1## Process this file with automake to produce Makefile.in
2
3SUBDIRS = acd data index
4
5AM_CFLAGS  = $(WARN_CFLAGS) $(DEVWARN_CFLAGS)
6if ISSHARED
7if ISAIXIA64
8AM_CFLAGS += -Wl,-bdynamic
9AM_CFLAGS += -Wl,-brtl
10AM_CFLAGS += -L../ajax/pcre/.libs
11AM_CFLAGS += -L../ajax/expat/.libs
12AM_CFLAGS += -L../ajax/zlib/.libs
13AM_CFLAGS += -L../ajax/core/.libs
14AM_CFLAGS += -L../ajax/graphics/.libs
15AM_CFLAGS += -L../ajax/ensembl/.libs
16AM_CFLAGS += -L../ajax/ajaxdb/.libs
17AM_CFLAGS += -L../ajax/acd/.libs
18AM_CFLAGS += -lacd
19AM_CFLAGS += -lajaxdb
20AM_CFLAGS += -lensembl
21AM_CFLAGS += -lajaxg
22AM_CFLAGS += -lajax
23AM_CFLAGS += -leexpat
24AM_CFLAGS += -lepcre
25AM_CFLAGS += -lezlib
26endif
27endif
28
29AM_CPPFLAGS  = -I$(top_srcdir)/ajax/acd
30AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb
31AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl
32AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics
33AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre
34if !ESYSTEMLIBS
35AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat
36AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib
37endif
38AM_CPPFLAGS += -I$(top_srcdir)/nucleus
39AM_CPPFLAGS += -I$(top_srcdir)/plplot
40AM_CPPFLAGS += $(AXIS2C_CPPFLAGS)
41AM_CPPFLAGS += $(JAVA_CPPFLAGS)
42
43LDADD  = ../nucleus/libnucleus.la
44LDADD += ../ajax/acd/libacd.la
45LDADD += ../ajax/ajaxdb/libajaxdb.la
46LDADD += ../ajax/ensembl/libensembl.la
47LDADD += ../ajax/graphics/libajaxg.la
48LDADD += ../ajax/core/libajax.la
49if !ESYSTEMLIBS
50LDADD += ../ajax/zlib/libezlib.la
51LDADD += ../ajax/expat/libeexpat.la
52endif
53LDADD += ../ajax/pcre/libepcre.la
54LDADD += ../plplot/libeplplot.la
55LDADD += $(XLIB)
56
57#if PURIFY
58#LINK = purify $(LIBTOOL) --mode=link $(CC) $(CFLAGS) $(LDFLAGS) -o $@
59#endif
60
61# Applications, which are not built.
62#
63# dbget
64# dbgeturl
65# dbshowdat
66# dbshowquery
67# dbtellquery
68# docxmlvalid
69# docxmlwell
70# entrygo
71# entrytax
72# goseq
73# isdbdata
74# isdbname
75# seqgo
76# seqtax
77# taxseq
78# template ###
79# texttotext
80# texttoxml
81# textvalid
82# xmltotext
83# xmltoxml
84# xmltransform
85
86check_PROGRAMS = \
87acdrelations \
88acdxsd \
89ajtest \
90complex \
91corbatest \
92dastest \
93dbfetchtest \
94domtesta \
95domtestb \
96domtestc \
97domtestd \
98edamclean \
99ensembltest \
100entrails \
101entrailsbook \
102entrailshtml \
103entrailswiki \
104histogramtest \
105intconv \
106martattributes \
107martdatasets \
108martfilters \
109martquery \
110martregistry \
111martseqs \
112newcoils \
113origsplitter \
114origunion \
115patmattest \
116prima \
117primers \
118seqinfo \
119seqretall \
120seqretallfeat \
121seqretset \
122seqretsingle \
123seqrettype \
124sqltest \
125testplot \
126treetypedisplay
127
128bin_PROGRAMS = \
129aaindexextract \
130abiview \
131acdc \
