makefile

   1 ###################################################\r
   2 #\r
   3 # Makefile for mothur\r
   4 # Creator [Xcode -> Makefile Ver: Feb 14 2007 09:18:41]\r
   5 # Created: April 16, 2010\r
   6 #\r
   7 ###################################################\r
   8 \r
   9 #\r
  10 # Macros\r
  11 #\r
  12 \r
  13 CC = mpic++\r
  14 CC_OPTIONS = -O3\r
  15 \r
  16 # if you do not want to use the readline library set to no, default yes.\r
  17 # make sure you have the library installed\r
  18 \r
  19 USEREADLINE ?= yes\r
  20 \r
  21 ifeq  ($(strip $(USEREADLINE)),yes)\r
  22     CC_OPTIONS += -DUSE_READLINE\r
  23         LNK_OPTIONS += \\r
  24       -lreadline\\r
  25       -lncurses\\r
  26       -L../readline-6.0\r
  27 endif\r
  28 \r
  29 USEMPI ?= no\r
  30 \r
  31 ifeq  ($(strip $(USEMPI)),yes)\r
  32     CC_OPTIONS += -DUSE_MPI\r
  33 endif\r
  34 \r
  35 #\r
  36 # INCLUDE directories for mothur\r
  37 #\r
  38
  39      INCLUDE = -I.
  40 \r
  41 #\r
  42 # Build mothur\r
  43 #\r
  44 \r
  45 mothur : \\r
  46                 ./sharedutilities.o\\r
  47                 ./treegroupscommand.o\\r
  48                 ./bootstrapsharedcommand.o\\r
  49                 ./matrixoutputcommand.o\\r
  50                 ./getoturepcommand.o\\r
  51                 ./screenseqscommand.o\\r
  52                 ./chimera.o\\r
  53                 ./decalc.o\\r
  54                 ./readotucommand.o\\r
  55                 ./readdistcommand.o\\r
  56                 ./commandfactory.o\\r
  57                 ./alignment.o\\r
  58                 ./alignmentcell.o\\r
  59                 ./gotohoverlap.o\\r
  60                 ./overlap.o\\r
  61                 ./needlemanoverlap.o\\r
  62                 ./blastalign.o\\r
  63                 ./noalign.o\\r
  64                 ./suffixdb.o\\r
  65                 ./suffixnodes.o\\r
  66                 ./suffixtree.o\\r
  67                 ./blastdb.o\\r
  68                 ./nast.o\\r
  69                 ./nastreport.o\\r
  70                 ./boneh.o\\r
  71                 ./efron.o\\r
  72                 ./solow.o\\r
  73                 ./unifracweightedcommand.o\\r
  74                 ./weighted.o\\r
  75                 ./unweighted.o\\r
  76                 ./unifracunweightedcommand.o\\r
  77                 ./getsabundcommand.o\\r
  78                 ./getrabundcommand.o\\r
  79                 ./bellerophon.o\\r
  80                 ./pintail.o\\r
  81                 ./sharedanderbergs.o\\r
  82                 ./venncommand.o\\r
  83                 ./venn.o\\r
  84                 ./fullmatrix.o\\r
  85                 ./heatmap.o\\r
  86                 ./heatmapcommand.o\\r
  87                 ./libshuffcommand.o\\r
  88                 ./nocommands.o\\r
  89                 ./sharedbraycurtis.o\\r
  90                 ./sharedkulczynski.o\\r
  91                 ./sharedlennon.o\\r
  92                 ./sharedkulczynskicody.o\\r
  93                 ./sharedmorisitahorn.o\\r
  94                 ./sharedochiai.o\\r
  95                 ./readcolumn.o\\r
  96                 ./readotu.o\\r
  97                 ./readphylip.o\\r
  98                 ./consensuscommand.o\\r
  99                 ./heatmapsimcommand.o\\r
 100                 ./heatmapsim.o\\r
 101                 ./optionparser.o\\r
 102                 ./filterseqscommand.o\\r
 103                 ./goodscoverage.o\\r
 104                 ./sequencedb.o\\r
 105                 ./sharedjackknife.o\\r
