1#   makefile for network demo programs and network entrez
2#
3#	$Id: makenet.unx,v 6.261 2016/08/25 15:37:04 ucko Exp $
4#   test, ignore
5#
6#   Sun with unbundled ANSI compiler [ make CC=acc RAN=ranlib ]
7#   Sun with Gnu C [ make CC=gcc RAN=ranlib ]
8#   Sun with Solaris 2.x OS [ make CC="cc -Xa" OTHERLIBS="-lsocket -lnsl -lresolv -lthread -lm" ]
9#   Silicon Graphics [ make OTHERLIBS="-lm -lPW -lsun" ]
10#   IBM 3090 with AIX [ make  ]
11#   ULTRIX [ make RAN=ranlib ]
12#   Apple AUX [ make SHELL=\usr\bin ]
13#   NeXt [ make CFLtxcprocAGS1="-c -ansi" RAN=ranlib ]
14#   DEC Alpha under OSF/1  [ make CC=cc RAN=ranlib ]
15#   BeOS [  make OTHERLIBS="" ]
16#
17#   Subsequent makes should make ... nocopy instead of make ... all
18#   to avoid recopying the include files
19#
20#   To Make the Motif version of demos and to make entrez add:
21#      VIBLIBS="-lXm -lXmu -lXt -lX11" VIBFLAG="-I/am/Motif/include -DWIN_MOTIF" VIB="Psequin Nentrez"
22#   to the argument list.  Substitute the path to your Motif includes for
23#    /am/Motif/include.
24#
25#   The build for RedHat Linux 2.XX with X11R6 requires:
26#     CC="gcc -ansi"
27#     VIBLIBS="-L/usr/X11R6/lib -lXm -lXpm -lXmu -lXp -lXt -lX11 -lXext"
28#
29#   To Make the network server and dispatcher tools, add 'servers' as an
30#   object to be made, e.g.:
31#     make all servers
32#          OR
33#     make nocopy servers
34#
35#   To make the seqget demo program for the network "make seqget"
36#
37#   This makefile may be run either before, after, or without 'makedemo'
38#   It must be run after 'makeall'
39#
40#
41#   NOTE: It is now possible to build using shared libraries, which
42#     consumes significantly less disk space.  To use shared libraries, try:
43#       make ... NCBI_SHLIBS=shlib NCBI_LINKINGLIBDIR=../shlib
44#             NCBI_OTHERLINKOPTIONS=-R`pwd`/../shlib
45#     Also note that building shared libraries using 'makenet' requires
46#     that the 'LCL' variable be set in the same manner as for 'makeall'
47#
48
49
50# default flags for compiling and loading
51
52SUFFIXLCL = $(LCL)
53CFLAGS1 = -c -O
54LDFLAGS1 = -O
55CC = cc
56RAN = ls -l
57AR = ar
58OTHERLIBS = -lm
59THREAD_OTHERLIBS = -lthread
60THREAD_OTHERLIBS =
61THREAD_OBJ = ncbithr.o
62THREAD_OBJ =
63VIBLIBS =
64VIBFLAG = -I/am/Motif/include -DWIN_MOTIF
65VIBFLAG =
66VIB = Nentrez ddv udv
67VIB =
68VIBLIBS= -lXm -lXmu -lXt -lX11
69VIBLIBS=
70SEQUIN_OPTS =
71LIBCOPY = cp -p
72SRCCOPY = ./ln-if-absent
73BINCOPY = cp -p
74
75SUFFIXENV = unx
76ASNDIR = asnstat
77
78BLIB5 = libncbiacc.a
79BLIB6 = libnetcli.a
80BLIB7 = libnetentr.a
81BLIB8 = libncbiNacc.a
82BLIB9 = libncbiCacc.a
83BLIB11 = libncbimla.a
84BLIB12 = libncbitax.a
85BLIB13 = libncbiid0.a
86#BLIB14 = libncbibls0.a
87BLIB19 = libncbispel.a
88BLIB22 = libncbimmdb.a
89BLIB23 = libncbitool.a
90BLIBCOMPADJ = libblastcompadj.a
91BLIB24 = libncbisugg.a
92BLIB25 = libncbiwww.a
93BLIB27 = libncbimsc1.a
94BLIB30 = libncbicn3d.a
95BLIB3000 = libncbicn3dOGL.a
96ULIB31 = libvibnet.a
97BLIB31 = $(ULIB31)
98BLIB31 =
99ULIB33 = libsmartnet.a
100BLIB33 = $(ULIB33)
101BLIB33 =
102BLIB35 = libssparse.a
103BLIB36 = libnetblast.a
104BLIB38 = libncbiprsn.a
105BLIB39 = libobjtax1.a
106BLIB40 = libncbitxc2.a
107BLIB41 = libncbiid1.a
108
109ULIB42 = libctutils.a
110BLIB42 = $(ULIB42)
111BLIB42 =
112
113ULIB43 = libosutils.a
114BLIB43 = $(ULIB43)
115BLIB43 =
116
117ULIB44 = libidload.a
118BLIB44 = $(ULIB44)
119BLIB44 =
120
121BLIB45 = libddvlib.a
122
123BLIB46 = libncbiid2.a
124
125BLIB60 = libblast.a
126BLIB61 = libblastapi.a
127
128#
129# Pseudo-dummy targets when Vibrant is not used
130#
131TLIB31 = D31$(ULIB31)
132DLIB31 = D31$(BLIB31)
133TLIB33 = D33$(ULIB33)
134DLIB33 = D33$(BLIB33)
135
136#
137# Pseudo-dummy explanation:
138#   By default the BLIB is NULL, so by default
139#      TLIB = DnLIBn and DLIBn = Dn and Dn: is a NO-OP
140#   IF BLIB is defined, then
141#      TLIB = DnLIBn and DLIBn = DnLIBn  (the same as TLIB)
142#  The trick is the nocopy depends on DLIBn, either a no-op or the real lib
143#   -Karl the detective
144
145#
146# Pseudo-dummy targets when Sybase is not used
147#
148TLIB42 = D42$(ULIB42)
149DLIB42 = D42$(BLIB42)
150TLIB43 = D43$(ULIB43)
151DLIB43 = D43$(BLIB43)
152TLIB44 = D44$(ULIB44)
153DLIB44 = D44$(BLIB44)
154
155
156LIB1 = -lncbi
157LIBTLS = -lconnssl
158LIB2 = -lncbiobj
159LIB3 = -lncbicdr
160LIB4 = -lvibrant
161LIB400 = -lvibrantOGL
162LIB5 = -lncbiacc
163LIB6 = -lnetcli
164LIB7 = -lnetentr
165LIB8 = -lncbiNacc
166LIB9 = -lncbiCacc
167# LIB10 is reserved for NCSA socket library
168LIB10 =
169LIB11 = -lncbimla
170LIB12 = -lncbitax
171LIB13 = -lncbiid0
172#LIB14 = -lncbibls0
173LIB19 = -lncbispel
174# LIB20 is for the NCBI desktop utilities
175LIB20 = -lncbidesk
176LIB22 = -lncbimmdb
177LIB23 = -lncbitool
178LIBCOMPADJ = -lblastcompadj
179LIB24 = -lncbisugg
180LIB25 = -lncbiwww
181LIB27 = -lncbimsc1
182LIB30 = -lncbicn3d
183LIB3000 = -lncbicn3dOGL
184LIB31 = -lvibnet
185LIB33 = -lsmartnet
186LIB35 = -lssparse
187LIB36 = -lnetblast
188LIB38 = -lncbiprsn
189LIB39 = -lobjtax1
190LIB40 = -lncbitxc2
191LIB41 = -lncbiid1
192LIB42 = -lctutils
193LIB_PS = -lctutils $(LMDB_LIBS) -lz
194LIB43 = -losutils
195LIB44 = -lidload
196LIB45 = -lddvlib
197LIB46 = -lncbiid2
198LIB60 = -lblast
199LIB61 = -lblastapi
200
201BNETCLILIB   = libnetcli.a
202NETCLILIB    = $(LIB6)
203BENTREZLIBS  = $(BLIB8) $(BLIB7) $(BNETCLILIB) $(BLIB3)
204ENTREZLIBS   = $(LIB8) $(LIB7) $(NETCLILIB) $(LIB3)
205
206BSRVNETCLILIB  = libnetcli.a
207SRVNETCLILIB   = $(LIB6)
208
209###
210NCBI_INCDIR = ../include
211NCBI_LIBDIR = ../lib
212NCBI_LINKINGLIBDIR = $(NCBI_LIBDIR)
213# A kludge which tells the linker not to try to use shared libraries
214# when linking programs which use main() instead of Nlm_Main()
215USES_MAIN_KLUDGE = -L$(NCBI_LIBDIR)
216NCBI_OTHERLINKOPTIONS =
217NCBI_SHLIBS = shlib
218NCBI_SHLIBS =
219MAKESHLIB = ../make/makeshlb.unx
220
221CFLAGS = $(CFLAGS1) -I$(NCBI_INCDIR) $(VIBFLAG) -DNETENTREZVERSION="\"$(NETENTREZVERSION) \""
222LDFLAGS = $(LDFLAGS1) -I$(NCBI_INCDIR) $(NCBI_OTHERLINKOPTIONS) -L$(NCBI_LINKINGLIBDIR) $(VIBFLAG)
223
224VIB_POST_LINK = :
225# VIB_POST_LINK = /Developer/Tools/Rez -t APPL ../link/macmet/Carbon.r -o
226
227##
228## some things to make
229##
230
231## sources for libraries
232
233SRC6  = ni_lib_.c ni_service.c ni_debug.c ni_error.c
234
235SRC7 = netentr.c netlib.c objneten.c
236
237SRC8 = accentr.c accutils.c
238
239SRC9 = $(SRC8)
240
241SRC11 = objmla.c medarch.c medutil.c
242
243SRC12 = objtaxon.c taxarch.c taxondt.c
244
245SRC13 = id0gen.c id0arch.c
246
247SRC19 = objspell.c spellapi.c
248
249SRC24 = suggadj.c suggapi.c suggen.c suggest.c suggslp.c
250
251SRC25 = www.c wtoolbar.c querydb.c
252
253SRCTAXCOMMON = objtax1.c taxutil.c
254
255SRC27 = indexlist.c isamlist.c memmap.c miscutils.c
256
257SRC31 = netcnfg.c trmlst.c docsum.c
258
259SRC33 = smartnet.c namedpipe.c
260
261SRC35 = ssputil.c
262
263SRC36 = objblst3.c netblap3.c
264
265SRC38 = ftanet.c
266
267SRC39 = objtax1.c
268