132acdgalaxy \
133acdlog \
134acdpretty \
135acdtable \
136acdtrace \
137acdvalid \
138aligncopy \
139aligncopypair \
140antigenic \
141assemblyget \
142backtranambig \
143backtranseq \
144banana \
145biosed \
146btwisted \
147cachedas \
148cachedbfetch \
149cacheebeyesearch \
150cacheensembl \
151cai \
152chaos \
153charge \
154checktrans \
155chips \
156cirdna \
157codcmp \
158codcopy \
159coderet \
160compseq \
161cons \
162consambig \
163cpgplot \
164cpgreport \
165cusp \
166cutgextract \
167cutseq \
168dan \
169dbiblast \
170dbifasta \
171dbiflat \
172dbigcg \
173dbtell \
174dbxcompress \
175dbxedam \
176dbxfasta \
177dbxflat \
178dbxgcg \
179dbxobo \
180dbxreport \
181dbxresource \
182dbxstat \
183dbxtax \
184dbxuncompress \
185degapseq \
186density \
187descseq \
188diffseq \
189distmat \
190dotmatcher \
191dotpath \
192dottup \
193dreg \
194drfinddata \
195drfindformat \
196drfindid \
197drfindresource \
198drget \
199drtext \
200edamdef \
201edamhasinput \
202edamhasoutput \
203edamisformat \
204edamisid \
205edamname \
206edialign \
207einverted \
208embossdata \
209embossupdate \
210embossversion \
211emma \
212emowse \
213entret \
214epestfind \
215eprimer3 \
216eprimer32 \
217equicktandem \
218est2genome \
219etandem \
220extractalign \
221extractfeat \
222extractseq \
223featcopy \
224featmerge \
225featreport \
226feattext \
227findkm \
228freak \
229fuzznuc \
230fuzzpro \
231fuzztran \
232garnier \
233geecee \
234getorf \
235godef \
236goname \
237helixturnhelix \
238hmoment \
239iep \
240infoalign \
241infoassembly \
242infobase \
243inforesidue \
244infoseq \
245isochore \
246jaspextract \
247jaspscan \
248jembossctl \
249lindna \
250listor \
251makenucseq \
252makeprotseq \
253marscan \
254maskambignuc \
255maskambigprot \
256maskfeat \
257maskseq \
258matcher \
259megamerger \
260merger \
261msbar \
262mwcontam \
263mwfilter \
264needle \
265needleall \
266newcpgreport \
267newcpgseek \
268newseq \
269nohtml \
270noreturn \
271nospace \
272notab \
273notseq \
274nthseq \
275nthseqset \
276octanol \
277oddcomp \
278ontocount \
279ontoget \
280ontogetcommon \
281ontogetdown \
282ontogetobsolete \
283ontogetroot \
284ontogetsibs \
285ontogetup \
286ontoisobsolete \
287ontotext \
288palindrome \
289pasteseq \
290patmatdb \
291patmatmotifs \
292pepcoil \
293pepdigest \
294pepinfo \
295pepnet \
296pepstats \
297pepwheel \
298pepwindow \
299pepwindowall \
300plotcon \
301plotorf \
302polydot \
303preg \
304prettyplot \
305prettyseq \
306primersearch \
307printsextract \
308profit \
309prophecy \
310prophet \
311prosextract \
312pscan \
313psiphi \
314rebaseextract \
315recoder \
316redata \
317refseqget \
318remap \
319restover \
320restrict \
321revseq \
322seealso \
323seqcount \
324seqmatchall \
325seqret \
326seqretsetall \
327seqretsplit \
328seqxref \
329seqxrefget \
330servertell \