 106                 ./sharedmarczewski.o\\r
 107                 ./aligncommand.o\\r
 108                 ./treemap.o\\r
 109                 ./parsimonycommand.o\\r
 110                 ./parsimony.o\\r
 111                 ./seqsummarycommand.o\\r
 112                 ./chimeraccodecommand.o\\r
 113                 ./chimerabellerophoncommand.o\\r
 114                 ./chimeracheckcommand.o\\r
 115                 ./chimeraslayercommand.o\\r
 116                 ./chimerapintailcommand.o\\r
 117                 ./chimeraseqscommand.o\\r
 118                 ./sharedlistvector.o\\r
 119                 ./tree.o\\r
 120                 ./readtree.o\\r
 121                 ./sharedsobscollectsummary.o\\r
 122                 ./deconvolutecommand.o\\r
 123                 ./listseqscommand.o\\r
 124                 ./getseqscommand.o\\r
 125                 ./removeseqscommand.o\\r
 126                 ./systemcommand.o\\r
 127                 ./binsequencecommand.o\\r
 128                 ./distancecommand.o\\r
 129                 ./ace.o\\r
 130                 ./averagelinkage.o\\r
 131                 ./bootstrap.o\\r
 132                 ./calculator.o\\r
 133                 ./chao1.o\\r
 134                 ./cluster.o\\r
 135                 ./clustercommand.o\\r
 136                 ./collect.o\\r
 137                 ./collectcommand.o\\r
 138                 ./collectsharedcommand.o\\r
 139                 ./commandoptionparser.o\\r
 140                 ./completelinkage.o\\r
 141                 ./database.o\\r
 142                 ./engine.o\\r
 143                 ./fastamap.o\\r
 144                 ./fileoutput.o\\r
 145                 ./globaldata.o\\r
 146                 ./groupmap.o\\r
 147                 ./helpcommand.o\\r
 148                 ./inputdata.o\\r
 149                 ./jackknife.o\\r
 150                 ./kmer.o\\r
 151                 ./kmerdb.o\\r
 152                 ./listvector.o\\r
 153                 ./mothur.o\\r
 154                 ./nameassignment.o\\r
 155                 ./npshannon.o\\r
 156                 ./ordervector.o\\r
 157                 ./progress.o\\r
 158                 ./quitcommand.o\\r
 159                 ./rabundvector.o\\r
 160                 ./rarecalc.o\\r
 161                 ./raredisplay.o\\r
 162                 ./rarefact.o\\r
 163                 ./rarefactcommand.o\\r
 164                 ./rarefactsharedcommand.o\\r
 165                 ./sabundvector.o\\r
 166                 ./sequence.o\\r
 167                 ./shannon.o\\r
 168                 ./sharedace.o\\r
 169                 ./sharedchao1.o\\r
 170                 ./sharedcommand.o\\r
 171                 ./sharedjabund.o\\r
 172                 ./sharedjclass.o\\r
 173                 ./sharedjest.o\\r
 174                 ./sharedordervector.o\\r
 175                 ./sharedrabundvector.o\\r
 176                 ./sharedsabundvector.o\\r
 177                 ./sharedsobs.o\\r
 178                 ./sharedsorabund.o\\r
 179                 ./sharedsorclass.o\\r
 180                 ./sharedsorest.o\\r
 181                 ./sharedthetan.o\\r
 182                 ./sharedthetayc.o\\r
 183                 ./simpson.o\\r
 184                 ./singlelinkage.o\\r
 185                 ./sparsematrix.o\\r
 186                 ./summarycommand.o\\r
 187                 ./summarysharedcommand.o\\r
 188                 ./uvest.o\\r
 189                 ./validcalculator.o\\r
