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authorRobin H. Johnson <robbat2@gentoo.org>2015-08-08 13:49:04 -0700
committerRobin H. Johnson <robbat2@gentoo.org>2015-08-08 17:38:18 -0700
commit56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch)
tree3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-biology/wise/files
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proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
Diffstat (limited to 'sci-biology/wise/files')
-rw-r--r--sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch301
-rw-r--r--sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch407
-rw-r--r--sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch302
-rw-r--r--sci-biology/wise/files/wise-api.tex.patch38
-rw-r--r--sci-biology/wise/files/wise-env1
5 files changed, 1049 insertions, 0 deletions
diff --git a/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch b/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch
new file mode 100644
index 00000000000..1ec433f1922
--- /dev/null
+++ b/sci-biology/wise/files/wise-2.2.0-glibc-2.10.patch
@@ -0,0 +1,301 @@
+diff -ur wise2.2.0.orig/src/HMMer2/sqio.c wise2.2.0/src/HMMer2/sqio.c
+--- wise2.2.0.orig/src/HMMer2/sqio.c 2001-06-18 16:59:51.000000000 +0300
++++ wise2.2.0/src/HMMer2/sqio.c 2009-08-05 22:39:04.000000000 +0300
+@@ -213,7 +213,7 @@
+ }
+ }
+
+-/* Function: getline()
++/* Function: get_line()
+ * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis]
+ *
+ * Purpose: read a line from a sequence file into V->sbuffer.
+@@ -229,7 +229,7 @@
+ * Returns: (void)
+ */
+ static void
+-getline(struct ReadSeqVars *V)
++get_line(struct ReadSeqVars *V)
+ {
+ char *cp;
+
+@@ -299,7 +299,7 @@
+ V->seqlen = 0;
+ if (addfirst) addseq(V->sbuffer, V);
+ do {
+- getline(V);
++ get_line(V);
+ /* feof() alone is a bug; files not necessarily \n terminated */
+ if (*(V->sbuffer) == '\0' && feof(V->f))
+ done = TRUE;
+@@ -327,7 +327,7 @@
+ char *sptr;
+ /* load first line of entry */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+- getline(V);
++ get_line(V);
+ if (feof(V->f)) return;
+
+ if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
+@@ -336,7 +336,7 @@
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
+ }
+ do {
+- getline(V);
++ get_line(V);
+ if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
+ SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
+ else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
+@@ -345,7 +345,7 @@
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
+ }
+ } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
+- getline(V); /* skip next line, coords */
++ get_line(V); /* skip next line, coords */
+
+ readLoop(0, endPIR, V);
+
+@@ -359,7 +359,7 @@
+ /* get next line
+ */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -377,7 +377,7 @@
+ char *nm;
+ /* position past ';' comments */
+ do {
+- getline(V);
++ get_line(V);
+ } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
+
+ if (!feof(V->f))
+@@ -389,7 +389,7 @@
+ }
+
+ while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
+- getline(V);
++ get_line(V);
+ }
+
+ static int
+@@ -411,7 +411,7 @@
+ if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
+ }
+- getline(V);
++ get_line(V);
+ }
+
+ if (! feof(V->f))
+@@ -420,7 +420,7 @@
+ /* load next line
+ */
+ while ((!feof(V->f)) && (*V->sbuffer != ';'))
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -438,7 +438,7 @@
+ int in_definition;
+
+ while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
+- getline(V);
++ get_line(V);
+
+ if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
+ {
+@@ -449,7 +449,7 @@
+ in_definition = FALSE;
+ while (! feof(V->f))
+ {
+- getline(V);
++ get_line(V);
+ if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
+ {
+ if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
+@@ -482,11 +482,11 @@
+
+
+ while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
+- getline(V);
++ get_line(V);
+ /* SRE: V->s now holds "//", so sequential
+ reads are wedged: fixed Tue Jul 13 1993 */
+ while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer)
+- getline(V);
++ get_line(V);
+ }
+
+ static int
+@@ -515,7 +515,7 @@
+ Die("bogus GCGdata format? %s", V->sbuffer);
+
+ /* second line contains free text description */
+- getline(V);
++ get_line(V);
+ SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
+
+ if (binary) {
+@@ -535,7 +535,7 @@
+ else readLoop(0, endGCGdata, V);
+
+ while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+- getline(V);
++ get_line(V);
+ }
+
+ static int
+@@ -555,12 +555,12 @@
+ if ((sptr = strtok(NULL, "\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
+ /* workaround for long NCBI NR lines */
+- while (V->longline && ! feof(V->f)) getline(V);