269SRC40 = objtax1.c taxutil.c tc2dproc.c txcdproc.c parttree.c taxcs.c taxblast.c
270
271SRC41 = id1gen.c id1arch.c accid1.c
272
273SRC42 = accpubseq.c ctliberr.c ctlibutils.c password.c gipropmmap.c gicache.c acclinkos.c accvdb.c
274
275SRC43 = os_mtutils.c already_running.c applog_wrap.c
276
277SRC44 = idload_lib.c
278
279SRC46 = id2.c id2sgen.c
280
281NET_LIBS_SRC = $(SRC6) $(SRC7) $(SRC8) $(SRC9)
282
283# objects for libraries
284
285OBJ6  = ni_lib_.o ni_debug.o ni_service.o ni_error.o
286
287OBJ7 = netentr.o netlib.o objneten.o
288
289OBJ8 = Naccentr.o accutils.o
290
291OBJ9 = Caccentr.o accutils.o
292
293OBJ11 = objmla.o medarch.o medutil.o
294
295OBJ12 = objtaxon.o taxarch.o taxondt.o
296
297OBJ13 = id0gen.o id0arch.o
298
299OBJ19 = objspell.o spellapi.o
300
301OBJ24 = suggadj.o suggapi.o suggen.o suggest.o suggslp.o
302
303OBJ25 = www.o wtoolbar.o querydb.o
304
305OBJ27 = indexlist.o isamlist.o memmap.o miscutils.o
306
307OBJ31 = netcnfg.o trmlst.o docsum.o
308
309OBJ33 = smartnet.o namedpipe.o
310
311OBJ35 = ssputil.o
312
313OBJ36 = objblst3.o netblap3.o
314
315OBJ38 = ftanet.o
316
317OBJ39 = objtax1.o
318
319OBJ40 = objtax1.o taxutil.o tc2dproc.o txcdproc.o parttree.o taxcs.o taxblast.o
320
321OBJ41 = id1gen.o id1arch.o accid1.o
322
323OBJ42 = accpubseq.o ctliberr.o ctlibutils.o password.o gipropmmap.o gicache.o acclinkos.o accvdb.o
324
325OBJ43 = os_mtutils.o already_running.o applog_wrap.o
326
327OBJ44 = idload_lib.o
328
329OBJ46 = id2.o id2sgen.o
330
331# objects & sources needed for versions of network demo programs
332
333OBJDDV = ddvmain.o
334
335OBJUDV = udvmain.o
336
337EXESUGGSRV = suggsrv
338
339EXEQUERY = query
340
341EXENQUERY = Nquery
342
343EXESEQUIN = sequin
344
345EXEPSEQUIN = Psequin
346
347EXESBTEDIT = sbtedit
348
349EXESTREAMER = streamer
350
351SRCDDV = ddvmain.c
352
353SRCUDV = udvmain.c
354
355SRCUTILCOPY = ../demo/srchnt.c ../demo/srchaa.c ../demo/mts.c ../demo/sigme.c \
356	../demo/dst.c ../demo/ccp.c ../demo/epi.c ../demo/twop.c \
357	../demo/cnsrt.c ../demo/cnsgn.c \
358	../demo/ccpv.c ../demo/dustv.c ../demo/epiv.c ../demo/sigmev.c \
359	../demo/twopv.c ../demo/cnsrtv.c ../demo/cnsgnv.c ../demo/searchv.c
360
361EXEUTIL = srchnt srchaa mts sigme dst ccp epi twop cnsrt cnsgn
362
363EXEUTILVIB = ccpv dustv epiv sigmev twopv cnsrtv cnsgnv searchv
364
365SRCSEQUIN = sequin1.c sequin2.c sequin3.c sequin4.c sequin5.c sequin6.c \
366	sequin7.c sequin8.c sequin9.c sequin10.c sequinx.c
367
368SRCSBTEDIT = sbtedit.c
369
370SRCSTREAMER = streamer.c
371
372CLI_SRC = $(SRCDDV) $(SRCUDV)
373
374CLIENTS = suggcli
375CLIENTS =
376
377SERV_SRC = $(SRCENTSRV)
378
379SERVERS = $(EXESUGGSRV) $(EXEQUERY) $(EXESEQUIN) $(EXEPSEQUIN) $(EXESBTEDIT) $(EXESTREAMER) $(EXENQUERY)
380
381ALL_SRC = $(NET_LIBS_SRC) $(CLI_SRC) $(SERV_SRC)
382
383## All things to make
384##
385all : ln-if-absent copy .WAIT nocopy
386
387ln-if-absent:	../make/ln-if-absent
388	rm -f ln-if-absent
389	ln -s ../make/ln-if-absent .
390
391nocopy : sources $(BLIB6) $(BLIB7) $(BLIB8) $(BLIB9) \
392	$(DLIB31) $(DLIB33) $(NCBI_SHLIBS) $(CLIENTS) $(VIB) \
393	$(DLIB42) $(DLIB43) $(DLIB44)
394
395sources : $(ALL_SRC)
396
397servers : $(SERV_SRC) $(SERVERS)
398
399utilities : $(EXEUTIL)
400
401vibutilities : $(EXEUTILVIB)
402
403.NO_PARALLEL: copy nocopy Tentrez sequin Psequin sbtedit streamer Ssequin elecpcr asn2fast asn2asn cleanasn cleanasn_psf cspeedtest sqn2agp sugint Nbatch Nbatch3 Nentrcmd seqget idfetch test_nc bi_socket test_ncbi_dsock debug_server rtestval rasn2ff asn2gb asn2gb_psf asn2fsa asn2fsa_psf tbl2asn tbl2asn_psf raw2delt aceread_tst asn2all gene2xml asnval asnval_psf asndisc asndisc_psf asnbarval demo_aceread_tst asnmacro asnstrip flint xlint diffshift gbseqget insdseqget trna2sap trna2tbl testent2 entrez2 spidey dotmatrix ingenue condense bl2seq src_chk src_chk_psf tbl_chk tbl_chk_psf
404
405.WAIT:
406	echo Waiting...go
407
408
409others : $(BLIB11) $(BLIB12) $(BLIB13) $(BLIB19) $(BLIB25) $(BLIB27) $(BLIB35) $(BLIB36) $(BLIB38) $(BLIB39) $(BLIB40) $(NCBI_SHLIBS).alt $(BLIB41) $(BLIB42) $(BLIB43) $(BLIB44) $(BLIB46)
410
411
412## To clean out the directory without removing make
413##
414clean :
415	- rm -f *.[acho]
416
417## use subordinate makefile for building shared libraries
418##
419shlib : shlib.$(LCL)
420
421## Special rules to allow shared libs to be built more than once within
422## a given 'make' invocation
423##
424shlib.alt :
425	make -f makenet.unx LCL=$(LCL) NCBI_LIBDIR=$(NCBI_LIBDIR) OTHERLIBS=$(OTHERLIBS) shlib
426
427shlib.alt2 :
428	make -f makenet.unx LCL=$(LCL) NCBI_LIBDIR=$(NCBI_LIBDIR) OTHERLIBS=$(OTHERLIBS) shlib
429
430## null rules
431##
432.alt :
433.alt2 :
434
435#
436# Solaris Intel shared libs are built the same in the same manner as for Solaris
437# Sparc
438#
439shlib.sin : shlib.sol
440
441shlib.sol :
442	-mkdir ../shlib
443	-rm -f ../shlib/*.a
444	ln $(NCBI_LIBDIR)/*.a ../shlib
445	cd ../shlib; make -f $(MAKESHLIB) `ls *.a | sed "s/\.a/.so/"` NCBI_OTHERLIBS=$(OTHERLIBS)
446	rm -f ../shlib/*.a
447
448#
449# Linux shared libs are built the same in the same manner as for SGI
450#
451shlib.lnx : shlib.sgi
452
453shlib.sgi :
454	-mkdir ../shlib
455	-rm -f ../shlib/*.a
456	ln $(NCBI_LIBDIR)/*.a ../shlib
457	cd ../shlib; make -f $(MAKESHLIB) `ls *.a | sed "s/\.a/.so/"` SH1="ld -o" SH2="-shared *.o"
458	rm -f ../shlib/*.a
459
460shlib.alf :
461	-mkdir ../shlib
462	-rm -f ../shlib/*.a
463	ln $(NCBI_LIBDIR)/*.a ../shlib
464	cd ../shlib; make -f $(MAKESHLIB) `ls *.a | sed "s/\.a/.so/"` SH1="ld -o" SH2="-expect_unresolved '*' -shared *.o"
465	rm -f ../shlib/*.a
466
467
468$(ALL_SRC) : copy
469
470copy :
471	$(SRCCOPY) ../connect/test/*.c .
472	$(SRCCOPY) ../network/entrez/client/*.h ../include
473	$(SRCCOPY) ../network/entrez/client/*.c .
474	-$(SRCCOPY) ../network/medarch/client/*.h ../include
475	-$(SRCCOPY) ../network/medarch/client/*.c .
476	-$(SRCCOPY) ../network/taxonomy/client/*.h ../include
477	-$(SRCCOPY) ../network/taxonomy/client/*.c .
478	-$(SRCCOPY) ../network/taxon1/common/*.h ../include
479	-$(SRCCOPY) ../network/taxon1/common/*.c .
480	-$(SRCCOPY) ../network/taxon1/taxon2/*.h ../include
481	-$(SRCCOPY) ../network/taxon1/taxon2/*.c .
482	-$(SRCCOPY) ../network/id0arch/client/*.h ../include
483	-$(SRCCOPY) ../network/id0arch/client/*.c .
484	-$(SRCCOPY) ../network/id1arch/*.h ../include
485	-$(SRCCOPY) ../network/id1arch/*.c .
486	-$(SRCCOPY) ../network/id2arch/*.h ../include
487	-$(SRCCOPY) ../network/id2arch/*.c .
488	-$(SRCCOPY) ../network/spell/client/*.h ../include
489	-$(SRCCOPY) ../network/spell/client/*.c .
490	-$(SRCCOPY) ../network/suggest/client/*.h ../include
491	-$(SRCCOPY) ../network/suggest/client/*.c .
492	-$(SRCCOPY) ../network/blast3/client/*.h ../include
493	-$(SRCCOPY) ../network/blast3/client/*.c .
494	-$(SRCCOPY) ../tools/taxblast.h ../include
495	-$(SRCCOPY) ../tools/taxblast.c .
496	-$(SRCCOPY) $(ENCRSRCDIR)/*.c .
497	-$(SRCCOPY) ../internal/misc/*.c .
498	-$(SRCCOPY) ../internal/misc/*.h ../include
499	-$(SRCCOPY) ../internal/ssparse/*.c .