 190                 ./validparameter.o\\r
 191                 ./treenode.o\\r
 192                 ./readtreecommand.o\\r
 193                 ./reversecommand.o\\r
 194                 ./trimseqscommand.o\\r
 195                 ./slibshuff.o\\r
 196                 ./libshuff.o\\r
 197                 ./dlibshuff.o\\r
 198                 ./mergefilecommand.o\\r
 199                 ./coverage.o\\r
 200                 ./whittaker.o\\r
 201                 ./preclustercommand.o\\r
 202                 ./otuhierarchycommand.o\\r
 203                 ./setdircommand.o\\r
 204                 ./getgroupcommand.o\\r
 205                 ./getlabelcommand.o\\r
 206                 ./secondarystructurecommand.o\\r
 207                 ./mothurout.o\\r
 208                 ./parselistscommand.o\\r
 209                 ./readblast.o\\r
 210                 ./chimeracheckrdp.o\\r
 211                 ./hclustercommand.o\\r
 212                 ./hcluster.o\\r
 213                 ./getlistcountcommand.o\\r
 214                 ./readcluster.o\\r
 215                 ./ccode.o\\r
 216                 ./taxonomyequalizer.o\\r
 217                 ./phylotypecommand.o\\r
 218                 ./classifyseqscommand.o\\r
 219                 ./parsesffcommand.o\\r
 220                 ./classify.o\\r
 221                 ./phylotree.o\\r
 222                 ./bayesian.o\
 223                 ./phylosummary.o\\r
 224                 ./alignmentdb.o\\r
 225                 ./knn.o\\r
 226                 ./distancedb.o\\r
 227                 ./chimeraslayer.o\\r
 228                 ./slayer.o\\r
 229                 ./pcacommand.o\\r
 230                 ./formatcolumn.o\\r
 231                 ./formatphylip.o\\r
 232                 ./mgclustercommand.o\\r
 233                 ./getsharedotucommand.o\\r
 234                 ./maligner.o\\r
 235                 ./chimerarealigner.o\\r
 236                 ./bergerparker.o\\r
 237                 ./bstick.o\\r
 238                 ./sharedkstest.o\\r
 239                 ./qstat.o\\r
 240                 ./shen.o\\r
 241                 ./logsd.o\\r
 242                 ./geom.o\
 243                 ./setlogfilecommand.o\r
 244         $(CC) $(LNK_OPTIONS) \\r
 245                 ./sharedutilities.o\\r
 246                 ./treegroupscommand.o\\r
 247                 ./bootstrapsharedcommand.o\\r
 248                 ./matrixoutputcommand.o\\r
 249                 ./getoturepcommand.o\\r
 250                 ./screenseqscommand.o\\r
 251                 ./chimera.o\\r
 252                 ./decalc.o\\r
 253                 ./readotucommand.o\\r
 254                 ./readdistcommand.o\\r
 255                 ./commandfactory.o\\r
 256                 ./alignment.o\\r
 257                 ./alignmentcell.o\\r
 258                 ./gotohoverlap.o\\r
 259                 ./overlap.o\\r
 260                 ./needlemanoverlap.o\\r
 261                 ./blastalign.o\\r
 262                 ./noalign.o\\r
 263                 ./suffixdb.o\\r
 264                 ./suffixnodes.o\\r
 265                 ./suffixtree.o\\r
 266                 ./blastdb.o\\r
 267                 ./nast.o\\r
 268                 ./nastreport.o\\r
 269                 ./boneh.o\\r
 270                 ./efron.o\\r
 271                 ./solow.o\\r
 272                 ./unifracweightedcommand.o\\r
 273                 ./weighted.o\\r
 274                 ./unweighted.o\\r
 275                 ./unifracunweightedcommand.o\\r