++ while (V->longline && ! feof(V->f)) get_line(V);
+
+ readLoop(0, endPearson, V);
+
+ while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -587,7 +587,7 @@
+
+ /* make sure we have first line */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
+- getline(V);
++ get_line(V);
+
+ if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
+ {
+@@ -596,7 +596,7 @@
+ }
+
+ do {
+- getline(V);
++ get_line(V);
+ if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
+ {
+ if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
+@@ -620,7 +620,7 @@
+
+ /* load next record's ID line */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -636,7 +636,7 @@
+ {
+ char *sptr;
+
+- getline(V); /*s == "seqLen seqid string..."*/
++ get_line(V); /*s == "seqLen seqid string..."*/
+
+ if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -647,7 +647,7 @@
+ readLoop(0, endZuker, V);
+
+ while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
+- getline(V);
++ get_line(V);
+ }
+
+ static void
+@@ -669,7 +669,7 @@
+
+ do {
+ done = feof(V->f);
+- getline(V);
++ get_line(V);
+ if (! done) addseq(V->sbuffer, V);
+ } while (!done);
+ }
+@@ -681,7 +681,7 @@
+ char *sptr;
+ int dostruc = FALSE;
+
+- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V);
+
+ if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -689,7 +689,7 @@
+ /*CONSTCOND*/
+ while (1)
+ {
+- getline(V);
++ get_line(V);
+ if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
+
+ if (strncmp(V->sbuffer, "SRC ", 4) == 0)
+@@ -721,14 +721,14 @@
+ while (1)
+ {
+ /* sequence line */
+- getline(V);
++ get_line(V);
+ if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0)
+ break;
+ addseq(V->sbuffer, V);
+ /* structure line */
+ if (dostruc)
+ {
+- getline(V);
++ get_line(V);
+ if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
+ addstruc(V->sbuffer, V);
+ }
+@@ -736,7 +736,7 @@
+
+
+ while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -816,7 +816,7 @@
+
+ /* Load the first line.
+ */
+- getline(dbfp);
++ get_line(dbfp);
+
+ return dbfp;
+ }
+@@ -833,7 +833,7 @@
+ Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
+
+ fseek(sqfp->f, offset, SEEK_SET);
+- getline(sqfp);
++ get_line(sqfp);
+ }
+
+
+@@ -853,7 +853,7 @@
+ if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
+ else {
+ rewind(sqfp->f);
+- getline(sqfp);
++ get_line(sqfp);
+ }
+ }
+
+@@ -949,7 +949,7 @@
+ do { /* skip leading comments on GCG file */
+ gotuw = (strstr(V->sbuffer,"..") != NULL);
+ if (gotuw) readUWGCG(V);
+- getline(V);
++ get_line(V);
+ } while (! feof(V->f));
+ break;
+
diff --git a/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch b/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch
new file mode 100644
index 00000000000..d3c17098105
--- /dev/null
+++ b/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch
@@ -0,0 +1,407 @@
+diff --git a/src/base/makefile b/src/base/makefile
+index 4620f19..a84e2c7 100644
+--- a/src/base/makefile
++++ b/src/base/makefile
+@@ -20,8 +20,8 @@ NBASEOBJ = wiseconfig.o \
+
+
+ #CFLAGS = -c -g -DUNIX -DWISE_MEMORY_WATCH
+-CFLAGS = -c -O2 -DUNIX -pthread
+-LFLAGS = -g -lm
++CFLAGS += -c -DUNIX -pthread
++LFLAGS = -lm
+ DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D
+ AR_OPTIONS = ru
+
+diff --git a/src/corba/makefile b/src/corba/makefile
+index df3dd78..237a1ba 100644
+--- a/src/corba/makefile
++++ b/src/corba/makefile
+@@ -1,10 +1,10 @@
+
+
+-CC = cc
++CC += gcc
+ INCFLAGS = -I../base/ -I../dynlibsrc
+ #gCFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/
+-#CFLAGS = -O2 -c -DUNIX -I../base/ `glib-config --cflags` -I/usr/local/include/orbit-1.0/
+-CFLAGS = -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client`
++#CFLAGS = -O2 -c -DUNIX -I../base/ `pkg-config glib-2.0 --cflags` -I/usr/local/include/orbit-1.0/
++CFLAGS += -pthread -c -DUNIX -I../base/ -I../dynlibsrc `pkg-config ORBit-2.0 --cflags`
+ LFLAGS = -L../base/ -lm -lpthread
+ AR_OPTIONS = ru
+
+@@ -14,18 +14,18 @@ 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) $(CFLAGS) $(LDFLAGS) -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
+
+ scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o
+- cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
++ $(CC) $(CFLAGS) $(LDFLAGS) -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
+
+
+ test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o
+- cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
++ $(CC) $(CFLAGS) $(LDFLAGS) -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
+
+
+ test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o
+- cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
++ $(CC) $(CFLAGS) $(LDFLAGS) -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
+
+ .c.o :
+ $(CC) $(CFLAGS) $(INCFLAGS) $?
