Version bump, #191982

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

6 files changed, 807 insertions, 9 deletions

diff --git a/sci-biology/wise/ChangeLog b/sci-biology/wise/ChangeLog
index c6f4c2a0cfa0..29d9c8389425 100644
--- a/sci-biology/wise/ChangeLog
+++ b/sci-biology/wise/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/wise
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/wise/ChangeLog,v 1.14 2009/08/05 19:42:00 ssuominen Exp $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/wise/ChangeLog,v 1.15 2010/06/23 13:10:09 jlec Exp $
+
+*wise-2.4.0_alpha (23 Jun 2010)
+
+  23 Jun 2010; Justin Lecher <jlec@gentoo.org> wise-2.2.0.ebuild,
+  +wise-2.4.0_alpha.ebuild, +files/wise-2.4.0_alpha-cflags.patch,
+  +files/wise-2.4.0_alpha-glibc-2.10.patch:
+  Version bump, #191982
 
   05 Aug 2009; Samuli Suominen <ssuominen@gentoo.org> wise-2.2.0.ebuild,
   +files/wise-2.2.0-glibc-2.10.patch:
diff --git a/sci-biology/wise/Manifest b/sci-biology/wise/Manifest
index 1c23935eedec..066eb461c30c 100644
--- a/sci-biology/wise/Manifest
+++ b/sci-biology/wise/Manifest
@@ -1,7 +1,21 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX wise-2.2.0-glibc-2.10.patch 7044 RMD160 bf7e9b784fee83bca6f532550a44911f65b83a44 SHA1 7b70e9734b18259c78e8ea4bb0362c4072a8afa5 SHA256 92086174f059ab9732cf502acd9619fc5c9e1c34c5018b6c493d5203ec629503
+AUX wise-2.4.0_alpha-cflags.patch 27241 RMD160 78ba87656ebb7206dd9e386c782ddbfdf971ae12 SHA1 2ba82038aba35e222e48e8ffe1bda444fdb5ffa8 SHA256 281c95e7f37f217a9bd730ba4d80640a6085dc134fb3dcd837f217b36f5b5b87
+AUX wise-2.4.0_alpha-glibc-2.10.patch 8068 RMD160 740e3f2ce7041be4c69520775620e08dc816efc6 SHA1 1a17a7e827418f6b3833c56056eaa63d3addb4f2 SHA256 caaacdde33b1f0b12aa0854fa27e3b2c4d6bab099dbc627e18057609763ce265
 AUX wise-api.tex.patch 2234 RMD160 c1780513680ad00562ba7589bd44ffa86ee996f4 SHA1 16c2b37efc603003448d37de2b67986b86020777 SHA256 31042f660669ea9df9bc608006cd40479e004f5cbb9aed055d3ec58a853c145d
 AUX wise-env 40 RMD160 2ac8408df8a36f789c28d8d55cf892dba78359c5 SHA1 76bce2a14ae2c2afa82e2c537383d4e730dfcb07 SHA256 de6f742147c43b3820ea261fd158647ae1d2d9e8fe562e0b5c4c0d7e878ced36
 DIST wise2.2.0.tar.gz 2108151 RMD160 a4292fbfb405d19b628fe5c829d746297e740862 SHA1 77cc08e9cda9416641370c9b45191192fc7cacd3 SHA256 192db34ffa76ef14a9804cc5a7ab72554498284c841f940f8951b4bfae96d780
-EBUILD wise-2.2.0.ebuild 2059 RMD160 d9b78053d4e682bd329305b384fa56618f293680 SHA1 19b2890f03ae0946d8c3d44b9d798496cce98ed6 SHA256 b149947b48b8ba989abf88a019b6b8c30562e90497c62a3c1e644fc8d264be01
-MISC ChangeLog 2003 RMD160 8882b890bf91663d54ba6e95b968d297827f2922 SHA1 b1cab908d796849e5a088c8f5c29f17ee9c8f49b SHA256 2b13ac8674e6d5774ea4e57f063466374f323ef6b6934a9efd3e05c8fb9c48e7
+DIST wise2.4.0alpha.tar.gz 3296399 RMD160 e4c56b965c83d961716c3870f57e4368757dd976 SHA1 97ee5997d2ffb7d1d9eec9d7d8ff7b68ce10a305 SHA256 6ec8be1ea6f0559d8a2659fe9c0626408fa2b3e327cae345d0e48bb971531853
+EBUILD wise-2.2.0.ebuild 2055 RMD160 9b854ae7ab949eec4d9bbebfd065192fd5190d66 SHA1 8c715486b6f50b0a32fc03c518fb8c1d64daba0d SHA256 4d6e796c75ada195d8e47f64038b8439ed4508335639f6b3e8adf24d29c69cd7
+EBUILD wise-2.4.0_alpha.ebuild 1976 RMD160 76591272f921c8ccd2035b223f40711dbc570f2a SHA1 1904b23c7b58523a00de3bd5abc1d93b364d2a84 SHA256 f504e3ec081bc7ea01c8f1f164ea9e87c97eba89dfa5d23a1c391ab244429af2
+MISC ChangeLog 2232 RMD160 096c9a07f42ded8d097e7b89acfce196f49e7d46 SHA1 62c3ad6f2e2e275428b54b2ac75a828e20924bae SHA256 c16fb4ab67ce762f416ebfc5c0028341bbe9891acef5afc270e1dfb53db0de05
 MISC metadata.xml 165 RMD160 b247a16b6552b292d1249ff4e8ea5060ad2c4372 SHA1 a9f91a3a303f4c85430e21eca09913e1c9426366 SHA256 560c375768c8e164d954d61924f110da785b4771012cb830963eaa267a319132
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.15 (GNU/Linux)
+
+iEYEARECAAYFAkwiB7cACgkQgAnW8HDreRYYDgCfaEtvFglR6p4pn3rPqOxlgq+k
+X2UAnRPwnxlIy9ewfQcNvElHrpTgc/0Y
+=qNTg
+-----END PGP SIGNATURE-----
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 000000000000..d3c17098105e
--- /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 000000000000..42af0c7e849b
--- /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/wise-2.2.0.ebuild b/sci-biology/wise/wise-2.2.0.ebuild
index da6d2419950e..6ec90c247754 100644
--- a/sci-biology/wise/wise-2.2.0.ebuild
+++ b/sci-biology/wise/wise-2.2.0.ebuild
@@ -1,26 +1,25 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/wise/wise-2.2.0.ebuild,v 1.10 2009/08/05 19:42:00 ssuominen Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/wise/wise-2.2.0.ebuild,v 1.11 2010/06/23 13:10:09 jlec Exp $
 