331showalign \
332showdb \
333showfeat \
334showorf \
335showpep \
336showseq \
337showserver \
338shuffleseq \
339sigcleave \
340silent \
341sirna \
342sixpack \
343sizeseq \
344skipredundant \
345skipseq \
346splitsource \
347splitter \
348stretcher \
349stssearch \
350supermatcher \
351syco \
352taxget \
353taxgetdown \
354taxgetrank \
355taxgetspecies \
356taxgetup \
357tcode \
358textget \
359textsearch \
360tfextract \
361tfm \
362tfscan \
363tmap \
364tranalign \
365transeq \
366trimest \
367trimseq \
368trimspace \
369twofeat \
370union \
371urlget \
372variationget \
373vectorstrip \
374water \
375whichdb \
376wobble \
377wordcount \
378wordfinder \
379wordmatch \
380wossdata \
381wossinput \
382wossname \
383wossoperation \
384wossoutput \
385wossparam \
386wosstopic \
387xmlget \
388xmltext \
389yank
390
391dist_pkgdata_DATA = \
392emboss.default.template \
393emboss.standard \
394server.biomart \
395server.dasregistry \
396server.dbfetch server.dkfz \
397server.ebeye \
398server.entrez \
399server.ensembl \
400server.ensemblgenomes \
401server.mrs \
402server.mrs3 \
403server.mrs4 \
404server.srs \
405server.wsdbfetch
406
407# EMBOSS bin application SOURCES
408
409aaindexextract_SOURCES = aaindexextract.c
410abiview_SOURCES = abiview.c
411acdc_SOURCES = acdc.c
412acdgalaxy_SOURCES = acdgalaxy.c
413acdpretty_SOURCES = acdpretty.c
414acdtable_SOURCES = acdtable.c
415acdtrace_SOURCES = acdtrace.c
416acdvalid_SOURCES = acdvalid.c
417aligncopy_SOURCES = aligncopy.c
418aligncopypair_SOURCES = aligncopypair.c
419antigenic_SOURCES = antigenic.c
420assemblyget_SOURCES = assemblyget.c
421backtranambig_SOURCES = backtranambig.c
422backtranseq_SOURCES = backtranseq.c
423banana_SOURCES = banana.c
424biosed_SOURCES = biosed.c
425btwisted_SOURCES = btwisted.c
426cachedas_SOURCES = cachedas.c
427cachedbfetch_SOURCES = cachedbfetch.c
428cacheebeyesearch_SOURCES = cacheebeyesearch.c
429cacheensembl_SOURCES = cacheensembl.c
430cai_SOURCES = cai.c
431chaos_SOURCES = chaos.c
432charge_SOURCES = charge.c
433checktrans_SOURCES = checktrans.c
434chips_SOURCES = chips.c
435cirdna_SOURCES = cirdna.c
436codcmp_SOURCES = codcmp.c
437codcopy_SOURCES = codcopy.c
438coderet_SOURCES = coderet.c
439compseq_SOURCES = compseq.c
440cons_SOURCES = cons.c
441consambig_SOURCES = consambig.c
442cpgplot_SOURCES = cpgplot.c
443cpgreport_SOURCES = cpgreport.c
444cusp_SOURCES = cusp.c
445cutgextract_SOURCES = cutgextract.c
446cutseq_SOURCES = cutseq.c
447dan_SOURCES = dan.c
448dbiblast_SOURCES = dbiblast.c
449dbifasta_SOURCES = dbifasta.c
450dbiflat_SOURCES = dbiflat.c
451dbigcg_SOURCES = dbigcg.c
452dbtell_SOURCES = dbtell.c
453dbxcompress_SOURCES = dbxcompress.c
454dbxedam_SOURCES = dbxedam.c
455dbxfasta_SOURCES = dbxfasta.c
456dbxflat_SOURCES = dbxflat.c
457dbxgcg_SOURCES = dbxgcg.c
458dbxobo_SOURCES = dbxobo.c
