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408 lines
27 KiB
408 lines
27 KiB
diff --git a/src/base/makefile b/src/base/makefile
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index 4620f19..a84e2c7 100644
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--- a/src/base/makefile
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+++ b/src/base/makefile
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@@ -20,8 +20,8 @@ NBASEOBJ = wiseconfig.o \
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#CFLAGS = -c -g -DUNIX -DWISE_MEMORY_WATCH
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-CFLAGS = -c -O2 -DUNIX -pthread
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-LFLAGS = -g -lm
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+CFLAGS += -c -DUNIX -pthread
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+LFLAGS = -lm
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DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D
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AR_OPTIONS = ru
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diff --git a/src/corba/makefile b/src/corba/makefile
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index df3dd78..237a1ba 100644
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--- a/src/corba/makefile
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+++ b/src/corba/makefile
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@@ -1,10 +1,10 @@
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-CC = cc
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+CC += gcc
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INCFLAGS = -I../base/ -I../dynlibsrc
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#gCFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/
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-#CFLAGS = -O2 -c -DUNIX -I../base/ `glib-config --cflags` -I/usr/local/include/orbit-1.0/
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-CFLAGS = -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client`
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+#CFLAGS = -O2 -c -DUNIX -I../base/ `pkg-config glib-2.0 --cflags` -I/usr/local/include/orbit-1.0/
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+CFLAGS += -pthread -c -DUNIX -I../base/ -I../dynlibsrc `pkg-config ORBit-2.0 --cflags`
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LFLAGS = -L../base/ -lm -lpthread
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AR_OPTIONS = ru
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@@ -14,18 +14,18 @@ hspscan_corba.c : hspscan_corba.idl
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orbit-idl hspscan_corba.idl
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test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o
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- 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
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+ $(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
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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
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- 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
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+ $(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
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test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o
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- 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
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+ $(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
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test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o
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- 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
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config glib-2.0 --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread
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.c.o :
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$(CC) $(CFLAGS) $(INCFLAGS) $?
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diff --git a/src/dnaindex/assembly/makefile b/src/dnaindex/assembly/makefile
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index ef3334a..3a0bc2a 100644
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--- a/src/dnaindex/assembly/makefile
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+++ b/src/dnaindex/assembly/makefile
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@@ -26,10 +26,10 @@ arraymatcher : arraymatcher.o assemblygraph.o assemblystats.o basegraph.o
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CC = cc
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-CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags`
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+CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config glib-2.0 --cflags`
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-LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm
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+LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm
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.c.o :
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diff --git a/src/dnaindex/makefile b/src/dnaindex/makefile
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index 285e6a0..8c6a0dc 100644
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--- a/src/dnaindex/makefile
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+++ b/src/dnaindex/makefile
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@@ -27,14 +27,14 @@ all: $(ASSEMBLY_OBJ)
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kwise : kwise.o $(ASSEMBLY_OBJ)
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- $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
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+ $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs`
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arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ)
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- $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
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+ $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs`
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findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ)
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- $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs`
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+ $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `pkg-config glib-2.0 --libs`
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make_shotgun : make_shotgun.o shotgun.o
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$(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS)
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@@ -70,10 +70,10 @@ show_euler : show_euler.o eulerindex.o singleseqspace.o
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$(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS)
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CC = cc
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-CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags`
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+CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config glib-2.0 --cflags`
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-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm
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+LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config glib-2.0 --libs` -lm
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.c.o :
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diff --git a/src/dynlibsrc/makefile b/src/dynlibsrc/makefile
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index d1d77af..cad8900 100644
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--- a/src/dynlibsrc/makefile
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+++ b/src/dynlibsrc/makefile
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@@ -78,11 +78,11 @@ DYNHELPEROBJ = packaln.o \
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-CC = cc
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+CC ?= gcc
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INCFLAGS = -I../base/
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#CFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/
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-CFLAGS = -Wall -g3 -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags`
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-#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `glib-config --cflags`
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+CFLAGS += -DPTHREAD -c -DUNIX -I../base/ `pkg-config glib-2.0 --cflags`
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+#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `pkg-config glib-2.0 --cflags`
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#CFLAGS = -O -c -DUNIX -DNOERROR -I../base/
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LFLAGS = -g -L../base/ -lm
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AR_OPTIONS = ru
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@@ -144,13 +144,13 @@ test_shadowindex : test_shadowindex.o shadowseqindex.o shadowseq.o libdyna.a
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$(CC) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm
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test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a
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- $(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
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+ $(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
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test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o
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- $(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`
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+ $(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`
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test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o
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- $(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`
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+ $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config glib-2.0 --libs`
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testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o
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diff --git a/src/external/mott/makefile b/src/external/mott/makefile
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index 8d7c1d4..940c438 100644
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--- a/src/external/mott/makefile
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+++ b/src/external/mott/makefile
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@@ -14,10 +14,10 @@ libmott.a : mott_api.o gaplib.o wise2_mott_bridge.o