 276                 ./getsabundcommand.o\\r
 277                 ./getrabundcommand.o\\r
 278                 ./bellerophon.o\\r
 279                 ./pintail.o\\r
 280                 ./sharedanderbergs.o\\r
 281                 ./venncommand.o\\r
 282                 ./venn.o\\r
 283                 ./fullmatrix.o\\r
 284                 ./heatmap.o\\r
 285                 ./heatmapcommand.o\\r
 286                 ./libshuffcommand.o\\r
 287                 ./nocommands.o\\r
 288                 ./sharedbraycurtis.o\\r
 289                 ./sharedkulczynski.o\\r
 290                 ./sharedlennon.o\\r
 291                 ./sharedkulczynskicody.o\\r
 292                 ./sharedmorisitahorn.o\\r
 293                 ./sharedochiai.o\\r
 294                 ./readcolumn.o\\r
 295                 ./readotu.o\\r
 296                 ./readphylip.o\\r
 297                 ./consensuscommand.o\\r
 298                 ./heatmapsimcommand.o\\r
 299                 ./heatmapsim.o\\r
 300                 ./optionparser.o\\r
 301                 ./filterseqscommand.o\\r
 302                 ./goodscoverage.o\\r
 303                 ./sequencedb.o\\r
 304                 ./sharedjackknife.o\\r
 305                 ./sharedmarczewski.o\\r
 306                 ./aligncommand.o\\r
 307                 ./treemap.o\\r
 308                 ./parsimonycommand.o\\r
 309                 ./parsimony.o\\r
 310                 ./seqsummarycommand.o\\r
 311                 ./chimeraccodecommand.o\\r
 312                 ./chimerabellerophoncommand.o\\r
 313                 ./chimeracheckcommand.o\\r
 314                 ./chimeraslayercommand.o\\r
 315                 ./chimerapintailcommand.o\\r
 316                 ./chimeraseqscommand.o\\r
 317                 ./sharedlistvector.o\\r
 318                 ./tree.o\\r
 319                 ./readtree.o\\r
 320                 ./sharedsobscollectsummary.o\\r
 321                 ./deconvolutecommand.o\\r
 322                 ./listseqscommand.o\\r
 323                 ./getseqscommand.o\\r
 324                 ./removeseqscommand.o\\r
 325                 ./systemcommand.o\\r
 326                 ./binsequencecommand.o\\r
 327                 ./distancecommand.o\\r
 328                 ./ace.o\\r
 329                 ./averagelinkage.o\\r
 330                 ./bootstrap.o\\r
 331                 ./calculator.o\\r
 332                 ./chao1.o\\r
 333                 ./cluster.o\\r
 334                 ./clustercommand.o\\r
 335                 ./collect.o\\r
 336                 ./collectcommand.o\\r
 337                 ./collectsharedcommand.o\\r
 338                 ./commandoptionparser.o\\r
 339                 ./completelinkage.o\\r
 340                 ./database.o\\r
 341                 ./engine.o\\r
 342                 ./fastamap.o\\r
 343                 ./fileoutput.o\\r
 344                 ./globaldata.o\\r
 345                 ./groupmap.o\\r
 346                 ./helpcommand.o\\r
 347                 ./inputdata.o\\r
 348                 ./jackknife.o\\r
 349                 ./kmer.o\\r
 350                 ./kmerdb.o\\r
 351                 ./listvector.o\\r
 352                 ./mothur.o\\r
 353                 ./nameassignment.o\\r
 354                 ./npshannon.o\\r
 355                 ./ordervector.o\\r
 356                 ./progress.o\\r
 357                 ./quitcommand.o\\r
 358                 ./rabundvector.o\\r
 359                 ./rarecalc.o\\r