500	-$(SRCCOPY) ../internal/ssparse/*.h ../include
501	-$(SRCCOPY) ../internal/libparsn/*.c .
502	-$(SRCCOPY) ../internal/libparsn/*.h ../include
503	-$(SRCCOPY) ../internal/smart/smartnet/*.c .
504	-$(SRCCOPY) ../internal/smart/smartnet/*.h ../include
505	-$(SRCCOPY) ../internal/www/*.c .
506	-$(SRCCOPY) ../internal/www/*.h ../include
507	-$(SRCCOPY) ../internal/query/*.c .
508	-$(SRCCOPY) ../internal/query/*.h ../include
509	-$(SRCCOPY) ../network/sybutils/ctlib/*.c .
510	-$(SRCCOPY) ../network/sybutils/ctlib/*.h ../include
511	-$(SRCCOPY) ../network/sybutils/oslib/*.c .
512	-$(SRCCOPY) ../network/sybutils/oslib/*.h ../include
513	-$(SRCCOPY) ../network/sybutils/idloadlib/*.c .
514	-$(SRCCOPY) ../network/sybutils/idloadlib/*.h ../include
515	$(SRCCOPY) ../network/nsclilib/*.h ../include
516	$(SRCCOPY) ../network/nsclilib/*.c .
517	$(SRCCOPY) ../network/vibnet/*.c .
518	$(SRCCOPY) ../network/vibnet/*.h ../include
519	$(SRCCOPY) ../cdromlib/*.h ../include
520	-$(SRCCOPY) ../network/wwwblast/Src/*.c .
521	-$(SRCCOPY) ../network/wwwblast/Src/*.h ../include
522	$(SRCCOPY) ../cdromlib/accentr.c .
523	$(SRCCOPY) ../cdromlib/accutils.c .
524	-$(SRCCOPY) ../sequin/*.* .
525	$(SRCCOPY) ../demo/entrez.c .
526	$(SRCCOPY) ../demo/seqget.c .
527	$(SRCCOPY) ../demo/entrcmd.c .
528	$(SRCCOPY) ../demo/batch.c .
529	$(SRCCOPY) ../demo/qbatch.c .
530	$(SRCCOPY) ../demo/elecpcr.c .
531	$(SRCCOPY) ../demo/asn2fast.c .
532	$(SRCCOPY) ../demo/asn2asn.c .
533	$(SRCCOPY) ../demo/cleanasn.c .
534	$(SRCCOPY) ../demo/cspeedtest.c .
535	$(SRCCOPY) ../demo/sqn2agp.c .
536	$(SRCCOPY) ../demo/sugint.c .
537	$(SRCCOPY) ../demo/fetchent.c .
538	$(SRCCOPY) ../demo/udvmain.c .
539	$(SRCCOPY) ../demo/rtestval.c .
540	$(SRCCOPY) ../demo/aceread_tst.c .
541	$(SRCCOPY) ../demo/asn2ff.c .
542	$(SRCCOPY) ../demo/asn2gb.c .
543	$(SRCCOPY) ../demo/asn2fsa.c .
544	$(SRCCOPY) ../demo/asn2all.c .
545	$(SRCCOPY) ../demo/gene2xml.c .
546	$(SRCCOPY) ../demo/asnval.c .
547	$(SRCCOPY) ../demo/asndisc.c .
548	$(SRCCOPY) ../demo/asnbarval.c .
549	$(SRCCOPY) ../demo/aceread_tst.c .
550	$(SRCCOPY) ../demo/asnmacro.c .
551	$(SRCCOPY) ../demo/asnstrip.c .
552	$(SRCCOPY) ../demo/tbl2asn.c .
553	$(SRCCOPY) ../demo/raw2delt.c .
554	$(SRCCOPY) ../demo/flint.c .
555	$(SRCCOPY) ../demo/xlint.c .
556	$(SRCCOPY) ../demo/diffshift.c .
557	$(SRCCOPY) ../demo/gbseqget.c .
558	$(SRCCOPY) ../demo/insdseqget.c .
559	$(SRCCOPY) ../demo/nps2gps.c .
560	$(SRCCOPY) ../demo/testent2.c .
561	$(SRCCOPY) ../demo/trna2sap.c .
562	$(SRCCOPY) ../demo/trna2tbl.c .
563	$(SRCCOPY) ../demo/entrez2.c .
564	$(SRCCOPY) ../demo/condense.c .
565	$(SRCCOPY) ../demo/spideymain.c .
566	$(SRCCOPY) ../demo/dotmain.c .
567	$(SRCCOPY) ../demo/ingenmain.c .
568	$(SRCCOPY) ../demo/bl2seq.c .
569	$(SRCCOPY) ../demo/blastall.c .
570	$(SRCCOPY) ../demo/blast_driver.c .
571	$(SRCCOPY) ../demo/src_chk.c .
572	$(SRCCOPY) ../demo/tbl_chk.c .
573	$(SRCCOPY) ../demo/export_cmt.c .
574	-$(SRCCOPY) ../internal/parser/flat2asn.c .
575	$(SRCCOPY) $(SRCUTILCOPY) .
576	-$(SRCCOPY) ../network/entrez/server/*.* .
577	-$(SRCCOPY) ../network/suggest/server/*.* .
578	-chmod -R ug+rw,o+r .
579
580
581## Implicit actions
582##
583
584.c.o :
585	$(CC) $(CFLAGS) $<
586
587## Special rules for network Acclib
588##
589Naccentr.o : accentr.c
590	$(SRCCOPY) accentr.c Naccentr.c
591	$(CC) $(CFLAGS) -D_NETENT_ Naccentr.c
592
593## Special rules for network/cd ("combo") Acclib
594##
595Caccentr.o : accentr.c
596	$(SRCCOPY) accentr.c Caccentr.c
597	$(CC) $(CFLAGS) -D_NET_AND_CD_ Caccentr.c
598
599## Special rules for automatically generated object loaders
600##
601objmla.o: objmla.c
602	$(CC) $(CFLAGS) -DNLM_OBJ_INCL=\"mapmla.h\" objmla.c
603
604objtaxon.o: objtaxon.c
605	$(CC) $(CFLAGS) -DNLM_OBJ_INCL=\"mappings.h\" objtaxon.c
606
607id0gen.o: id0gen.c
608	$(CC) $(CFLAGS) -DNLM_OBJ_INCL=\"id0map.h\" id0gen.c
609
610id1gen.o: id1gen.c
611	$(CC) $(CFLAGS) id1gen.c
612
613## Special rule for ni_lib_.c (with allowed WWW stateless mode)
614##
615ni_lib_.o : ni_lib_.c
616	$(CC) $(CFLAGS) $(IN_HOUSE_CFLAGS) ni_lib_.c
617
618## Explicit rules for SunOS and Solaris make utilities,
619## which can't seem to figure out how to make some objects
620## using the default rules
621medarch.o: medarch.c
622	$(CC) $(CFLAGS) medarch.c
623medutil.o: medutil.c
624	$(CC) $(CFLAGS) medutil.c
625taxarch.o: taxarch.c
626	$(CC) $(CFLAGS) taxarch.c
627taxondt.o: taxondt.c
628	$(CC) $(CFLAGS) taxondt.c
629id0arch.o: id0arch.c
630	$(CC) $(CFLAGS) id0arch.c
631accid1.o: accid1.c
632	$(CC) $(CFLAGS) accid1.c
633id1arch.o: id1arch.c
634	$(CC) $(CFLAGS) id1arch.c
635id2.o: id2.c
636	$(CC) $(CFLAGS) id2.c
637id2sgen.o: id2sgen.c
638	$(CC) $(CFLAGS) id2sgen.c
639objbl1p1.o : objbl1p1.c
640	$(CC) $(CFLAGS) objbl1p1.c
641objbl1p2.o : objbl1p2.c
642	$(CC) $(CFLAGS) objbl1p2.c
643netblap1.o : netblap1.c
644	$(CC) $(CFLAGS) netblap1.c
645blstout1.o : blstout1.c
646	$(CC) $(CFLAGS) blstout1.c
647objspell.o : objspell.c
648	$(CC) $(CFLAGS) objspell.c
649spellapi.o : spellapi.c
650	$(CC) $(CFLAGS) spellapi.c
651suggadj.o : suggadj.c
652	$(CC) $(CFLAGS) suggadj.c
653suggapi.o : suggapi.c
654	$(CC) $(CFLAGS) suggapi.c
655suggen.o : suggen.c
656	$(CC) $(CFLAGS) suggen.c
657suggest.o : suggest.c
658	$(CC) $(CFLAGS) suggest.c
659suggslp.o : suggslp.c
660	$(CC) $(CFLAGS) suggslp.c
661www.o : www.c
662	$(CC) $(CFLAGS) www.c
663wtoolbar.o : wtoolbar.c
664	$(CC) $(CFLAGS) wtoolbar.c
665querydb.o : querydb.c
666	$(CC) $(CFLAGS) querydb.c
667indexlist.o : indexlist.c
668	$(CC) $(CFLAGS) indexlist.c
669isamlist.o : isamlist.c
670	$(CC) $(CFLAGS) isamlist.c
671memmap.o : memmap.c
672	$(CC) $(CFLAGS) memmap.c
673miscutils.o : miscutils.c
674	$(CC) $(CFLAGS) miscutils.c
675division.o : division.c
676	$(CC) $(CFLAGS) division.c
677fs1proc.o : fs1proc.c
678	$(CC) $(CFLAGS) fs1proc.c
679fsutils.o : fsutils.c
680	$(CC) $(CFLAGS) fsutils.c
681gc.o : gc.c
682	$(CC) $(CFLAGS) gc.c
683nmclass.o : nmclass.c
684	$(CC) $(CFLAGS) nmclass.c
685objtax1.o : objtax1.c
686	$(CC) $(CFLAGS) objtax1.c
687objtax0.o : objtax0.c
688	$(CC) $(CFLAGS) objtax0.c
689tax1proc.o : tax1proc.c
690	$(CC) $(CFLAGS) tax1proc.c
691rank.o : rank.c
692	$(CC) $(CFLAGS) rank.c
693rex_util.o : rex_util.c
694	$(CC) $(CFLAGS) rex_util.c
695taxutil.o : taxutil.c
696	$(CC) $(CFLAGS) taxutil.c
697taxctl.o : taxctl.c
698	$(CC) $(CFLAGS) taxctl.c
699taxname.o : taxname.c
700	$(CC) $(CFLAGS) taxname.c
701taxtree.o : taxtree.c
702	$(CC) $(CFLAGS) taxtree.c
703fscproc.o : fscproc.c
704	$(CC) $(CFLAGS) fscproc.c
705tc2dproc.o : tc2proc.c
706	$(CC) $(CFLAGS) -c -o $@ -DTAXSERVICE tc2proc.c
707txcdproc.o : txcdproc.c
