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