 360                 ./raredisplay.o\\r
 361                 ./rarefact.o\\r
 362                 ./rarefactcommand.o\\r
 363                 ./rarefactsharedcommand.o\\r
 364                 ./sabundvector.o\\r
 365                 ./sequence.o\\r
 366                 ./shannon.o\\r
 367                 ./sharedace.o\\r
 368                 ./sharedchao1.o\\r
 369                 ./sharedcommand.o\\r
 370                 ./sharedjabund.o\\r
 371                 ./sharedjclass.o\\r
 372                 ./sharedjest.o\\r
 373                 ./sharedordervector.o\\r
 374                 ./sharedrabundvector.o\\r
 375                 ./sharedsabundvector.o\\r
 376                 ./sharedsobs.o\\r
 377                 ./sharedsorabund.o\\r
 378                 ./sharedsorclass.o\\r
 379                 ./sharedsorest.o\\r
 380                 ./sharedthetan.o\\r
 381                 ./sharedthetayc.o\\r
 382                 ./simpson.o\\r
 383                 ./singlelinkage.o\\r
 384                 ./sparsematrix.o\\r
 385                 ./summarycommand.o\\r
 386                 ./summarysharedcommand.o\\r
 387                 ./uvest.o\\r
 388                 ./validcalculator.o\\r
 389                 ./validparameter.o\\r
 390                 ./treenode.o\\r
 391                 ./readtreecommand.o\\r
 392                 ./reversecommand.o\\r
 393                 ./trimseqscommand.o\\r
 394                 ./slibshuff.o\\r
 395                 ./libshuff.o\\r
 396                 ./dlibshuff.o\\r
 397                 ./mergefilecommand.o\\r
 398                 ./coverage.o\\r
 399                 ./whittaker.o\\r
 400                 ./preclustercommand.o\\r
 401                 ./otuhierarchycommand.o\\r
 402                 ./setdircommand.o\\r
 403                 ./getgroupcommand.o\\r
 404                 ./getlabelcommand.o\\r
 405                 ./secondarystructurecommand.o\\r
 406                 ./mothurout.o\\r
 407                 ./parselistscommand.o\\r
 408                 ./readblast.o\\r
 409                 ./chimeracheckrdp.o\\r
 410                 ./hclustercommand.o\\r
 411                 ./hcluster.o\\r
 412                 ./getlistcountcommand.o\\r
 413                 ./readcluster.o\\r
 414                 ./ccode.o\\r
 415                 ./taxonomyequalizer.o\\r
 416                 ./phylotypecommand.o\\r
 417                 ./classifyseqscommand.o\\r
 418                 ./parsesffcommand.o\\r
 419                 ./classify.o\\r
 420                 ./phylotree.o\\r
 421                 ./bayesian.o\
 422                 ./phylosummary.o\\r
 423                 ./alignmentdb.o\\r
 424                 ./knn.o\\r
 425                 ./distancedb.o\\r
 426                 ./chimeraslayer.o\\r
 427                 ./slayer.o\\r
 428                 ./pcacommand.o\\r
 429                 ./formatcolumn.o\\r
 430                 ./formatphylip.o\\r
 431                 ./mgclustercommand.o\\r
 432                 ./getsharedotucommand.o\\r
 433                 ./maligner.o\\r
 434                 ./chimerarealigner.o\\r
 435                 ./bergerparker.o\\r
 436                 ./bstick.o\\r
 437                 ./sharedkstest.o\\r
 438                 ./qstat.o\\r
 439                 ./shen.o\\r
 440                 ./logsd.o\\r
 441                 ./geom.o\
 442                 ./setlogfilecommand.o\\r
 443                 -o ../Release/mothur\r
 444 \r
 445 clean : \r
 446                 rm \\r