708	$(CC) $(CFLAGS) -c -o $@ -DTAXSERVICE txcdproc.c
709parttree.o : parttree.c
710	$(CC) $(CFLAGS) parttree.c
711taxcs.o : taxcs.c
712	$(CC) $(CFLAGS) taxcs.c
713taxblast.o : taxblast.c
714	$(CC) $(CFLAGS) taxblast.c
715objtaxc0.o : objtaxc0.c
716	$(CC) $(CFLAGS) objtaxc0.c
717tax0.o : tax0.c
718	$(CC) $(CFLAGS) tax0.c
719netcnfg.o : netcnfg.c
720	$(CC) $(CFLAGS) netcnfg.c
721trmlst.o : trmlst.c
722	$(CC) $(CFLAGS) trmlst.c
723docsum.o : docsum.c
724	$(CC) $(CFLAGS) docsum.c
725smartnet.o : smartnet.c
726	$(CC) $(CFLAGS) smartnet.c
727namedpipe.o : namedpipe.c
728	$(CC) $(CFLAGS) namedpipe.c
729ssputil.o : ssputil.c
730	$(CC) $(CFLAGS) ssputil.c
731objblst3.o : objblst3.c
732	$(CC) $(CFLAGS) objblst3.c
733netblap3.o : netblap3.c
734	$(CC) $(CFLAGS) netblap3.c
735ftanet.o : ftanet.c
736	$(CC) $(CFLAGS) ftanet.c
737already_running.o : already_running.c
738	$(CC) $(CFLAGS) already_running.c
739## get all the source files
740##
741
742## make libraries
743##
744
745$(BLIB6) : $(OBJ6)
746	- rm -f $(BLIB6)
747	$(AR) cru $(BLIB6) $(OBJ6)
748	$(LIBCOPY) $(BLIB6) $(NCBI_LIBDIR)
749	$(RAN) $(NCBI_LIBDIR)/$(BLIB6)
750
751$(BLIB7) : $(OBJ7)
752	- rm -f $(BLIB7)
753	$(AR) cru $(BLIB7) $(OBJ7)
754	$(LIBCOPY) $(BLIB7) $(NCBI_LIBDIR)
755	$(RAN) $(NCBI_LIBDIR)/$(BLIB7)
756
757$(BLIB8) : $(OBJ8)
758	- rm -f $(BLIB8)
759	$(AR) cru $(BLIB8) $(OBJ8)
760	$(LIBCOPY) $(BLIB8) $(NCBI_LIBDIR)
761	$(RAN) $(NCBI_LIBDIR)/$(BLIB8)
762
763$(BLIB9) : $(OBJ9)
764	- rm -f $(BLIB9)
765	$(AR) cru $(BLIB9) $(OBJ9)
766	$(LIBCOPY) $(BLIB9) $(NCBI_LIBDIR)
767	$(RAN) $(NCBI_LIBDIR)/$(BLIB9)
768
769$(BLIB11) : $(OBJ11)
770	- rm -f $(BLIB11)
771	$(AR) cru $(BLIB11) $(OBJ11)
772	$(LIBCOPY) $(BLIB11) $(NCBI_LIBDIR)
773	$(RAN) $(NCBI_LIBDIR)/$(BLIB11)
774
775$(BLIB12) : $(OBJ12)
776	- rm -f $(BLIB12)
777	$(AR) cru $(BLIB12) $(OBJ12)
778	$(LIBCOPY) $(BLIB12) $(NCBI_LIBDIR)
779	$(RAN) $(NCBI_LIBDIR)/$(BLIB12)
780
781$(BLIB13) : $(OBJ13)
782	- rm -f $(BLIB13)
783	$(AR) cru $(BLIB13) $(OBJ13)
784	$(LIBCOPY) $(BLIB13) $(NCBI_LIBDIR)
785	$(RAN) $(NCBI_LIBDIR)/$(BLIB13)
786
787$(BLIB19) : $(OBJ19)
788	- rm -f $(BLIB19)
789	$(AR) cru $(BLIB19) $(OBJ19)
790	$(LIBCOPY) $(BLIB19) $(NCBI_LIBDIR)
791	$(RAN) $(NCBI_LIBDIR)/$(BLIB19)
792
793$(BLIB24) : $(OBJ24)
794	- rm -f $(BLIB24)
795	$(AR) cru $(BLIB24) $(OBJ24)
796	$(LIBCOPY) $(BLIB24) $(NCBI_LIBDIR)
797	$(RAN) $(NCBI_LIBDIR)/$(BLIB24)
798
799$(BLIB25) : $(OBJ25)
800	- rm -f $(BLIB25)
801	$(AR) cru $(BLIB25) $(OBJ25)
802	$(LIBCOPY) $(BLIB25) $(NCBI_LIBDIR)
803	$(RAN) $(NCBI_LIBDIR)/$(BLIB25)
804
805$(BLIB27) : $(OBJ27)
806	- rm -f $(BLIB27)
807	$(AR) cru $(BLIB27) $(OBJ27)
808	$(LIBCOPY) $(BLIB27) $(NCBI_LIBDIR)
809	$(RAN) $(NCBI_LIBDIR)/$(BLIB27)
810
811$(BLIB35) : $(OBJ35)
812	- rm -f $(BLIB35)
813	$(AR) cru $(BLIB35) $(OBJ35)
814	$(LIBCOPY) $(BLIB35) $(NCBI_LIBDIR)
815	$(RAN) $(NCBI_LIBDIR)/$(BLIB35)
816
817$(BLIB36) : $(OBJ36)
818	- rm -f $(BLIB36)
819	$(AR) cru $(BLIB36) $(OBJ36)
820	$(LIBCOPY) $(BLIB36) $(NCBI_LIBDIR)
821	$(RAN) $(NCBI_LIBDIR)/$(BLIB36)
822
823
824$(BLIB38) : $(OBJ38)
825	- rm -f $(BLIB38)
826	$(AR) cru $(BLIB38) $(OBJ38)
827	$(LIBCOPY) $(BLIB38) $(NCBI_LIBDIR)
828	$(RAN) $(NCBI_LIBDIR)/$(BLIB38)
829
830$(BLIB39) : $(OBJ39)
831	- rm -f $(BLIB39)
832	$(AR) cru $(BLIB39) $(OBJ39)
833	$(LIBCOPY) $(BLIB39) $(NCBI_LIBDIR)
834	$(RAN) $(NCBI_LIBDIR)/$(BLIB39)
835
836$(BLIB40) : $(OBJ40)
837	- rm -f $(BLIB40)
838	$(AR) cru $(BLIB40) $(OBJ40)
839	$(LIBCOPY) $(BLIB40) $(NCBI_LIBDIR)
840	$(RAN) $(NCBI_LIBDIR)/$(BLIB40)
841
842$(BLIB41) : $(OBJ41)
843	- rm -f $(BLIB41)
844	$(AR) cru $(BLIB41) $(OBJ41)
845	$(LIBCOPY) $(BLIB41) $(NCBI_LIBDIR)
846	$(RAN) $(NCBI_LIBDIR)/$(BLIB41)
847
848$(BLIB46) : $(OBJ46)
849	- rm -f $(BLIB46)
850	$(AR) cru $(BLIB46) $(OBJ46)
851	$(LIBCOPY) $(BLIB46) $(NCBI_LIBDIR)
852	$(RAN) $(NCBI_LIBDIR)/$(BLIB46)
853
854#
855# Dummy target used when Vibrant is not used
856#
857D31:
858
859$(TLIB31) : $(ULIB31)
860
861$(ULIB31) : $(OBJ31)
862	- rm -f $(BLIB31)
863	$(AR) cru $(BLIB31) $(OBJ31)
864	$(LIBCOPY) $(BLIB31) $(NCBI_LIBDIR)
865	$(RAN) $(NCBI_LIBDIR)/$(BLIB31)
866
867D33:
868
869$(TLIB33) : $(ULIB33)
870
871$(ULIB33) : $(OBJ33)
872	- rm -f $(BLIB33)
873	$(AR) cru $(BLIB33) $(OBJ33)
874	$(LIBCOPY) $(BLIB33) $(NCBI_LIBDIR)
875	$(RAN) $(NCBI_LIBDIR)/$(BLIB33)
876
877#
878# Dummy targets for no Sybase
879#
880D42:
881
882$(TLIB42) : $(ULIB42)
883
884$(ULIB42) : $(OBJ42)
885	- rm -f $(BLIB42)
886	$(AR) cru $(BLIB42) $(OBJ42)
887	$(LIBCOPY) $(BLIB42) $(NCBI_LIBDIR)
888	$(RAN) $(NCBI_LIBDIR)/$(BLIB42)
889
890D43:
891
892$(TLIB43) : $(ULIB43)
893
894$(ULIB43) : $(OBJ43)
895	- rm -f $(BLIB43)
896	$(AR) cru $(BLIB43) $(OBJ43)
897	$(LIBCOPY) $(BLIB43) $(NCBI_LIBDIR)
898	$(RAN) $(NCBI_LIBDIR)/$(BLIB43)
899
900D44:
901
902$(TLIB44) : $(ULIB44)
903
904$(ULIB44) : $(OBJ44)
905	- rm -f $(BLIB44)
906	$(AR) cru $(BLIB44) $(OBJ44)
907	$(LIBCOPY) $(BLIB44) $(NCBI_LIBDIR)
908	$(RAN) $(NCBI_LIBDIR)/$(BLIB44)
909
910#   below applies to both 42 (ctlib) and 43 (oslib) and 44 (idloadlib)
911# Since Sybase needs special include, and becuase of the TLIB/DLIB trick
912#  this will not be invoked unless BLIB42 defined on the make line, we
913#  can safely have an NCBI-only rule here
914# SRC42 = accpubseq.c ctliberr.c ctlibutils.c password.c gipropmmap.c acclinkos.c accvdb.c
915
916ctlibutils.o : ctlibutils.c
917	$(CC) $(CFLAGS) $(IN_HOUSE_CFLAGS) -c ctlibutils.c
918
919ctliberr.o : ctliberr.c
920	$(CC) $(CFLAGS) $(IN_HOUSE_CFLAGS) -c ctliberr.c
921
922accpubseq.o : accpubseq.c
923# Disable optimization to work around a bug in ICC 8. :-/
924	$(CC) $(CFLAGS) $(IN_HOUSE_CFLAGS) -O0 -c accpubseq.c
925
926password.o : password.c
927	$(CC) $(CFLAGS) $(IN_HOUSE_CFLAGS) -c password.c
928
929gipropmmap.o : gipropmmap.c
930	$(CC) $(CFLAGS) $(IN_HOUSE_CFLAGS) -c gipropmmap.c
931
932gicache.o : gicache.c
933	$(CC) $(CFLAGS) $(IN_HOUSE_CFLAGS) $(LMDB_INCLUDE) -c gicache.c
934
935os_mtutils.o : os_mtutils.c
936	$(CC) $(CFLAGS) $(IN_HOUSE_CFLAGS) -c os_mtutils.c
937
938applog_wrap.o : applog_wrap.c
939	$(CC) $(CFLAGS) $(IN_HOUSE_CFLAGS) -c applog_wrap.c
940
941
942idload_lib.o : idload_lib.c
943	$(CC) $(CFLAGS) $(IN_HOUSE_CFLAGS) -c idload_lib.c
944
945acclinkos.o : acclinkos.c
946	$(CC) $(CFLAGS) $(IN_HOUSE_CFLAGS) -c acclinkos.c
947
948accvdb.o : accvdb.c
949	$(CC) $(CFLAGS) $(IN_HOUSE_CFLAGS) -c accvdb.c
950
951## make applications
952##
953
954
955ddv    : $(OBJDDV)
956	$(CC) -o ddv $(LDFLAGS) $(OBJDDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
957	$(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) $(LIB23) \
958	$(LIBCOMPADJ) $(LIB2) $(LIB1) \
959	$(VIBLIBS) $(OTHERLIBS)
960
