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-rw-r--r--sci-biology/wise/Manifest3
-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
-rw-r--r--sci-biology/wise/wise-2.4.0_alpha.ebuild11
6 files changed, 8 insertions, 754 deletions
diff --git a/sci-biology/wise/Manifest b/sci-biology/wise/Manifest
index fc9cf9f0083..f9c6fa852c5 100644
--- a/sci-biology/wise/Manifest
+++ b/sci-biology/wise/Manifest
@@ -1 +1,2 @@
-DIST wise2.4.0alpha.tar.gz 3296399 SHA256 6ec8be1ea6f0559d8a2659fe9c0626408fa2b3e327cae345d0e48bb971531853 SHA512 a2288d7304e7768328689514a986aeff62a0ca6538ee61177a434fb08065f83ab5db39e0cb9101dd8ae9a91f7d95d05528d7ad23df0c394587717c584bf2341c WHIRLPOOL cb6b34dc7d6b758d83a97af491e803230f8dfbd0d0600600fc4c2513b9450d7b6da988d5d584bf9db6193f938df59899e49f2a4e26d5f29c5e089a741d00f6ec
+DIST wise-2.4.0_alpha-patchset.tar.bz2 7244 BLAKE2B 3c921b61e6a30515d790abd8168b5fbc4f8add44f1133cf7d163a98a6935a74ae7c9f79b72874a509bb743aa5b340c92a049ad091380f9cd33b0b9154cca5974 SHA512 ca73f1b03e14cef44d84484c64d06c4856d6ef33b7434de5ac58725cea1d071d875a7b073fc181da33a7490c4f086f674a9a52db4d36e78f4f5b75b28b855cfe
+DIST wise2.4.0alpha.tar.gz 3296399 BLAKE2B a7fbac022c62606ce865250f4091497e9c86331d2d2050fc4f69614aa5e95313eac3a0fcd49451c724c9b50bc6ac63700cd44828736b7a4d15eff2bc21fc29ec SHA512 a2288d7304e7768328689514a986aeff62a0ca6538ee61177a434fb08065f83ab5db39e0cb9101dd8ae9a91f7d95d05528d7ad23df0c394587717c584bf2341c
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
deleted file mode 100644
index d3c17098105..00000000000
--- a/sci-biology/wise/files/wise-2.4.0_alpha-cflags.patch
+++ /dev/null
@@ -1,407 +0,0 @@
-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
deleted file mode 100644
index 42af0c7e849..00000000000
--- a/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10.patch
+++ /dev/null
@@ -1,302 +0,0 @@
-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
deleted file mode 100644
index 827ce4cdfa7..00000000000
--- a/sci-biology/wise/files/wise-api.tex.patch
+++ /dev/null
@@ -1,38 +0,0 @@
---- 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
deleted file mode 100644
index 3f781c80833..00000000000
--- a/sci-biology/wise/files/wise-env
+++ /dev/null
@@ -1 +0,0 @@
-WISECONFIGDIR="/usr/share/wise/wisecfg"
diff --git a/sci-biology/wise/wise-2.4.0_alpha.ebuild b/sci-biology/wise/wise-2.4.0_alpha.ebuild
index 3d4f0955d84..aa971e0c693 100644
--- a/sci-biology/wise/wise-2.4.0_alpha.ebuild
+++ b/sci-biology/wise/wise-2.4.0_alpha.ebuild
@@ -7,7 +7,8 @@ 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"
+SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${PN}$(delete_version_separator 3).tar.gz
+ https://dev.gentoo.org/~mgorny/dist/${P}-patchset.tar.bz2"
LICENSE="BSD"
SLOT="0"
@@ -25,12 +26,12 @@ S="${WORKDIR}"/${PN}$(delete_version_separator 3)
src_prepare() {
epatch \
- "${FILESDIR}"/${P}-glibc-2.10.patch \
- "${FILESDIR}"/${P}-cflags.patch
+ "${WORKDIR}"/${P}-patchset/${P}-glibc-2.10.patch \
+ "${WORKDIR}"/${P}-patchset/${P}-cflags.patch
cd "${S}"/docs || die
cat "${S}"/src/models/*.tex "${S}"/src/dynlibsrc/*.tex | perl gettex.pl > temp.tex || die
cat wise2api.tex temp.tex apiend.tex > api.tex || die
- epatch "${FILESDIR}"/${PN}-api.tex.patch
+ epatch "${WORKDIR}"/${P}-patchset/${PN}-api.tex.patch
}
src_compile() {
@@ -68,5 +69,5 @@ src_install() {
insinto /usr/share/doc/${PF}
doins "${S}"/docs/*.ps
fi
- newenvd "${FILESDIR}"/${PN}-env 24wise || die "Failed to install env file"
+ newenvd "${WORKDIR}"/${P}-patchset/${PN}-env 24wise || die "Failed to install env file"
}