459dbxreport_SOURCES = dbxreport.c
460dbxresource_SOURCES = dbxresource.c
461dbxstat_SOURCES = dbxstat.c
462dbxtax_SOURCES = dbxtax.c
463dbxuncompress_SOURCES = dbxuncompress.c
464degapseq_SOURCES = degapseq.c
465density_SOURCES = density.c
466descseq_SOURCES = descseq.c
467diffseq_SOURCES = diffseq.c
468distmat_SOURCES = distmat.c
469dotmatcher_SOURCES = dotmatcher.c
470dotpath_SOURCES = dotpath.c
471dottup_SOURCES = dottup.c
472dreg_SOURCES = dreg.c
473drfinddata_SOURCES = drfinddata.c
474drfindformat_SOURCES = drfindformat.c
475drfindid_SOURCES = drfindid.c
476drfindresource_SOURCES = drfindresource.c
477drget_SOURCES = drget.c
478drtext_SOURCES = drtext.c
479edamdef_SOURCES = edamdef.c
480edamhasinput_SOURCES = edamhasinput.c
481edamhasoutput_SOURCES = edamhasoutput.c
482edamisformat_SOURCES = edamisformat.c
483edamisid_SOURCES = edamisid.c
484edamname_SOURCES = edamname.c
485edialign_SOURCES = edialign.c
486einverted_SOURCES = einverted.c
487embossdata_SOURCES = embossdata.c
488embossversion_SOURCES = embossversion.c
489emma_SOURCES = emma.c
490emowse_SOURCES = emowse.c
491entret_SOURCES = entret.c
492epestfind_SOURCES = epestfind.c
493eprimer3_SOURCES = eprimer3.c
494eprimer32_SOURCES = eprimer32.c
495equicktandem_SOURCES = equicktandem.c
496est2genome_SOURCES = est2genome.c
497etandem_SOURCES = etandem.c
498extractalign_SOURCES = extractalign.c
499extractfeat_SOURCES = extractfeat.c
500extractseq_SOURCES = extractseq.c
501featcopy_SOURCES = featcopy.c
502featmerge_SOURCES = featmerge.c
503featreport_SOURCES = featreport.c
504feattext_SOURCES = feattext.c
505findkm_SOURCES = findkm.c
506freak_SOURCES = freak.c
507fuzznuc_SOURCES = fuzznuc.c
508fuzzpro_SOURCES = fuzzpro.c
509fuzztran_SOURCES = fuzztran.c
510garnier_SOURCES = garnier.c
511geecee_SOURCES = geecee.c
512getorf_SOURCES = getorf.c
513godef_SOURCES = godef.c
514goname_SOURCES = goname.c
515helixturnhelix_SOURCES = helixturnhelix.c
516hmoment_SOURCES = hmoment.c
517iep_SOURCES = iep.c
518infoalign_SOURCES = infoalign.c
519infoassembly_SOURCES = infoassembly.c
520infobase_SOURCES = infobase.c
521inforesidue_SOURCES = inforesidue.c
522infoseq_SOURCES = infoseq.c
523isochore_SOURCES = isochore.c
524jaspextract_SOURCES = jaspextract.c
525jaspscan_SOURCES = jaspscan.c
526jembossctl_SOURCES = jembossctl.c
527lindna_SOURCES = lindna.c
528listor_SOURCES = listor.c
529makenucseq_SORCES = makenucseq.c
530makeprotseq_SOURCES = makeprotseq.c
531marscan_SOURCES = marscan.c
532maskambignuc_SOURCES = maskambignuc.c
533maskambigprot_SOURCES = maskambigprot.c
534maskfeat_SOURCES = maskfeat.c
535maskseq_SOURCES = maskseq.c
536matcher_SOURCES = matcher.c
537megamerger_SOURCES = megamerger.c
538merger_SOURCES = merger.c
539msbar_SOURCES = msbar.c
540mwcontam_SOURCES = mwcontam.c
541mwfilter_SOURCES = mwfilter.c
542needle_SOURCES = needle.c
543needleall_SOURCES = needleall.c