+diff --git a/src/dnaindex/assembly/makefile b/src/dnaindex/assembly/makefile
+index ef3334a..3a0bc2a 100644
+--- a/src/dnaindex/assembly/makefile
++++ b/src/dnaindex/assembly/makefile
+@@ -26,10 +26,10 @@ arraymatcher : arraymatcher.o assemblygraph.o assemblystats.o basegraph.o
+
+
+ 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/ `pkg-config glib-2.0 --cflags`
+
+
+-LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm
++LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm
+
+
+ .c.o :
+diff --git a/src/dnaindex/makefile b/src/dnaindex/makefile
+index 285e6a0..8c6a0dc 100644
+--- 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 $(LFLAGS) `glib-config --libs`
++ $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs`
+
+ arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ)
+- $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
++ $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs`
+
+
+ findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ)
+- $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
++ $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs`
+
+ make_shotgun : make_shotgun.o shotgun.o
+ $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS)
+@@ -70,10 +70,10 @@ show_euler : show_euler.o eulerindex.o singleseqspace.o
+ $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS)
+
+ CC = cc
+-CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags`
++CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags`
+
+
+-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm
++LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm
+
+
+ .c.o :
+diff --git a/src/dynlibsrc/makefile b/src/dynlibsrc/makefile
+index d1d77af..cad8900 100644
+--- a/src/dynlibsrc/makefile
++++ b/src/dynlibsrc/makefile
+@@ -78,11 +78,11 @@ DYNHELPEROBJ = packaln.o \
+
+
+
+-CC = cc
++CC ?= gcc
+ INCFLAGS = -I../base/
+ #CFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/
+-CFLAGS = -Wall -g3 -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags`
+-#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `glib-config --cflags`
++CFLAGS += -DPTHREAD -c -DUNIX -I../base/ `pkg-config glib-2.0 --cflags`
++#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `pkg-config glib-2.0 --cflags`
+ #CFLAGS = -O -c -DUNIX -DNOERROR -I../base/
+ LFLAGS = -g -L../base/ -lm
+ AR_OPTIONS = ru
+@@ -144,13 +144,13 @@ 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
+
+ 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 `pkg-config glib-2.0 --libs` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm
+
+ test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o
+- $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs`
++ $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs`
+
+ test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o
+- $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs`
++ $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs`
+
+
+ testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o
+diff --git a/src/external/mott/makefile b/src/external/mott/makefile
+index 8d7c1d4..940c438 100644
+--- a/src/external/mott/makefile
++++ b/src/external/mott/makefile
+@@ -14,10 +14,10 @@ libmott.a : mott_api.o gaplib.o wise2_mott_bridge.o
+ wise2_mott_bridge.o : wise2_mott_bridge.c
+ $(CC) $(CFLAGS) -I../../dynlibsrc -I../../base wise2_mott_bridge.c
+
+-CC = cc
++CC ?= gcc
+
+-CFLAGS = -Wall -g3 -DPTHREAD -O2 -c
+-LFLAGS = -g -L../base/ -lm
++CFLAGS += -DPTHREAD -c
++LFLAGS = -L../base/ -lm
+ AR_OPTIONS = ru
+
+
+diff --git a/src/makefile b/src/makefile
+index bdff4ff..0d7c871 100644
+--- a/src/makefile
++++ b/src/makefile
+@@ -26,12 +26,12 @@
+
+ # Change the cc line to gcc if you get compiler errors
+ # Most likely you have a non ANSI C compiler
+-CC ?= cc
++CC ?= gcc
+
+ # These are the CFLAGS to use. These days Wise2 is inherently
+ # pthreaded, and everything is compiled with threads. More
+ # info on running threads can be found in the documentation
+-CFLAGS = -c -pthread -O2 `glib-config --cflags`
++CFLAGS += -c -pthread `pkg-config glib-2.0 --cflags`
+
+
+
+diff --git a/src/models/makefile b/src/models/makefile
+index f518d0c..a297eff 100644
+--- a/src/models/makefile
++++ b/src/models/makefile
+@@ -50,6 +50,8 @@ NEWG = geneparser21.o \
+ proteinsw.o \
+ estquick3.o
+
++EXTRALIBS += `pkg-config glib-2.0 --libs`
++
+ all : dnal psw pswdb dba estwise genewise genewisedb estwisedb genomewise sywise pseudowise promoterwise scanwisep scanwisep_wiseserver libmodel.a
+
+ libmodel.a : $(NEWG)
+@@ -180,7 +182,7 @@ 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 -lm
++ $(CC) $(LDFLAGS) -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm
+
+ testdna : testdna.o dnaalign.o seqaligndisplay.o
+ $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
+@@ -192,10 +194,10 @@ 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 -lm $(EXTRALIBS)
+
+ scanwisep.o : scanwisep.c
+- $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $?