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wise2_mott_bridge.o : wise2_mott_bridge.c
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$(CC) $(CFLAGS) -I../../dynlibsrc -I../../base wise2_mott_bridge.c
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-CC = cc
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+CC ?= gcc
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-CFLAGS = -Wall -g3 -DPTHREAD -O2 -c
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-LFLAGS = -g -L../base/ -lm
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+CFLAGS += -DPTHREAD -c
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+LFLAGS = -L../base/ -lm
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AR_OPTIONS = ru
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diff --git a/src/makefile b/src/makefile
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index bdff4ff..0d7c871 100644
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--- a/src/makefile
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+++ b/src/makefile
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@@ -26,12 +26,12 @@
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# Change the cc line to gcc if you get compiler errors
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# Most likely you have a non ANSI C compiler
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-CC ?= cc
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+CC ?= gcc
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# These are the CFLAGS to use. These days Wise2 is inherently
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# pthreaded, and everything is compiled with threads. More
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# info on running threads can be found in the documentation
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-CFLAGS = -c -pthread -O2 `glib-config --cflags`
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+CFLAGS += -c -pthread `pkg-config glib-2.0 --cflags`
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diff --git a/src/models/makefile b/src/models/makefile
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index f518d0c..a297eff 100644
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--- a/src/models/makefile
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+++ b/src/models/makefile
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@@ -50,6 +50,8 @@ NEWG = geneparser21.o \
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proteinsw.o \
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estquick3.o
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+EXTRALIBS += `pkg-config glib-2.0 --libs`
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+
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all : dnal psw pswdb dba estwise genewise genewisedb estwisedb genomewise sywise pseudowise promoterwise scanwisep scanwisep_wiseserver libmodel.a
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libmodel.a : $(NEWG)
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@@ -180,7 +182,7 @@ fivestarscan.o : fivestarscan.c
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$(CC) $(CFLAGS) fivestarscan.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I.
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oldpostwise : oldpostwise.o $(NEWG)
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- $(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm
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+ $(CC) $(LDFLAGS) -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm
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testdna : testdna.o dnaalign.o seqaligndisplay.o
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$(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
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@@ -192,10 +194,10 @@ psw : psw.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o
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$(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
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scanwisep.o : scanwisep.c
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- $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $?
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+ $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config glib-2.0 --cflags` $?
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hsp2aln_sw.o : hsp2aln_sw.c
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- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
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+ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
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scanwisep_mysql.o : scanwisep.c
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$(CC) $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c
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@@ -212,10 +214,10 @@ scanwisep_corba : scanwisep_corba.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.
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scanwisep_wiseserver.o : scanwisep.c
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- $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c
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+ $(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`
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scanwisep_wiseserver : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
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- $(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
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+ $(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 $(EXTRALIBS) -lpthread `pkg-config glib-2.0 --libs`
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scanwisep_compress.o : scanwisep.c
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$(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c
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@@ -226,25 +228,25 @@ scanwisep_compress : scanwisep_compress.o seqaligndisplay.o proteinsw.o sw_wrap.
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scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
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- $(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
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+ $(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
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test_gwhsp : test_gwhsp.o genewisehsp.o
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- $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS) `glib-config --libs` -lpthread
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+ $(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
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localcishit.o : localcishit.c
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- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
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+ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
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promoterwise.o : promoterwise.c
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- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $?
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+ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config glib-2.0 --cflags` $?
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promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o
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- $(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
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+ $(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
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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
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- $(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
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+ $(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
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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
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- $(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
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+ $(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 $(EXTRALIBS) `pkg-config glib-2.0 --libs` -lpthread
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dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o
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$(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm -lpthread
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@@ -275,66 +277,66 @@ makerandomdb : makerandomdb.o
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$(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
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genewise : genewise.o $(NEWG)
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- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
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+ $(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`
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cdnawise : cdnawise.o $(NEWG) cdnawise10.o
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- $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
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|
+ $(CC) $(LDFLAGS) -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -lm $(EXTRALIBS)
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fivestar : fivestar.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o
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|
- $(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)
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|
+ $(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)
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|
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|
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|
fivestarsearch : fivestarsearch.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o
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|
- $(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)
|
|
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|
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)
|
|
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|
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
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|
|
|
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|
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
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|
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|
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|
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`
|
|
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|
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`
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|
|
|
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
|
|
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|
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
|