544newcpgreport_SOURCES = newcpgreport.c
545newcpgseek_SOURCES = newcpgseek.c
546newseq_SOURCES = newseq.c
547nohtml_SOURCES = nohtml.c
548noreturn_SOURCES = noreturn.c
549nospace_SOURCES = nospace.c
550notab_SOURCES = notab.c
551notseq_SOURCES = notseq.c
552nthseq_SOURCES = nthseq.c
553nthseqset_SOURCES = nthseqset.c
554octanol_SOURCES = octanol.c
555oddcomp_SOURCES = oddcomp.c
556ontocount_SOURCES = ontocount.c
557ontoget_SOURCES = ontoget.c
558ontogetcommon_SOURCES = ontogetcommon.c
559ontogetdown_SOURCES = ontogetdown.c
560ontogetobsolete_SOURCES = ontogetobsolete.c
561ontogetroot_SOURCES = ontogetroot.c
562ontogetsibs_SOURCES = ontogetsibs.c
563ontogetup_SOURCES = ontogetup.c
564ontoisobsolete_SOURCES = ontoisobsolete.c
565ontotext_SOURCES = ontotext.c
566palindrome_SOURCES = palindrome.c
567pasteseq_SOURCES = pasteseq.c
568patmatdb_SOURCES = patmatdb.c
569patmatmotifs_SOURCES = patmatmotifs.c
570pepcoil_SOURCES = pepcoil.c
571pepdigest_SOURCES = pepdigest.c
572pepinfo_SOURCES = pepinfo.c
573pepnet_SOURCES = pepnet.c
574pepstats_SOURCES = pepstats.c
575pepwheel_SOURCES = pepwheel.c
576pepwindow_SOURCES = pepwindow.c
577pepwindowall_SOURCES = pepwindowall.c
578plotcon_SOURCES = plotcon.c
579plotorf_SOURCES = plotorf.c
580polydot_SOURCES = polydot.c
581preg_SOURCES = preg.c
582prettyplot_SOURCES = prettyplot.c
583prettyseq_SOURCES = prettyseq.c
584primersearch_SOURCES = primersearch.c
585printsextract_SOURCES = printsextract.c
586profit_SOURCES = profit.c
587prophecy_SOURCES = prophecy.c
588prophet_SOURCES = prophet.c
589prosextract_SOURCES = prosextract.c
590pscan_SOURCES = pscan.c
591psiphi_SOURCES = psiphi.c
592rebaseextract_SOURCES = rebaseextract.c
593recoder_SOURCES = recoder.c
594redata_SOURCES = redata.c
595refseqget_SOURCES = refseqget.c
596remap_SOURCES = remap.c
597restover_SOURCES = restover.c
598restrict_SOURCES = restrict.c
599revseq_SOURCES = revseq.c
600seealso_SOURCES = seealso.c
601seqcount_SOURCES = seqcount.c
602seqmatchall_SOURCES = seqmatchall.c
603seqret_SOURCES = seqret.c
604seqretsetall_SOURCES = seqretsetall.c
605seqretsplit_SOURCES = seqretsplit.c
606seqxref_SOURCES = seqxref.c
607seqxrefget_SOURCES = seqxrefget.c
608servertell_SOURCES = servertell.c
609showalign_SOURCES = showalign.c
610showdb_SOURCES = showdb.c
611showfeat_SOURCES = showfeat.c
612showorf_SOURCES = showorf.c
613showpep_SOURCES = showpep.c
614showseq_SOURCES = showseq.c
615showserver_SOURCES = showserver.c
616shuffleseq_SOURCES = shuffleseq.c
617sigcleave_SOURCES = sigcleave.c
618silent_SOURCES = silent.c
619sirna_SOURCES = sirna.c
620sixpack_SOURCES = sixpack.c
621sizeseq_SOURCES = sizeseq.c
622skipredundant_SOURCES = skipredundant.c
623skipseq_SOURCES = skipseq.c
624splitsource_SOURCES = splitsource.c
625splitter_SOURCES = splitter.c
626stretcher_SOURCES = stretcher.c
627stssearch_SOURCES = stssearch.c