++ $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config glib-2.0 --cflags` $?
+
+ hsp2aln_sw.o : hsp2aln_sw.c
+- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
+
+ scanwisep_mysql.o : scanwisep.c
+ $(CC) $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c
+@@ -212,10 +214,10 @@ scanwisep_corba : scanwisep_corba.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.
+
+
+ scanwisep_wiseserver.o : scanwisep.c
+- $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c
++ $(CC) $(LDFLAGS) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c `pkg-config glib-2.0 --libs`
+
+ scanwisep_wiseserver : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
+- $(CC) -o scanwisep_wiseserver scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm $(EXTRALIBS) -lpthread
++ $(CC) -o scanwisep_wiseserver scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm $(EXTRALIBS) -lpthread `pkg-config glib-2.0 --libs`
+
+ scanwisep_compress.o : scanwisep.c
+ $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c
+@@ -226,25 +228,25 @@ scanwisep_compress : scanwisep_compress.o seqaligndisplay.o proteinsw.o sw_wrap.
+
+
+ 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 -lm $(EXTRALIBS) `glib-config --libs` -lpthread
++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
+
+ test_gwhsp : test_gwhsp.o genewisehsp.o
+- $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread
++ $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
+
+ localcishit.o : localcishit.c
+- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
+
+ promoterwise.o : promoterwise.c
+- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
+
+ promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o
+- $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread
++ $(CC) $(LDFLAGS) -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 -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
+
+ test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o
+- $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread
++ $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
+
+ promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o
+- $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread
++ $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
+
+ dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o
+ $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm -lpthread
+@@ -275,66 +277,66 @@ makerandomdb : makerandomdb.o
+ $(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
+
+ genewise : genewise.o $(NEWG)
+- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs`
+
+ cdnawise : cdnawise.o $(NEWG) cdnawise10.o
+- $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(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 -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(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 -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(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 -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(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 -lm
++ $(CC) $(LDFLAGS) -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm
+
+
+ efgw : genewise.o $(NEWG)
+- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence
++ $(CC) $(LDFLAGS) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence
+
+
+ genewisedb : genewisedb.o $(NEWG)
+- $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs`
+
+ estwisedb : estwisedb.o $(NEWG)
+- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs`
+
+ edb : estwisedb.o $(NEWG)
+- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence
++ $(CC) $(LDFLAGS) -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) -lefence
+
+ estwise : estwise.o $(NEWG)
+- $(CC) -g -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs`
+
+
+ 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 -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(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 -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(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 -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(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 -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(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 -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(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 -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
+
+ pseudowise : pseudowise.o pseudowise7.o $(NEWG)
+- $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `pkg-config glib-2.0 --libs`
+
+ clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o
+- $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
++ $(CC) $(LDFLAGS) -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
+
+
+ HMMER_LIBS = ../HMMer2/
+@@ -345,11 +347,11 @@ HMMER_DEFINE =
+ CC = cc
+ #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/
+ #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I.