 447                 ./sharedutilities.o\\r
 448                 ./treegroupscommand.o\\r
 449                 ./bootstrapsharedcommand.o\\r
 450                 ./matrixoutputcommand.o\\r
 451                 ./getoturepcommand.o\\r
 452                 ./screenseqscommand.o\\r
 453                 ./chimera.o\\r
 454                 ./decalc.o\\r
 455                 ./readotucommand.o\\r
 456                 ./readdistcommand.o\\r
 457                 ./commandfactory.o\\r
 458                 ./alignment.o\\r
 459                 ./alignmentcell.o\\r
 460                 ./gotohoverlap.o\\r
 461                 ./overlap.o\\r
 462                 ./needlemanoverlap.o\\r
 463                 ./blastalign.o\\r
 464                 ./noalign.o\\r
 465                 ./suffixdb.o\\r
 466                 ./suffixnodes.o\\r
 467                 ./suffixtree.o\\r
 468                 ./blastdb.o\\r
 469                 ./nast.o\\r
 470                 ./nastreport.o\\r
 471                 ./boneh.o\\r
 472                 ./efron.o\\r
 473                 ./solow.o\\r
 474                 ./unifracweightedcommand.o\\r
 475                 ./weighted.o\\r
 476                 ./unweighted.o\\r
 477                 ./unifracunweightedcommand.o\\r
 478                 ./getsabundcommand.o\\r
 479                 ./getrabundcommand.o\\r
 480                 ./bellerophon.o\\r
 481                 ./pintail.o\\r
 482                 ./sharedanderbergs.o\\r
 483                 ./venncommand.o\\r
 484                 ./venn.o\\r
 485                 ./fullmatrix.o\\r
 486                 ./heatmap.o\\r
 487                 ./heatmapcommand.o\\r
 488                 ./libshuffcommand.o\\r
 489                 ./nocommands.o\\r
 490                 ./sharedbraycurtis.o\\r
 491                 ./sharedkulczynski.o\\r
 492                 ./sharedlennon.o\\r
 493                 ./sharedkulczynskicody.o\\r
 494                 ./sharedmorisitahorn.o\\r
 495                 ./sharedochiai.o\\r
 496                 ./readcolumn.o\\r
 497                 ./readotu.o\\r
 498                 ./readphylip.o\\r
 499                 ./consensuscommand.o\\r
 500                 ./heatmapsimcommand.o\\r
 501                 ./heatmapsim.o\\r
 502                 ./optionparser.o\\r
 503                 ./filterseqscommand.o\\r
 504                 ./goodscoverage.o\\r
 505                 ./sequencedb.o\\r
 506                 ./sharedjackknife.o\\r
 507                 ./sharedmarczewski.o\\r
 508                 ./aligncommand.o\\r
 509                 ./treemap.o\\r
 510                 ./parsimonycommand.o\\r
 511                 ./parsimony.o\\r
 512                 ./seqsummarycommand.o\\r
 513                 ./chimeraccodecommand.o\\r
 514                 ./chimerabellerophoncommand.o\\r
 515                 ./chimeracheckcommand.o\\r
 516                 ./chimeraslayercommand.o\\r
 517                 ./chimerapintailcommand.o\\r
 518                 ./chimeraseqscommand.o\\r
 519                 ./sharedlistvector.o\\r
 520                 ./tree.o\\r
 521                 ./readtree.o\\r
 522                 ./sharedsobscollectsummary.o\\r
 523                 ./deconvolutecommand.o\\r
 524                 ./listseqscommand.o\\r
 525                 ./getseqscommand.o\\r
 526                 ./removeseqscommand.o\\r
 527                 ./systemcommand.o\\r
 528                 ./binsequencecommand.o\\r
 529                 ./distancecommand.o\\r