628supermatcher_SOURCES = supermatcher.c
629syco_SOURCES = syco.c
630taxget_SOURCES = taxget.c
631taxgetdown_SOURCES = taxgetdown.c
632taxgetrank_SOURCES = taxgetrank.c
633taxgetspecies_SOURCES = taxgetspecies.c
634taxgetup_SOURCES = taxgetup.c
635tcode_SOURCES = tcode.c
636textget_SOURCE = textget.c
637textsearch_SOURCES = textsearch.c
638tfextract_SOURCES = tfextract.c
639tfm_SOURCES = tfm.c
640tfscan_SOURCES = tfscan.c
641tmap_SOURCES = tmap.c
642tranalign_SOURCES = tranalign.c
643transeq_SOURCES = transeq.c
644trimest_SOURCES = trimest.c
645trimseq_SOURCES = trimseq.c
646trimspace_SOURCES = trimspace.c
647twofeat_SOURCES = twofeat.c
648union_SOURCES = union.c
649urlget_SOURCES = urlget.c
650variationget_SOURCES = variationget.c
651vectorstrip_SOURCES = vectorstrip.c
652water_SOURCES = water.c
653whichdb_SOURCES = whichdb.c
654wobble_SOURCES = wobble.c
655wordcount_SOURCES = wordcount.c
656wordfinder_SOURCES = wordfinder.c
657wordmatch_SOURCES = wordmatch.c
658wossdata_SOURCES = wossdata.c
659wossinput_SOURCES = wossinput.c
660wossname_SOURCES = wossname.c
661wossoperation_SOURCES = wossoperation.c
662wossoutput_SOURCES = wossoutput.c
663wossparam_SOURCES = wossparam.c
664wosstopic_SOURCES = wosstopic.c
665xmlget_SOURCES = xmlget.c
666xmltext_SOURCES = xmltext.c
667yank_SOURCES = yank.c
668
669# EMBOSS check application SOURCES
670
671acdlog_SOURCES = acdlog.c
672acdrelations_SOURCES = acdrelations.c
673acdxsd_SOURCES = acdxsd.c
674ajtest_SOURCES = ajtest.c
675complex_SOURCES = complex.c
676corbatest_SOURCES = corbatest.c
677dastest_SOURCES = dastest.c
678dbfetchtest_SOURCES = dbfetchtest.c
679domtesta_SOURCES = domtesta.c
680domtestb_SOURCES = domtestb.c
681domtestc_SOURCES = domtestc.c
682domtestd_SOURCES = domtestd.c
683edamclean_SOURCES = edamclean.c
684ensembltest_SOURCES = ensembltest.c
685entrails_SOURCES = entrails.c
686entrailsbook_SOURCES = entrailsbook.c
687entrailshtml_SOURCES = entrailshtml.c
688entrailswiki_SOURCES = entrailswiki.c
689histogramtest_SOURCES = histogramtest.c
690intconv_SOURCES = intconv.c
691martattributes_SOURCES = martattributes.c
692martdatasets_SOURCES = martdatasets.c
693martfilters_SOURCES = martfilters.c
694martquery_SOURCES = martquery.c
695martregistry_SOURCES = martregistry.c
696martseqs_SOURCES = martseqs.c
697newcoils_SOURCES = newcoils.c
698origsplitter_SOURCES = origsplitter.c
699origunion_SOURCES = origunion.c
700patmattest_SOURCES = patmattest.c
701prima_SOURCES = prima.c
702primers_SOURCES = primers.c
703seqinfo_SOURCES = seqinfo.c
704seqretall_SOURCES = seqretall.c
705seqretallfeat_SOURCES = seqretallfeat.c
706seqretset_SOURCES = seqretset.c
707seqretsingle_SOURCES = seqretsingle.c
708seqrettype_SOURCES = seqrettype.c
709sqltest_SOURCES = sqltest.c
710testplot_SOURCES = testplot.c
711treetypedisplay_SOURCES = treetypedisplay.c
712