+-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags`
+-#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags`
++CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0 --cflags`
++#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags`
+ #LFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/
+
+-LFLAGS = -g -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs`
++LFLAGS = -g -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config glib-2.0 --libs`
+ AR_OPTIONS = ru
+
+ RANLIB_NEEDED = 0
+diff --git a/src/network/makefile b/src/network/makefile
+index 303c2da..e607310 100644
+--- a/src/network/makefile
++++ b/src/network/makefile
+@@ -3,8 +3,8 @@
+
+ CC = cc
+ INCFLAGS = -I../base/ -I../socket -I../dynlibsrc -I../dnaindex
+-CFLAGS = -O2 -g3 -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 -g3 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config glib-2.0 --cflags`
++LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config glib-2.0 --libs`
+ AR_OPTIONS = ru
+
+ RANLIB_NEEDED = 0
+diff --git a/src/snp/makefile b/src/snp/makefile
+index ccf750a..2b83c43 100644
+--- a/src/snp/makefile
++++ b/src/snp/makefile
+@@ -2,12 +2,12 @@
+ .SUFFIXES : .dy
+
+
+-CC = cc
++CC ?= gcc
+ #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/
+ #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I.
+-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags`
++CFLAGS += -c -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config glib-2.0 --cflags`
+
+-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm
++LFLAGS = -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lpthread -lm
+ AR_OPTIONS = ru
+
+ RANLIB_NEEDED = 0
+@@ -16,7 +16,7 @@ RANLIB_NEEDED = 0
+ $(CC) $(CFLAGS) $(INCFLAGS) $?
+
+ test_est : test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o
+- $(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS)
++ $(CC) $(LDFLAGS) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS)
+
+ INCFLAGS = -I../base/ -I../dynlibsrc/
+ DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn
diff --git a/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch b/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch
new file mode 100644
index 00000000000..42af0c7e849
--- /dev/null
+++ b/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch
@@ -0,0 +1,302 @@
+diff --git a/src/HMMer2/sqio.c b/src/HMMer2/sqio.c
+index 5889e7d..bc95629 100644
+--- a/src/HMMer2/sqio.c
++++ b/src/HMMer2/sqio.c
+@@ -213,7 +213,7 @@ readline(FILE *f, char *s)
+ }
+ }
+
+-/* Function: getline()
++/* Function: get_line()
+ * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis]
+ *
+ * Purpose: read a line from a sequence file into V->sbuffer.
+@@ -229,7 +229,7 @@ readline(FILE *f, char *s)
+ * Returns: (void)
+ */
+ static void
+-getline(struct ReadSeqVars *V)
++get_line(struct ReadSeqVars *V)
+ {
+ char *cp;
+
+@@ -299,7 +299,7 @@ readLoop(int addfirst, int (*endTest)(char *,int *), struct ReadSeqVars *V)
+ V->seqlen = 0;
+ if (addfirst) addseq(V->sbuffer, V);
+ do {
+- getline(V);
++ get_line(V);
+ /* feof() alone is a bug; files not necessarily \n terminated */
+ if (*(V->sbuffer) == '\0' && feof(V->f))
+ done = TRUE;
+@@ -327,7 +327,7 @@ readPIR(struct ReadSeqVars *V)
+ char *sptr;
+ /* load first line of entry */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+- getline(V);
++ get_line(V);
+ if (feof(V->f)) return;
+
+ if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
+@@ -336,7 +336,7 @@ readPIR(struct ReadSeqVars *V)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
+ }
+ do {
+- getline(V);
++ get_line(V);
+ if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
+ SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
+ else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
+@@ -345,7 +345,7 @@ readPIR(struct ReadSeqVars *V)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
+ }
+ } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
+- getline(V); /* skip next line, coords */
++ get_line(V); /* skip next line, coords */
+
+ readLoop(0, endPIR, V);
+
+@@ -359,7 +359,7 @@ readPIR(struct ReadSeqVars *V)
+ /* get next line
+ */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -377,7 +377,7 @@ readIG(struct ReadSeqVars *V)
+ char *nm;
+ /* position past ';' comments */
+ do {
+- getline(V);
++ get_line(V);
+ } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
+
+ if (!feof(V->f))
+@@ -389,7 +389,7 @@ readIG(struct ReadSeqVars *V)
