gcc if you get compiler errors
+ # Most likely you have a non ANSI C compiler
+ # CC = /opt/intel_cc_80/bin/icc
+-CC = cc
++CC = gcc
+
+ # These are the CFLAGS to use. These days Wise2 is inherently
+ # pthreaded, and everything is compiled with threads. However
+@@ -37,7 +37,7 @@ CC = cc
+ # CFLAGS = -c -O3 -pthread `glib-config --cflags`
+
+ # normal linux/bsd/mac flags
+-CFLAGS = -c -O3 `glib-config --cflags`
++CFLAGS = -c -O3
+
+
+ EXTRALIBS = -lm
diff --git a/wise3/patches/patch-models_makefile b/wise3/patches/patch-models_makefile
new file mode 100644
index 0000000000..b641432905
--- /dev/null
+++ b/wise3/patches/patch-models_makefile
@@ -0,0 +1,138 @@
+$NetBSD$
+
+--- models/makefile.orig 2014-06-19 15:10:23.000000000 +0000
++++ models/makefile
+@@ -110,10 +110,10 @@ gw21 : $(MODELOBJ) $(GENEWISEMODEL) gene
+ 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 -lwisebase ../dynlibsrc/matrix.o $(LFLAGS)
+
+ 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 $(LFLAGS) -lhmmer -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
+@@ -129,10 +129,10 @@ motifdiff : motifdiff.o transfactor.o tr
+
+
+ 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 -lwisebase $(LFLAGS)
+
+ prob2bits : prob2bits.o
+- $(CC) -o prob2bits $(LFLAGS) -ldyna_glib -ldyna -lwisebase
++ $(CC) -o prob2bits $(LFLAGS) -ldyna -lwisebase
+
+ quick :
+ cc -O -c -I../dynlibsrc/ -I../base/ genewise6.c
+@@ -179,74 +179,74 @@ fivestarscan.o : fivestarscan.c
+ $(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) $(LFLAGS) -lhmmer -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 $(LFLAGS) -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 $(LFLAGS) -ldyna -lwisebase $(EXTRALIBS)
+
+ foldback : foldback.o foldbackmat.o seqaligndisplay.o
+- $(CC) -o foldback foldback.o foldbackmat.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
++ $(CC) -o foldback foldback.o foldbackmat.o seqaligndisplay.o $(LFLAGS) -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 $(LFLAGS) -ldyna -lwisebase $(EXTRALIBS)
+
+ scanwisep.o : scanwisep.c
+- $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $?
++ $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott $?
+
+ hsp2aln_sw.o : hsp2aln_sw.c
+- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
++ $(CC) $(CFLAGS) $(INCFLAGS) $?
+
+ 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 $(LFLAGS) -L../external/mott -L/usr/local/mysql/lib -ldyna ott -lwisebase -lmysqlclient -lm $(EXTRALIBS) -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 $(LFLAGS) -L../external/mott -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 $(LFLAGS) -L../external/mott -L../socket -lmott -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 $(LFLAGS) -L../external/mott -L../socket -lmott -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 $(LFLAGS) -L../external/mott -lmott -ldyna -lwisebase $(EXTRALIBS) -lpthread
+
+ test_gwhsp : test_gwhsp.o genewisehsp.o
+- $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread
++ $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna -lwisebase $(EXTRALIBS) -lpthread
+
+ localcishit.o : localcishit.c
+- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
++ $(CC) $(CFLAGS) $(INCFLAGS) $?
+
+ promoterwise.o : promoterwise.c
+- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
++ $(CC) $(CFLAGS) $(INCFLAGS) $?
+
+ 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 -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread
++ $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna -lwisebase $(EXTRALIBS) -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 -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread
++ $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna -lwisebase $(EXTRALIBS) -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 -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread
++ $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna -lwisebase $(EXTRALIBS) -lpthread
+
+ dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o
+ $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LFLAGS) -ldyna -lwisebase -lpthread
+@@ -355,11 +355,11 @@ HMMER_DEFINE =
+ CC = cc
+ #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/
+ #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I.
+-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags`
+-#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags`
++CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread
++#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/
+ #LFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/
+
+-LFLAGS = -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs`
++LFLAGS = -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread
+ AR_OPTIONS = ru
+
+ RANLIB_NEEDED = 0
diff --git a/wise3/patches/patch-network_makefile b/wise3/patches/patch-network_makefile
new file mode 100644
index 0000000000..a46afc1aeb
--- /dev/null
+++ b/wise3/patches/patch-network_makefile
@@ -0,0 +1,15 @@
+$NetBSD$
+
+--- network/makefile.orig 2014-06-19 15:10:23.000000000 +0000
++++ 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 = -O2 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex
++LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm
+ AR_OPTIONS = ru
+
+ RANLIB_NEEDED = 0
diff --git a/wise3/patches/patch-other__programs_makefile b/wise3/patches/patch-other__programs_makefile
new file mode 100644
index 0000000000..c3a82b3d34
--- /dev/null
+++ b/wise3/patches/patch-other__programs_makefile
@@ -0,0 +1,15 @@
+$NetBSD$
+
+--- other_programs/makefile.orig 2014-06-19 15:10:23.000000000 +0000
++++ other_programs/makefile
+@@ -3,8 +3,8 @@
+ .SUFFIXES : .dy
+
+ CC = cc
+-CFLAGS = -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `glib-config --cflags`
+-LFLAGS = -g -L../base/ -L../dynlibsrc -lm `glib-config --libs`
++CFLAGS = -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc
++LFLAGS = -g -L../base/ -L../dynlibsrc -lm
+ AR_OPTIONS = ru
+
+ RANLIB_NEEDED = 0
diff --git a/wise3/patches/patch-snp_makefile b/wise3/patches/patch-snp_makefile
new file mode 100644
index 0000000000..eacc337685
--- /dev/null
+++ b/wise3/patches/patch-snp_makefile
@@ -0,0 +1,16 @@
+$NetBSD$
+
+--- snp/makefile.orig 2014-06-19 15:10:23.000000000 +0000
++++ 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 = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread
+
+-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm
++LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread -lpthread -lm
+ AR_OPTIONS = ru
+
+ RANLIB_NEEDED = 0
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