 530                 ./ace.o\\r
 531                 ./averagelinkage.o\\r
 532                 ./bootstrap.o\\r
 533                 ./calculator.o\\r
 534                 ./chao1.o\\r
 535                 ./cluster.o\\r
 536                 ./clustercommand.o\\r
 537                 ./collect.o\\r
 538                 ./collectcommand.o\\r
 539                 ./collectsharedcommand.o\\r
 540                 ./commandoptionparser.o\\r
 541                 ./completelinkage.o\\r
 542                 ./database.o\\r
 543                 ./engine.o\\r
 544                 ./fastamap.o\\r
 545                 ./fileoutput.o\\r
 546                 ./globaldata.o\\r
 547                 ./groupmap.o\\r
 548                 ./helpcommand.o\\r
 549                 ./inputdata.o\\r
 550                 ./jackknife.o\\r
 551                 ./kmer.o\\r
 552                 ./kmerdb.o\\r
 553                 ./listvector.o\\r
 554                 ./mothur.o\\r
 555                 ./nameassignment.o\\r
 556                 ./npshannon.o\\r
 557                 ./ordervector.o\\r
 558                 ./progress.o\\r
 559                 ./quitcommand.o\\r
 560                 ./rabundvector.o\\r
 561                 ./rarecalc.o\\r
 562                 ./raredisplay.o\\r
 563                 ./rarefact.o\\r
 564                 ./rarefactcommand.o\\r
 565                 ./rarefactsharedcommand.o\\r
 566                 ./sabundvector.o\\r
 567                 ./sequence.o\\r
 568                 ./shannon.o\\r
 569                 ./sharedace.o\\r
 570                 ./sharedchao1.o\\r
 571                 ./sharedcommand.o\\r
 572                 ./sharedjabund.o\\r
 573                 ./sharedjclass.o\\r
 574                 ./sharedjest.o\\r
 575                 ./sharedordervector.o\\r
 576                 ./sharedrabundvector.o\\r
 577                 ./sharedsabundvector.o\\r
 578                 ./sharedsobs.o\\r
 579                 ./sharedsorabund.o\\r
 580                 ./sharedsorclass.o\\r
 581                 ./sharedsorest.o\\r
 582                 ./sharedthetan.o\\r
 583                 ./sharedthetayc.o\\r
 584                 ./simpson.o\\r
 585                 ./singlelinkage.o\\r
 586                 ./sparsematrix.o\\r
 587                 ./summarycommand.o\\r
 588                 ./summarysharedcommand.o\\r
 589                 ./uvest.o\\r
 590                 ./validcalculator.o\\r
 591                 ./validparameter.o\\r
 592                 ./treenode.o\\r
 593                 ./readtreecommand.o\\r
 594                 ./reversecommand.o\\r
 595                 ./trimseqscommand.o\\r
 596                 ./slibshuff.o\\r
 597                 ./libshuff.o\\r
 598                 ./dlibshuff.o\\r
 599                 ./mergefilecommand.o\\r
 600                 ./coverage.o\\r
 601                 ./whittaker.o\\r
 602                 ./preclustercommand.o\\r
 603                 ./otuhierarchycommand.o\\r
 604                 ./setdircommand.o\\r
 605                 ./getgroupcommand.o\\r
 606                 ./getlabelcommand.o\\r
 607                 ./secondarystructurecommand.o\\r
 608                 ./mothurout.o\\r
 609                 ./parselistscommand.o\\r
 610                 ./readblast.o\\r
 611                 ./chimeracheckrdp.o\\r
 612                 ./hclustercommand.o\\r
 613                 ./hcluster.o\\r
 614                 ./getlistcountcommand.o\\r
 615                 ./readcluster.o\\r