+ }
+
+ while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
+- getline(V);
++ get_line(V);
+ }
+
+ static int
+@@ -411,7 +411,7 @@ readStrider(struct ReadSeqVars *V)
+ if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
+ }
+- getline(V);
++ get_line(V);
+ }
+
+ if (! feof(V->f))
+@@ -420,7 +420,7 @@ readStrider(struct ReadSeqVars *V)
+ /* load next line
+ */
+ while ((!feof(V->f)) && (*V->sbuffer != ';'))
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -438,7 +438,7 @@ readGenBank(struct ReadSeqVars *V)
+ int in_definition;
+
+ while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
+- getline(V);
++ get_line(V);
+
+ if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
+ {
+@@ -449,7 +449,7 @@ readGenBank(struct ReadSeqVars *V)
+ in_definition = FALSE;
+ while (! feof(V->f))
+ {
+- getline(V);
++ get_line(V);
+ if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
+ {
+ if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
+@@ -482,11 +482,11 @@ readGenBank(struct ReadSeqVars *V)
+
+
+ while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
+- getline(V);
++ get_line(V);
+ /* SRE: V->s now holds "//", so sequential
+ reads are wedged: fixed Tue Jul 13 1993 */
+ while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer)
+- getline(V);
++ get_line(V);
+ }
+
+ static int
+@@ -515,7 +515,7 @@ readGCGdata(struct ReadSeqVars *V)
+ Die("bogus GCGdata format? %s", V->sbuffer);
+
+ /* second line contains free text description */
+- getline(V);
++ get_line(V);
+ SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
+
+ if (binary) {
+@@ -535,7 +535,7 @@ readGCGdata(struct ReadSeqVars *V)
+ else readLoop(0, endGCGdata, V);
+
+ while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+- getline(V);
++ get_line(V);
+ }
+
+ static int
+@@ -555,12 +555,12 @@ readPearson(struct ReadSeqVars *V)
+ if ((sptr = strtok(NULL, "\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
+ /* workaround for long NCBI NR lines */
+- while (V->longline && ! feof(V->f)) getline(V);
++ while (V->longline && ! feof(V->f)) get_line(V);
+
+ readLoop(0, endPearson, V);
+
+ while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -587,7 +587,7 @@ readEMBL(struct ReadSeqVars *V)
+
+ /* make sure we have first line */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
+- getline(V);
++ get_line(V);
+
+ if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
+ {
+@@ -596,7 +596,7 @@ readEMBL(struct ReadSeqVars *V)
+ }
+
+ do {
+- getline(V);
++ get_line(V);
+ if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
+ {
+ if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
+@@ -620,7 +620,7 @@ readEMBL(struct ReadSeqVars *V)
+
+ /* load next record's ID line */
+ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -636,7 +636,7 @@ readZuker(struct ReadSeqVars *V)
+ {
+ char *sptr;
+
+- getline(V); /*s == "seqLen seqid string..."*/
++ get_line(V); /*s == "seqLen seqid string..."*/
+
+ if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -647,7 +647,7 @@ readZuker(struct ReadSeqVars *V)
+ readLoop(0, endZuker, V);
+
+ while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
+- getline(V);
++ get_line(V);
+ }
+
+ static void
+@@ -669,7 +669,7 @@ readUWGCG(struct ReadSeqVars *V)
+
+ do {
+ done = feof(V->f);
+- getline(V);
++ get_line(V);
+ if (! done) addseq(V->sbuffer, V);
+ } while (!done);
+ }
+@@ -681,7 +681,7 @@ readSquid(struct ReadSeqVars *V)
+ char *sptr;
+ int dostruc = FALSE;
+
+- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V);
+
+ if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -689,7 +689,7 @@ readSquid(struct ReadSeqVars *V)
+ /*CONSTCOND*/
+ while (1)
+ {
+- getline(V);
++ get_line(V);
+ if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
+
+ if (strncmp(V->sbuffer, "SRC ", 4) == 0)
+@@ -721,14 +721,14 @@ readSquid(struct ReadSeqVars *V)
+ while (1)
+ {
+ /* sequence line */
+- getline(V);
++ get_line(V);
+ if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0)
+ break;
+ addseq(V->sbuffer, V);
+ /* structure line */
+ if (dostruc)
+ {
+- getline(V);
++ get_line(V);
+ if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
+ addstruc(V->sbuffer, V);
+ }
+@@ -736,7 +736,7 @@ readSquid(struct ReadSeqVars *V)
+
+
+ while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
+- getline(V);
++ get_line(V);
+ }
+
+
+@@ -816,7 +816,7 @@ SeqfileOpen(char *filename, int format, char *env)
+
+ /* Load the first line.