 inherit eutils toolchain-funcs
 
 DESCRIPTION="Intelligent algorithms for DNA searches"
-LICENSE="BSD"
 HOMEPAGE="http://www.ebi.ac.uk/Wise2/"
 SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/unix/${PN}2/${PN}${PV}.tar.gz"
 
+LICENSE="BSD"
 SLOT="0"
 IUSE=""
 KEYWORDS="~alpha ia64 ~sparc x86 ~amd64"
 
 RDEPEND="=sci-biology/hmmer-2.3.2-r1"
-
 DEPEND="${RDEPEND}
 	app-shells/tcsh
 	dev-lang/perl
 	virtual/latex-base"
 
-S=${WORKDIR}/${PN}${PV}
+S="${WORKDIR}"/${PN}${PV}
 
 src_unpack() {
 	unpack ${A}
diff --git a/sci-biology/wise/wise-2.4.0_alpha.ebuild b/sci-biology/wise/wise-2.4.0_alpha.ebuild
new file mode 100644
index 000000000000..36f36b411c76
--- /dev/null
+++ b/sci-biology/wise/wise-2.4.0_alpha.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/wise/wise-2.4.0_alpha.ebuild,v 1.1 2010/06/23 13:10:09 jlec Exp $
+
+EAPI="3"
+
+inherit eutils toolchain-funcs versionator
+
+DESCRIPTION="Intelligent algorithms for DNA searches"
+HOMEPAGE="http://www.ebi.ac.uk/Wise2/"
+SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${PN}$(delete_version_separator 3).tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="doc"
+KEYWORDS="~alpha ~amd64 ~ia64 ~sparc ~x86"
+
+RDEPEND="=sci-biology/hmmer-2.3.2-r1"
+DEPEND="
+	${RDEPEND}
+	app-shells/tcsh
+	dev-lang/perl
+	virtual/latex-base"
+
+S="${WORKDIR}"/${PN}$(delete_version_separator 3)
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-glibc-2.10.patch
+	epatch "${FILESDIR}"/${P}-cflags.patch
+	cd "${S}"/docs
+	cat "${S}"/src/models/*.tex "${S}"/src/dynlibsrc/*.tex | perl gettex.pl > temp.tex
+	cat wise2api.tex temp.tex apiend.tex > api.tex
+	epatch "${FILESDIR}"/${PN}-api.tex.patch
+}
+
+src_compile() {
+	emake \
+		-C src \
+		CC="$(tc-getCC)" \
+		all || die
+	if use doc; then
+		cd "${S}"/docs
+		for i in api appendix dynamite wise2 wise3arch; do
+			latex ${i} || die
+			latex ${i} || die
+			dvips ${i}.dvi -o || die
+		done
+	fi
+}
+
+src_test() {
+	cd "${S}"/src
+	WISECONFIGDIR="${S}/wisecfg" make test || die
+}
+
+src_install() {
+	dobin "${S}"/src/bin/* || die "Failed to install program"
+	dolib.a "${S}"/src/base/libwisebase.a || die "Failed to install libwisebase"
+	dolib.a "${S}"/src/dynlibsrc/libdyna.a || die "Failed to install libdyna"
+	dobin "${S}"/src/dynlibsrc/testgendb || die "Failed to install testgendb"
+	dolib.a "${S}"/src/models/libmodel.a || die "Failed to install libmodel"
+	insinto /usr/share/${PN}
+	doins -r "${S}"/wisecfg || die "Failed to install wisecfg"
+	if use doc; then
+		insinto /usr/share/doc/${PF}
+		doins "${S}"/docs/*.ps || die "Failed to install documentation"
+	fi
+	newenvd "${FILESDIR}"/${PN}-env 24wise || die "Failed to install env file"
+}