961udv    : $(OBJUDV)
962	$(CC) -o udv $(LDFLAGS) $(OBJUDV) $(LIB41) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
963	$(LIB8) $(LIB7) $(NETCLILIB) $(LIB3) $(LIB4) \
964	$(LIB23) $(LIBCOMPADJ) $(LIB2) \
965	$(LIB1) $(VIBLIBS) $(OTHERLIBS)
966
967Nentrez : entrez.c $(ULIB31)
968	$(CC) -o Nentrez $(LDFLAGS) entrez.c $(LIB41) $(LIB31) $(LIB30) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
969	$(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
970
971# left this in (Tentrez) for script backwards compatibility
972Tentrez : entrez.c $(ULIB31)
973	$(CC) -o Tentrez $(LDFLAGS) entrez.c $(LIB41) $(LIB31) $(LIB30) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) \
974	$(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB8) $(LIB7) $(NETCLILIB) $(LIB5) $(LIB4) $(LIB3) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
975
976
977# demo program (network version of "seqget")
978
979seqget : seqget.c $(BENTREZLIBS)
980	$(CC) -o seqget $(LDFLAGS) seqget.c $(ENTREZLIBS) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
981
982# demo program (network version of "entrcmd")
983
984Nentrcmd : entrcmd.c
985	$(CC) -o Nentrcmd $(LDFLAGS) entrcmd.c $(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS)
986
987# demo program (batch entrez)
988
989Nbatch : batch.c
990	$(CC) -o Nbatch $(LDFLAGS) batch.c $(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS)
991
992Nbatch3 : qbatch.c
993	$(CC) -o Nbatch3 $(LDFLAGS) qbatch.c $(LIB41) $(LIB6) $(LIB2) $(LIB1) $(OTHERLIBS)
994
995# demo program (rtestval)
996rtestval :	rtestval.c
997	$(CC) -o rtestval $(LDFLAGS) rtestval.c $(LIB41) $(LIB6) $(LIB2) $(LIB1) $(OTHERLIBS)
998
999# remote asn2ff program (rasn2ff)
1000rasn2ff :	asn2ff.c
1001	$(CC) -o rasn2ff -DENABLE_ENTREZ -DENABLE_ID1 $(LDFLAGS) asn2ff.c $(LIB8) $(LIB3) $(LIB7) $(LIB6) $(LIB41) $(LIB2) $(LIB1) $(OTHERLIBS)
1002
1003# aceread_tst program (aceread_tst)
1004aceread_tst :	aceread_tst.c
1005	$(CC) -g -o aceread_tst $(LDFLAGS) aceread_tst.c $(THREAD_OBJ) $(LIB41) \
1006		$(NETCLILIB) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) \
1007		$(OTHERLIBS) $(THREAD_OTHERLIBS)
1008
1009# asn2gb program (asn2gb)
1010asn2gb :	asn2gb.c
1011	$(CC) -g -o asn2gb $(LDFLAGS) asn2gb.c $(LIB41) $(NETCLILIB) \
1012	    $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIBTLS) $(LIB1) \
1013	    $(GNUTLS_LIBS) $(OTHERLIBS)
1014
1015# asn2gb_psf, uses PUBSEQBioseqFetchEnable instead of PubSeqFetchEnable
1016# should be used only internally within NCBI.
1017asn2gb_psf :	asn2gb_psf.o
1018	$(CC) -g -o asn2gb_psf $(LDFLAGS) asn2gb_psf.o \
1019	    $(LIB_PS) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIBTLS) $(LIB1) \
1020	    $(NCBI_SYBLIBS_CT) $(GNUTLS_LIBS) $(OTHERLIBS)
1021
1022asn2gb_psf.o :	asn2gb.c
1023	$(CC) $(CFLAGS) -c -DINTERNAL_NCBI_ASN2GB -g -o asn2gb_psf.o asn2gb.c
1024
1025# asn2fsa program (asn2fsa)
1026asn2fsa :	asn2fsa.c
1027	$(CC) -g -o asn2fsa $(LDFLAGS) asn2fsa.c $(THREAD_OBJ) $(LIB41) \
1028	    $(NETCLILIB) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIBTLS) $(LIB1) \
1029	    $(GNUTLS_LIBS) $(OTHERLIBS) $(THREAD_OTHERLIBS)
1030
1031# asn2fsa_psf, uses PUBSEQBioseqFetchEnable instead of PubSeqFetchEnable
1032# should be used only internally within NCBI.
1033asn2fsa_psf :	asn2fsa_psf.o
1034	$(CC) -g -o asn2fsa_psf $(LDFLAGS) asn2fsa_psf.o $(THREAD_OBJ) $(LIB_PS) \
1035	    $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIBTLS) $(LIB1) \
1036            $(NCBI_SYBLIBS_CT_r) $(GNUTLS_LIBS) $(OTHERLIBS) $(THREAD_OTHERLIBS)
1037
1038asn2fsa_psf.o :	asn2fsa.c
1039	$(CC) $(CFLAGS) -c -DINTERNAL_NCBI_ASN2FSA -g -o asn2fsa_psf.o asn2fsa.c
1040
1041# asn2all program (asn2all)
1042asn2all :	asn2all.c
1043	$(CC) -g -o asn2all $(LDFLAGS) asn2all.c $(THREAD_OBJ) $(LIB41) \
1044	    $(NETCLILIB) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIBTLS) $(LIB1) \
1045	    $(GNUTLS_LIBS) $(OTHERLIBS) $(THREAD_OTHERLIBS)
1046
1047# tbl2asn
1048tbl2asn : tbl2asn.c
1049	$(CC) -o tbl2asn $(LDFLAGS) tbl2asn.c $(LIB23) $(LIBCOMPADJ) \
1050	    $(LIB2) $(NETCLILIB) $(LIBTLS) $(LIB1) $(GNUTLS_LIBS) $(OTHERLIBS)
1051
1052# tbl2asn_psf, uses PUBSEQBioseqFetchEnable instead of PubSeqFetchEnable
1053# should be used only internally within NCBI.
1054tbl2asn_psf : tbl2asn_psf.o
1055	$(CC) -g -o tbl2asn_psf $(LDFLAGS) tbl2asn_psf.o $(THREAD_OBJ) $(LIB_PS) \
1056	$(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIBTLS) $(LIB1) \
1057	$(NCBI_SYBLIBS_CT_r) $(GNUTLS_LIBS) $(OTHERLIBS) $(THREAD_OTHERLIBS)
1058
1059tbl2asn_psf.o :	tbl2asn.c
1060	$(CC) $(CFLAGS) -c -DINTERNAL_NCBI_TBL2ASN -g -o tbl2asn_psf.o tbl2asn.c
1061
1062# raw2delt
1063raw2delt : raw2delt.c
1064	$(CC) -o raw2delt $(LDFLAGS) raw2delt.c $(LIB22) $(LIBCOMPADJ) \
1065		$(LIB2) $(NETCLILIB) $(LIB1) $(OTHERLIBS)
1066
1067# gene2xml program (gene2xml)
1068gene2xml :	gene2xml.c
1069	$(CC) -g -o gene2xml $(LDFLAGS) gene2xml.c $(NETCLILIB) $(LIB2) $(LIB1) $(OTHERLIBS)
1070
1071# asnval program (asnval)
1072asnval :	asnval.c
1073	$(CC) -g -o asnval $(LDFLAGS) asnval.c $(THREAD_OBJ) $(LIB41) \
1074	    $(NETCLILIB) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIBTLS) $(LIB1) \
1075	    $(GNUTLS_LIBS) $(OTHERLIBS) $(THREAD_OTHERLIBS)
1076
1077# asnval_psf, uses PUBSEQBioseqFetchEnable instead of PubSeqFetchEnable
1078# should be used only internally within NCBI.
1079asnval_psf :	asnval_psf.o
1080	$(CC) -g -o asnval_psf $(LDFLAGS) asnval_psf.o $(THREAD_OBJ) $(LIB_PS) \
1081	    $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIBTLS) $(LIB1) \
1082	    $(NCBI_SYBLIBS_CT_r) $(GNUTLS_LIBS) $(OTHERLIBS) $(THREAD_OTHERLIBS)
1083
1084asnval_psf.o :	asnval.c
1085	$(CC) $(CFLAGS) -c -DINTERNAL_NCBI_ASN2VAL -g -o asnval_psf.o asnval.c
1086
1087# asnval_dbx_psf, -- debug version -- uses PUBSEQBioseqFetchEnable instead of PubSeqFetchEnable
1088# should be used only internally within NCBI.
1089asnval_dbx_psf :	asnval_dbx_psf.o
1090	$(CC) -g -o asnval_dbx_psf $(LDFLAGS) asnval_dbx_psf.o $(THREAD_OBJ) $(LIB_PS) \
1091	$(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) $(NCBI_SYBLIBS_CT_r) \
1092	$(OTHERLIBS) $(THREAD_OTHERLIBS)
1093
1094asnval_dbx_psf.o :	asnval.c
1095	$(CC) $(CFLAGS) -c -DINTERNAL_NCBI_ASN2VAL -g -o asnval_psf.o asnval.c
1096
1097# asndisc program (asndisc)
1098asndisc :	asndisc.c
1099	$(CC) -g -o asndisc $(LDFLAGS) asndisc.c $(THREAD_OBJ) $(LIB41) \
1100		$(NETCLILIB) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) \
1101		$(OTHERLIBS) $(THREAD_OTHERLIBS)
1102
1103# asndisc_psf, uses PUBSEQBioseqFetchEnable instead of PubSeqFetchEnable
1104# should be used only internally within NCBI.