+ */
+- getline(dbfp);
++ get_line(dbfp);
+
+ return dbfp;
+ }
+@@ -833,7 +833,7 @@ SeqfilePosition(SQFILE *sqfp, long offset)
+ Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
+
+ fseek(sqfp->f, offset, SEEK_SET);
+- getline(sqfp);
++ get_line(sqfp);
+ }
+
+
+@@ -853,7 +853,7 @@ SeqfileRewind(SQFILE *sqfp)
+ if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
+ else {
+ rewind(sqfp->f);
+- getline(sqfp);
++ get_line(sqfp);
+ }
+ }
+
+@@ -949,7 +949,7 @@ ReadSeq(SQFILE *V, int format, char **ret_seq, SQINFO *sqinfo)
+ do { /* skip leading comments on GCG file */
+ gotuw = (strstr(V->sbuffer,"..") != NULL);
+ if (gotuw) readUWGCG(V);
+- getline(V);
++ get_line(V);
+ } while (! feof(V->f));
+ break;
+
diff --git a/sci-biology/wise/files/wise-api.tex.patch b/sci-biology/wise/files/wise-api.tex.patch
new file mode 100644
index 00000000000..827ce4cdfa7
--- /dev/null
+++ b/sci-biology/wise/files/wise-api.tex.patch
@@ -0,0 +1,38 @@
+--- api.tex.old 2005-03-06 11:31:59.862760952 -0500
++++ api.tex 2005-03-06 11:42:31.375756384 -0500
+@@ -204,7 +204,7 @@
+ \item Build two Sequence objects, from a file or strings (\ref{object_Sequence})
+ \item Optionally convert the Sequence objects into Protein objects (\ref{object_Protein}). This ensures you have proteins
+ \item Read in the comparison matrix using CompMat (\ref{object_CompMat})
+-\item Use one of the algorithm calls in sw_wrap module (\ref{module_sw_wrap})
++\item Use one of the algorithm calls in sw\_wrap module (\ref{module_sw_wrap})
+ \item Show the alignment using a call in the seqaligndisaply module (\ref{module_seqaligndisplay})
+ \end{itemize}
+
+@@ -213,7 +213,7 @@
+ \item Read in a sequence object and convert it to a protein object (\ref{object_Protein},\ref{object_Sequence})
+ \item Make a protein database from the single protein object (\ref{object_ProteinDB})
+ \item Make a protein database from a single fasta file (\ref{object_ProteinDB})
+-\item Using one of the calls to the sw_wrap module, make a Hscore object (\ref{module_sw_wrap})
++\item Using one of the calls to the sw\_wrap module, make a Hscore object (\ref{module_sw_wrap})
+ \item Show the Hscore object using a show function (\ref{object_Hscore})
+ \item Retrieve individual protein objects from the database by taking out the
+ DataEntry objects (\ref{object_DataEntry}) and passing them into the ProteinDB object (\ref{object_ProteinDB}), giving you a protein object
+@@ -232,7 +232,7 @@
+ \item Read in a codon table (\ref{object_CodonTable})
+ \item Make a random DNA model (\ref{object_RandomModelDNA})
+ \item Make an algorithm type (\ref{module_gwrap})
+-\item Build an entire parameter set for genewise using Wise2::GeneParameter21_wrap (\ref{module_gwrap})
++\item Build an entire parameter set for genewise using Wise2::GeneParameter21\_wrap (\ref{module_gwrap})
+ \item Run the actual algorithm (\ref{module_gwrap})
+ \item show the alignment using genedisplay (\ref{module_gwrap})
+ \end{itemize}
+@@ -5055,7 +5055,7 @@
+ Member functions of RandomModel
+
+ \section{sequence\_codon}
+-\label{module_sequence\_codon}
++\label{module_sequence_codon}
+ This module only contains factory methods
+
+ \subsection{sequence\_codon factory methods}
diff --git a/sci-biology/wise/files/wise-env b/sci-biology/wise/files/wise-env
new file mode 100644
index 00000000000..3f781c80833
--- /dev/null
+++ b/sci-biology/wise/files/wise-env
@@ -0,0 +1 @@
+WISECONFIGDIR="/usr/share/wise/wisecfg"