1105asndisc_psf :	asndisc_psf.o
1106	$(CC) -g -o asndisc_psf $(LDFLAGS) asndisc_psf.o $(THREAD_OBJ) $(LIB_PS) \
1107	$(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) $(NCBI_SYBLIBS_CT_r) \
1108	$(OTHERLIBS) $(THREAD_OTHERLIBS)
1109
1110asndisc_psf.o :	asndisc.c
1111	$(CC) $(CFLAGS) -c -DINTERNAL_NCBI_ASNDISC -g -o asndisc_psf.o asndisc.c
1112
1113# asnbarval program (asnbarval)
1114asnbarval :	asnbarval.c
1115	$(CC) -g -o asnbarval $(LDFLAGS) asnbarval.c $(THREAD_OBJ) $(LIB41) \
1116		$(NETCLILIB) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) \
1117		$(OTHERLIBS) $(THREAD_OTHERLIBS)
1118
1119# demo_aceread_tst program (demo_aceread_tst)
1120demo_aceread_tst :	aceread_tst.c
1121	$(CC) -g -o demo_aceread_tst $(LDFLAGS) aceread_tst.c $(THREAD_OBJ) $(LIB41) \
1122		$(NETCLILIB) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) \
1123		$(OTHERLIBS) $(THREAD_OTHERLIBS)
1124
1125# asnmacro
1126asnmacro : asnmacro.c
1127	$(CC) -o asnmacro $(LDFLAGS) asnmacro.c $(LIB61) $(LIB60) $(LIB23) $(LIBCOMPADJ) \
1128		$(LIB2) $(LIB1) $(OTHERLIBS)
1129
1130# asnstrip program (asnstrip)
1131asnstrip : asnstrip.c
1132	$(CC) -o asnstrip $(LDFLAGS) asnstrip.c $(LIB23) $(LIBCOMPADJ) \
1133		$(LIB2) $(NETCLILIB) $(LIB1) $(OTHERLIBS)
1134
1135# flint program (flint)
1136flint :	flint.c
1137	$(CC) -g -o flint $(LDFLAGS) flint.c $(LIB41) $(NETCLILIB) \
1138		$(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS)
1139
1140# xlint program (xlint)
1141xlint :	xlint.c
1142	$(CC) -g -o xlint $(LDFLAGS) xlint.c $(LIB41) $(NETCLILIB) \
1143		$(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS)
1144
1145# diffshift program (diffshift)
1146diffshift :	diffshift.c
1147	$(CC) -g -o diffshift $(LDFLAGS) diffshift.c $(LIB41) $(NETCLILIB) \
1148		$(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS)
1149
1150# gbseqget program (gbseqget)
1151gbseqget :	gbseqget.c
1152	$(CC) -g -o gbseqget $(LDFLAGS) gbseqget.c $(LIB41) $(NETCLILIB) \
1153		$(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS)
1154
1155# insdseqget program (insdseqget)
1156insdseqget :	insdseqget.c
1157	$(CC) -g -o insdseqget $(LDFLAGS) insdseqget.c $(LIB41) $(NETCLILIB) \
1158		$(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) $(OTHERLIBS)
1159
1160# nps2gps program (nps2gps)
1161nps2gps :	nps2gps.c
1162	$(CC) -g -o nps2gps $(LDFLAGS) nps2gps.c $(LIB23) $(LIBCOMPADJ) \
1163		$(LIB2) $(LIB1) $(OTHERLIBS)
1164
1165# trna2sap program (trna2sap)
1166trna2sap :	trna2sap.c
1167	$(CC) -g -o trna2sap $(LDFLAGS) trna2sap.c $(LIB23) $(LIBCOMPADJ) \
1168		$(LIB2) $(LIB1) $(OTHERLIBS)
1169
1170# trna2tbl program (trna2tbl)
1171trna2tbl :	trna2tbl.c
1172	$(CC) -g -o trna2tbl $(LDFLAGS) trna2tbl.c $(LIB23) $(LIBCOMPADJ) \
1173		$(LIB2) $(LIB1) $(OTHERLIBS)
1174
1175# Entrez2 service test program (testent2)
1176testent2 :	testent2.c
1177	$(CC) -g -o testent2 $(LDFLAGS) testent2.c $(LIB23) $(LIBCOMPADJ) \
1178		$(LIB22) $(LIB61) $(LIB60) $(LIB2) $(LIB1) $(OTHERLIBS)
1179
1180# network Entrez2 application (entrez2)
1181entrez2 :	entrez2.c
1182	$(CC) -g -o entrez2 $(LDFLAGS) entrez2.c $(LIB41) $(LIB6) $(LIB20) \
1183		$(LIB61) $(LIB60) $(LIB22) $(LIB23) $(LIBCOMPADJ) \
1184		$(LIB2) $(LIB4) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
1185	$(VIB_POST_LINK) entrez2
1186
1187# demo program (spidey)
1188spidey :	spideymain.c
1189	$(CC) -o spidey $(LDFLAGS) spideymain.c $(LIB41) $(LIB23) \
1190		$(LIBCOMPADJ) $(LIB6) $(LIB2) $(LIB1) $(OTHERLIBS)
1191
1192# demo program dotmatrix
1193dotmatrix :	dotmain.c
1194	$(CC) -o dotmatrix $(LDFLAGS) dotmain.c $(LIB41) $(LIB6) \
1195		$(LIB20) $(LIB61) $(LIB60) $(LIB23) $(LIBCOMPADJ) $(LIB2) \
1196		$(LIB4) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
1197
1198# demo program ingenue
1199ingenue :	ingenmain.c
1200	$(CC) -o ingenue $(LDFLAGS) ingenmain.c $(LIB41) $(LIB6) $(LIB20) \
1201		$(LIB61) $(LIB60) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB4) \
1202		$(LIB1) $(VIBLIBS) $(OTHERLIBS)
1203
1204# demo program (electronic PCR)
1205
1206elecpcr : elecpcr.c
1207	$(CC) -o elecpcr $(LDFLAGS) elecpcr.c $(LIB23) $(LIBCOMPADJ) \
1208		$(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS)
1209
1210# demo program (asn2fast)
1211
1212asn2fast : asn2fast.c
1213	$(CC) -o asn2fast $(LDFLAGS) asn2fast.c $(LIB41) $(LIB6) $(LIB2) $(LIB1) $(OTHERLIBS)
1214
1215# demo program (asn2asn)
1216
1217asn2asn : asn2asn.c
1218	$(CC) -o asn2asn $(LDFLAGS) asn2asn.c $(LIB41) $(LIB6) $(LIB2) $(LIB1) $(OTHERLIBS)
1219
1220# demo program (cleanasn)
1221
1222cleanasn : cleanasn.c
1223	$(CC) -o cleanasn $(LDFLAGS) cleanasn.c $(LIB61) $(LIB60) $(LIB41) \
1224	    $(LIB23) $(LIBCOMPADJ) $(LIB6) $(LIB2) $(LIBTLS) $(LIB1) \
1225	    $(GNUTLS_LIBS) $(OTHERLIBS)
1226
1227# cleanasn_psf, uses PUBSEQBioseqFetchEnable instead of PubSeqFetchEnable
1228# should be used only internally within NCBI.
1229cleanasn_psf : cleanasn_psf.o
1230	$(CC) -g -o cleanasn_psf $(LDFLAGS) cleanasn_psf.o \
1231	    $(LIB_PS) $(LIB61) $(LIB60) $(LIB41) $(LIB23) $(LIB6) \
1232	    $(LIBCOMPADJ) $(LIB2) $(LIBTLS) $(LIB1) \
1233	    $(NCBI_SYBLIBS_CT) $(GNUTLS_LIBS) $(OTHERLIBS)
1234
1235cleanasn_psf.o :	cleanasn.c
1236	$(CC) $(CFLAGS) -c -DINTERNAL_NCBI_CLEANASN -g -o cleanasn_psf.o cleanasn.c
1237
1238# demo program (cspeedtest)
1239
1240cspeedtest : cspeedtest.c
1241	$(CC) -o cspeedtest $(LDFLAGS) cspeedtest.c $(LIB41) $(LIB23) $(LIB6) $(LIB2) $(LIB1) $(OTHERLIBS)
1242
1243# demo program (sqn2agp)
1244
1245sqn2agp : sqn2agp.c
1246	$(CC) -o sqn2agp $(LDFLAGS) sqn2agp.c $(LIB41) $(LIB23) $(LIB6) $(LIB2) $(LIB1) $(OTHERLIBS)
1247
1248# demo program (sugint)
1249
1250sugint : sugint.c
1251	$(CC) -o sugint $(LDFLAGS) sugint.c $(LIB23) $(LIB2) $(LIB1) $(OTHERLIBS)
1252
1253# demo program (fetchent)
1254
1255fetchent : fetchent.c
1256	$(CC) -o fetchent $(LDFLAGS) fetchent.c $(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS)
1257
1258# demo program (condense)
1259condense :	condense.c
1260	$(CC) $(IN_HOUSE_CFLAGS) -o condense $(LDFLAGS) condense.c $(LIB_PS) $(LIB2) $(LIB1) $(NCBI_SYBLIBS_CT) $(OTHERLIBS)
1261
1262# test client for the id0 network service
1263
1264id0test: id0test.c $(BNETCLILIB) $(BLIB13)
1265	$(CC) -g -o id0test $(LDFLAGS) id0test.c $(LIB13) $(NETCLILIB) $(LIB2) $(LIB1) $(OTHERLIBS)
1266
1267idfetch: idfetch.c $(BNETCLILIB) $(BLIB41)
1268	$(CC) -g -o idfetch $(LDFLAGS) idfetch.c $(LIB41) $(NETCLILIB) $(LIB2) $(LIBTLS) $(LIB1) $(GNUTLS_LIBS) $(OTHERLIBS)
1269
1270# gapped BLAST client
1271# blastcl3 now has the same source code as blastall but should be compiled
1272# with -DBLAST_CS_API flag
1273blastcl3: blastall.c $(BNETCLILIB) $(BLIB36)
1274	$(CC) -g -o blastcl3 $(LDFLAGS) -DBLAST_CS_API blastall.c \
1275		$(LIB61) $(LIB60) $(LIB36) $(LIB23) $(LIBCOMPADJ) \
1276		$(NETCLILIB) $(LIB2) $(LIB1) $(OTHERLIBS)
1277
1278# BLAST 2 sequences
1279# Uses network libraries to access Entrez for retrieving sequences by gi/accession
1280bl2seq : bl2seq.c
1281	$(CC) -o bl2seq $(LDFLAGS) bl2seq.c $(LIB61) $(LIB60) $(LIB23) \
1282		$(LIBCOMPADJ) $(LIB41) $(NETCLILIB) $(LIB2) $(LIB1) \
1283		$(OTHERLIBS)
1284
1285taxblast: taxblast_main.c $(BLIB41) $(BLIB40)
1286	$(CC) -g -o taxblast $(LDFLAGS) taxblast_main.c \
1287		$(LIB61) $(LIB60) $(LIB36) $(LIB41) $(LIB40) $(LIB23) $(LIBCOMPADJ) \
1288		$(NETCLILIB) $(LIB2) $(LIB1) $(OTHERLIBS)
1289
1290# test client for the suggest network service
1291suggcli: suggcli.c $(BNETCLILIB) $(BLIB24)
1292	$(CC) -g -o suggcli $(LDFLAGS) suggcli.c $(LIB24) $(NETCLILIB) $(LIB2) $(LIB1) $(OTHERLIBS)
1293
1294# server for the suggest network service
1295suggsrv : suggsrv.c $(BSRVNETCLILIB) $(BLIB24) $(NCBI_SHLIBS).alt2
1296	$(CC) -o suggsrv $(LDFLAGS) suggsrv.c $(LIB24) $(SRVNETCLILIB) $(LIB3) $(LIB2) $(LIB1) $(OTHERLIBS)
1297
1298# 'query' program used as WWW Entrez server
1299query : query.c sumutils.c $(BLIB27) $(BLIB25) $(BLIB22)
1300	$(CC) -o query $(LDFLAGS) query.c sumutils.c $(LIB25) $(LIB27) $(LIB22) $(LIB5) $(LIB3) $(LIB2) $(LIB1) $(OTHERLIBS)
1301
1302# 'query' program used as WWW Entrez server
1303Nquery : query.c sumutils.c $(BLIB27) $(BLIB25) $(BLIB22) $(BENTREZLIBS)
1304	$(CC) -o Nquery $(LDFLAGS) query.c sumutils.c $(LIB25) $(LIB27) $(LIB22) $(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS)
1305
1306
1307# srchnt - pattern match REN search
1308
1309srchnt : srchnt.c
1310	$(CC) -o srchnt $(LDFLAGS) srchnt.c $(LIB23) $(LIBCOMPADJ) \
1311		$(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS)
1312
1313# srchaa - pattern match Prosite search or endopeptidase fragment report
1314
1315srchaa.o : srchaa.c
1316	$(CC) $(CFLAGS) -DNO_TAX_NET srchaa.c
1317
1318srchaa : srchaa.o
1319	$(CC) -o srchaa $(LDFLAGS) srchaa.o $(LIB23) $(LIBCOMPADJ) \
1320		$(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS)
1321
1322#srchaa : srchaa.c
1323#	$(CC) -o srchaa $(LDFLAGS) srchaa.c $(LIB40) $(LIB23) $(LIBCOMPADJ) \
1324		$(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS)
1325
1326# searchv - patterns - Vibrant version
1327
1328searchv : searchv.c
1329	$(CC) -o searchv $(LDFLAGS) searchv.c $(LIB20) $(LIB61) $(LIB60) \
1330		$(LIB23) $(LIBCOMPADJ) $(ENTREZLIBS) $(LIB4) $(LIB2) \
1331		 $(LIB1) $(VIBLIBS) $(OTHERLIBS)
1332
1333# mts - profile search
1334
1335mts : mts.c
1336	$(CC) -o mts $(LDFLAGS) mts.c $(LIB23) $(LIBCOMPADJ) $(ENTREZLIBS) \
1337		$(LIB2) $(LIB1) $(OTHERLIBS)
1338
1339# sigme - signal peptides and transmembrane regions
1340
1341sigme : sigme.c
1342	$(CC) -o sigme $(LDFLAGS) sigme.c $(LIB23) $(LIBCOMPADJ) \
1343		$(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS)
1344
1345# sigmev - signal peptides and transmembrane regions - Vibrant version
1346
1347sigmev : sigmev.c
1348	$(CC) -o sigmev $(LDFLAGS) sigmev.c $(LIB20) $(LIB61) $(LIB60) \
1349		$(LIB23) $(LIBCOMPADJ) $(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) \
1350		$(VIBLIBS) $(OTHERLIBS)
1351
1352# dst - low complexity nucleic acids
1353
1354dst : dst.c
1355	$(CC) -o dst $(LDFLAGS) dst.c $(LIB23) $(LIBCOMPADJ) $(ENTREZLIBS) \
1356		$(LIB2) $(LIB1) $(OTHERLIBS)
1357
1358# dustv - low complexity nucleic acids - Vibrant version
1359
1360dustv : dustv.c
1361	$(CC) -o dustv $(LDFLAGS) dustv.c $(LIB20) $(LIB61) $(LIB60) $(LIB23) \
1362		$(LIBCOMPADJ) $(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) \
1363		$(VIBLIBS) $(OTHERLIBS)
1364
1365# coiled coil prediction
1366
1367ccp : ccp.c
1368	$(CC) -o ccp $(LDFLAGS) ccp.c $(LIB23) $(LIBCOMPADJ) $(ENTREZLIBS) \
1369		$(LIB2) $(LIB1) $(OTHERLIBS)
1370
1371# coiled coil prediction - Vibrant version
1372
1373ccpv : ccpv.c
1374	$(CC) -o ccpv $(LDFLAGS) ccpv.c $(LIB20) $(LIB61) $(LIB60) $(LIB23) \
1375		$(LIBCOMPADJ) $(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) \
1376		$(VIBLIBS) $(OTHERLIBS)
1377
1378# low complexity
1379
1380epi : epi.c
1381	$(CC) -o epi $(LDFLAGS) epi.c $(LIB23) $(LIBCOMPADJ) \
1382		$(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS)
1383
1384# epiv - low complexity - Vibrant version
1385
1386epiv : epiv.c
1387	$(CC) -o epiv $(LDFLAGS) epiv.c $(LIB20) $(LIB61) $(LIB60) $(LIB23) \
1388		$(LIBCOMPADJ) $(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) \
1389		$(VIBLIBS) $(OTHERLIBS)
1390
1391# twop - identity in longest blast hit
1392
1393twop : twop.c
1394	$(CC) -o twop $(LDFLAGS) twop.c $(LIB23) $(LIBCOMPADJ) \
1395		$(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS)
1396
1397# twopv - identity in longest blast hit - Vibrant version
1398
1399twopv : twopv.c
1400	$(CC) -o twopv $(LDFLAGS) twopv.c $(LIB20) $(LIB61) $(LIB60) \
1401		$(LIB23) $(LIBCOMPADJ) $(ENTREZLIBS) $(LIB4) $(LIB2) \
1402		$(LIB1) $(VIBLIBS) $(OTHERLIBS)
1403
1404# cnsrt - codon usage relationship
1405
1406cnsrt : cnsrt.c
1407	$(CC) -o cnsrt $(LDFLAGS) cnsrt.c $(LIB23) $(LIBCOMPADJ) \
1408		$(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS)
1409
1410# cnsrtv - codon usage tree - Vibrant version
1411
1412cnsrtv : cnsrtv.c
1413	$(CC) -o cnsrtv $(LDFLAGS) cnsrtv.c $(LIB20) $(LIB61) $(LIB60) \
1414		$(LIB23) $(LIBCOMPADJ) $(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) \
1415		 $(VIBLIBS) $(OTHERLIBS)
1416
1417# cnsgn - orf selection by codon bias
1418
1419cnsgn.o : cnsgn.c
1420	$(CC) $(CFLAGS) -DNO_BLS_NET cnsgn.c
1421
1422cnsgn : cnsgn.o
1423	$(CC) -o cnsgn $(LDFLAGS) cnsgn.o $(LIB23) $(LIBCOMPADJ) \
1424		$(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS)
1425
1426#cnsgn : cnsgn.c
1427#	$(CC) -o cnsgn $(LDFLAGS) cnsgn.c $(LIB36) $(LIB23) $(LIBCOMPADJ) \
1428		$(ENTREZLIBS) $(LIB2) $(LIB1) $(OTHERLIBS)
1429
1430# cnsgnv - orf selection by codon bias - Vibrant version
1431
1432cnsgnv : cnsgnv.c
1433	$(CC) -o cnsgnv $(LDFLAGS) cnsgnv.c $(LIB20) $(LIB61) $(LIB60) \
1434		$(LIB23) $(LIBCOMPADJ) $(ENTREZLIBS) $(LIB4) $(LIB2) \
1435		$(LIB1) $(VIBLIBS) $(OTHERLIBS)
1436
1437
1438# 'sequin' direct submission tool
1439sequin : $(SRCSEQUIN) $(BENTREZLIBS) $(BLIB61) $(BLIB60) $(BLIB23) \
1440	$(BLIBCOMPADJ) $(BLIB30) $(BLIB20) \
1441	$(BLIB22) $(BLIB19) $(BLIB40) $(BLIB41) $(BLIB36) $(BLIB45) \
1442	$(BLIB11) $(BLIB8) $(BLIB7) $(NETCLIBLIB) $(BLIB5) $(BLIB4) $(BLIB3) \
1443	$(BLIB2) $(BLIB1) $(ULIB31)
1444	$(CC) -o sequin $(SEQUIN_OPTS) -I. $(LDFLAGS) $(SRCSEQUIN) \
1445	$(LIB31) $(LIB30) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB45) $(LIB19) $(LIB40) $(LIB41) \
1446	$(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) $(ENTREZLIBS) $(LIB4) \
1447	$(LIB2) $(LIBTLS) $(LIB1) $(VIBLIBS) $(GNUTLS_LIBS) $(OTHERLIBS)
1448	$(VIB_POST_LINK) sequin
1449
1450# 'sequin' direct submission tool with interprocess communication capability
1451Ssequin : $(SRCSEQUIN) $(BENTREZLIBS) $(BLIB61) $(BLIB60) $(BLIB23) \
1452	$(BLIBCOMPADJ) $(BLIB30) $(BLIB20) \
1453	$(BLIB22) $(BLIB19) $(BLIB40) $(BLIB41) $(BLIB36) $(BLIB45) \
1454	$(BLIB11) $(BLIB8) $(BLIB7) $(NETCLIBLIB) $(BLIB5) $(BLIB4) $(BLIB3) \
1455	$(BLIB2) $(BLIB1) $(ULIB31) $(ULIB33) $(THREAD_OBJ)
1456	$(CC) -o Ssequin $(SEQUIN_OPTS) -DUSE_SMARTNET -I. $(LDFLAGS) $(SRCSEQUIN) \
1457	$(THREAD_OBJ) $(LIB33) $(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) $(LIB19) $(LIB40) \
1458	$(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) \
1459	$(LIB11) $(ENTREZLIBS) $(LIB4) $(LIB2) $(LIBTLS) $(LIB1) \
1460	$(VIBLIBS) $(GNUTLS_LIBS) $(OTHERLIBS) $(THREAD_OTHERLIBS)
1461
1462# 'Psequin' ("Public Network Sequin") direct submission tool
1463Psequin : $(SRCSEQUIN) $(BENTREZLIBS) $(BLIB61) $(BLIB60) $(BLIB23) \
1464	$(BLIBCOMPADJ) $(BLIB45) $(BLIB30) $(BLIB20) \
1465	$(BLIB22) $(BLIB40) $(BLIB41) $(BLIB36) \
1466	$(BLIB11) $(BLIB8) $(BLIB7) $(NETCLIBLIB) $(BLIB5) $(BLIB4) $(BLIB3) \
1467	$(BLIB2) $(BLIB1) $(ULIB31)
1468	$(CC) -o Psequin -I. $(LDFLAGS) -UINTERNAL_NCBI_SEQUIN $(SRCSEQUIN) \
1469	$(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) \
1470	$(LIB40) $(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) \
1471	$(ENTREZLIBS) $(LIB4) $(LIB2) $(LIBTLS) $(LIB1) \
1472	$(VIBLIBS) $(GNUTLS_LIBS) $(OTHERLIBS)
1473	$(VIB_POST_LINK) Psequin
1474
1475# 'sbtedit' Submission Template Editor
1476sbtedit : $(SRCSBTEDIT) $(BENTREZLIBS) $(BLIB61) $(BLIB60) $(BLIB23) \
1477	$(BLIBCOMPADJ) $(BLIB45) $(BLIB30) $(BLIB20) \
1478	$(BLIB22) $(BLIB40) $(BLIB41) $(BLIB36) \
1479	$(BLIB11) $(BLIB8) $(BLIB7) $(NETCLIBLIB) $(BLIB5) $(BLIB4) $(BLIB3) \
1480	$(BLIB2) $(BLIB1) $(ULIB31)
1481	$(CC) -o sbtedit -I. $(LDFLAGS) -UINTERNAL_NCBI_SEQUIN $(SRCSBTEDIT) \
1482	$(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) \
1483	$(LIB40) $(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) \
1484	$(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
1485	$(VIB_POST_LINK) sbtedit
1486
1487# 'streamer' Sequinesque Stream Editor
1488streamer : $(SRCSTREAMER) $(BENTREZLIBS) $(BLIB61) $(BLIB60) $(BLIB23) \
1489	$(BLIBCOMPADJ) $(BLIB45) $(BLIB30) $(BLIB20) \
1490	$(BLIB22) $(BLIB40) $(BLIB41) $(BLIB36) \
1491	$(BLIB11) $(BLIB8) $(BLIB7) $(NETCLIBLIB) $(BLIB5) $(BLIB4) $(BLIB3) \
1492	$(BLIB2) $(BLIB1) $(ULIB31)
1493	$(CC) -o streamer -I. $(LDFLAGS) -UINTERNAL_NCBI_SEQUIN $(SRCSTREAMER) \
1494	$(LIB30) $(LIB45) $(LIB31) $(LIB20) $(LIB61) $(LIB60) $(LIB22) \
1495	$(LIB40) $(LIB41) $(LIB36) $(LIB23) $(LIBCOMPADJ) $(LIB11) \
1496	$(ENTREZLIBS) $(LIB4) $(LIB2) $(LIB1) $(VIBLIBS) $(OTHERLIBS)
1497	$(VIB_POST_LINK) streamer
1498
1499salogif.o:	salogif.c
1500	$(CC) $(CFLAGS) salogif.c
1501
1502xmlblast.o:	xmlblast.c
1503	$(CC) $(CFLAGS) xmlblast.c
1504
1505bxmlobj.o:	bxmlobj.c
1506	$(CC) $(CFLAGS) bxmlobj.c
1507
1508# test_ncbi_socket
1509
1510test_ncbi_socket : test_ncbi_socket.c
1511	$(CC) -o test_ncbi_socket $(LDFLAGS) test_ncbi_socket.c -DNCBI_C $(LIB1) $(OTHERLIBS)
1512
1513# test_ncbi_dsock
1514
1515test_ncbi_dsock : test_ncbi_dsock.c
1516	$(CC) -o test_ncbi_dsock $(LDFLAGS) test_ncbi_dsock.c -DNCBI_C $(LIB1) $(OTHERLIBS)
1517
1518# debug_server
1519
1520debug_server : debug_server.c
1521	$(CC) -o debug_server $(LDFLAGS) debug_server.c $(LIB1) $(OTHERLIBS)
1522
1523# blast www server
1524
1525psiblast.REAL : psiblast.c wwwbutl.c
1526	$(CC) -o psiblast.REAL $(LDFLAGS) psiblast.c wwwbutl.c $(THREAD_OBJ) \
1527	$(LIB20) $(LIB61) $(LIB60) $(LIB23) $(LIBCOMPADJ) \
1528	-lvibgif $(LIB2) $(LIB1) $(OTHERLIBS) $(THREAD_OTHERLIBS)
1529
1530psiblast_cs.REAL : psiblast.c wwwbutl.c
1531	$(CC) -o psiblast_cs.REAL $(LDFLAGS) -DNCBI_ENTREZ_CLIENT psiblast.c wwwbutl.c \
1532	$(THREAD_OBJ) $(LIB40) $(LIB41) $(LIB36) $(LIB6) $(LIB20) $(LIB61) \
1533	$(LIB60) $(LIB23) $(LIBCOMPADJ) -lvibgif \
1534	$(LIB2) $(LIB1) $(OTHERLIBS) 	$(THREAD_OTHERLIBS)
1535
1536blast.REAL : wwwblast.c wwwbutl.c
1537	$(CC) -o blast.REAL $(LDFLAGS) wwwblast.c wwwbutl.c $(THREAD_OBJ) \
1538	$(LIB20) $(LIB61) $(LIB60) $(LIB23) $(LIBCOMPADJ) -lvibgif $(LIB2) \
1539	$(LIB1) $(OTHERLIBS) $(THREAD_OTHERLIBS)
1540
1541blast_cs.REAL : wwwblast.c wwwbutl.c
1542	$(CC) -o blast_cs.REAL $(LDFLAGS) -DNCBI_ENTREZ_CLIENT wwwblast.c wwwbutl.c \
1543	$(THREAD_OBJ) $(LIB40) $(LIB41) $(LIB36) $(LIB6) $(LIB20) $(LIB61) \
1544	$(LIB60) $(LIB23) $(LIBCOMPADJ) -lvibgif \
1545	$(LIB2) $(LIB1) $(OTHERLIBS) $(THREAD_OTHERLIBS)
1546
1547nph-viewgif.cgi : viewgif.c
1548	$(CC) -o nph-viewgif.cgi $(LDFLAGS) viewgif.c
1549
1550wblast2.REAL : wblast2.c
1551	$(CC) -o wblast2.REAL $(LDFLAGS) -DBL2SEQ_STANDALONE wblast2.c \
1552	$(LIB61) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB60) $(LIB1) $(OTHERLIBS)
1553
1554
1555wblast2_cs.REAL : wblast2.c
1556	$(CC) -o wblast2_cs.REAL $(LDFLAGS) -DNCBI_ENTREZ_CLIENT -DBL2SEQ_STANDALONE \
1557	wblast2.c $(LIB41) $(LIB6) $(LIB61) $(LIB23) $(LIBCOMPADJ) \
1558	$(LIB2) $(LIB60) $(LIB1) \
1559	$(OTHERLIBS)
1560
1561bl2bag.cgi : bl2bag.c
1562	$(CC) -o bl2bag.cgi $(LDFLAGS) bl2bag.c $(LIB1) $(OTHERLIBS)
1563
1564# src_chk
1565
1566src_chk : src_chk.c
1567	$(CC) -o src_chk $(LDFLAGS) src_chk.c $(LIB2) $(LIB1) $(OTHERLIBS)
1568
1569src_chk_psf : src_chk_psf.o
1570	$(CC) -g -o src_chk_psf $(LDFLAGS) src_chk_psf.o.c \
1571		$(LIB_PS) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) \
1572		$(NCBI_SYBLIBS_CT) $(OTHERLIBS)
1573
1574src_chk_psf.o :	src_chk.c
1575	$(CC) $(CFLAGS) -c -DINTERNAL_NCBI_SRC_CHK -g -o src_chk_psf.o src_chk.c
1576
1577# tbl_chk
1578
1579tbl_chk : tbl_chk.c
1580	$(CC) -o tbl_chk $(LDFLAGS) tbl_chk.c $(LIB2) $(LIB1) $(OTHERLIBS)
1581
1582tbl_chk_psf : tbl_chk_psf.o
1583	$(CC) -g -o tbl_chk_psf $(LDFLAGS) tbl_chk_psf.o \
1584		$(LIB_PS) $(LIB23) $(LIBCOMPADJ) $(LIB2) $(LIB1) \
1585		$(NCBI_SYBLIBS_CT) $(OTHERLIBS)
1586
1587tbl_chk_psf.o :	tbl_chk.c
1588	$(CC) $(CFLAGS) -c -DINTERNAL_NCBI_TBL_CHK -g -o tbl_chk_psf.o tbl_chk.c
1589
1590# export_cmt
1591
1592export_cmt : export_cmt.c
1593	$(CC) -o export_cmt $(LDFLAGS) export_cmt.c $(LIB23) $(LIB8) $(LIB7) \
1594		$(LIB6) $(LIB3) $(LIB2) $(LIB1) $(OTHERLIBS)
1595
1596# flat2asn
1597
1598flat2asn : flat2asn.c
1599	$(CC) -o flat2asn $(LDFLAGS) flat2asn.c $(LIB38) $(LIB37) $(LIB34) \
1600	    $(LIB40) $(LIB11) $(LIB_PS) $(LIB23) $(LIB6) $(LIB2) $(LIB1) \
1601	    $(NCBI_SYBLIBS_CT) $(OTHERLIBS)
1602
1603##
1604