 616                 ./ccode.o\\r
 617                 ./taxonomyequalizer.o\\r
 618                 ./phylotypecommand.o\\r
 619                 ./classifyseqscommand.o\\r
 620                 ./parsesffcommand.o\\r
 621                 ./classify.o\\r
 622                 ./phylotree.o\\r
 623                 ./bayesian.o\
 624                 ./phylosummary.o\\r
 625                 ./alignmentdb.o\\r
 626                 ./knn.o\\r
 627                 ./distancedb.o\\r
 628                 ./chimeraslayer.o\\r
 629                 ./slayer.o\\r
 630                 ./pcacommand.o\\r
 631                 ./formatcolumn.o\\r
 632                 ./formatphylip.o\\r
 633                 ./mgclustercommand.o\\r
 634                 ./getsharedotucommand.o\\r
 635                 ./maligner.o\\r
 636                 ./chimerarealigner.o\\r
 637                 ./bergerparker.o\\r
 638                 ./bstick.o\\r
 639                 ./sharedkstest.o\\r
 640                 ./qstat.o\\r
 641                 ./shen.o\\r
 642                 ./logsd.o\\r
 643                 ./geom.o\
 644                 ./setlogfilecommand.o\\r
 645                 mothur\r
 646 \r
 647 install : mothur\r
 648                 #cp mothur ../Release/mothur\r
 649 \r
 650 #\r
 651 # Build the parts of mothur\r
 652 #\r
 653 \r
 654 \r
 655 # Item # 1 -- sharedutilities --\r
 656 ./sharedutilities.o : sharedutilities.cpp\r
 657         $(CC) $(CC_OPTIONS) sharedutilities.cpp -c $(INCLUDE) -o ./sharedutilities.o\r
 658 \r
 659 \r
 660 # Item # 2 -- treegroupscommand --\r
 661 ./treegroupscommand.o : treegroupscommand.cpp\r
 662         $(CC) $(CC_OPTIONS) treegroupscommand.cpp -c $(INCLUDE) -o ./treegroupscommand.o\r
 663 \r
 664 \r
 665 # Item # 3 -- bootstrapsharedcommand --\r
 666 ./bootstrapsharedcommand.o : bootstrapsharedcommand.cpp\r
 667         $(CC) $(CC_OPTIONS) bootstrapsharedcommand.cpp -c $(INCLUDE) -o ./bootstrapsharedcommand.o\r
 668 \r
 669 \r
 670 # Item # 4 -- matrixoutputcommand --\r
 671 ./matrixoutputcommand.o : matrixoutputcommand.cpp\r
 672         $(CC) $(CC_OPTIONS) matrixoutputcommand.cpp -c $(INCLUDE) -o ./matrixoutputcommand.o\r
 673 \r
 674 \r
 675 # Item # 5 -- getoturepcommand --\r
 676 ./getoturepcommand.o : getoturepcommand.cpp\r
 677         $(CC) $(CC_OPTIONS) getoturepcommand.cpp -c $(INCLUDE) -o ./getoturepcommand.o\r
 678 \r
 679 \r
 680 # Item # 6 -- screenseqscommand --\r
 681 ./screenseqscommand.o : screenseqscommand.cpp\r
 682         $(CC) $(CC_OPTIONS) screenseqscommand.cpp -c $(INCLUDE) -o ./screenseqscommand.o\r
 683 \r
 684 \r
 685 # Item # 7 -- chimera --\r
 686 ./chimera.o : chimera.cpp\r
 687         $(CC) $(CC_OPTIONS) chimera.cpp -c $(INCLUDE) -o ./chimera.o\r
 688 \r
 689 \r
 690 # Item # 8 -- decalc --\r
 691 ./decalc.o : decalc.cpp\r
 692         $(CC) $(CC_OPTIONS) decalc.cpp -c $(INCLUDE) -o ./decalc.o\r
 693 \r
 694 \r
 695 # Item # 9 -- readotucommand --\r
 696 ./readotucommand.o : readotucommand.cpp\r
 697         $(CC) $(CC_OPTIONS) readotucommand.cpp -c $(INCLUDE) -o ./readotucommand.o\r
 698 \r
 699 \r
 700 # Item # 10 -- readdistcommand --\r
 701 ./readdistcommand.o : readdistcommand.cpp\r
 702         $(CC) $(CC_OPTIONS) readdistcommand.cpp -c $(INCLUDE) -o ./readdistcommand.o\r
 703 \r
 704 \r
 705 # Item # 11 -- commandfactory --\r
 706 ./commandfactory.o : commandfactory.cpp\r
 707         $(CC) $(CC_OPTIONS) commandfactory.cpp -c $(INCLUDE) -o ./commandfactory.o\r
 708 \r
 709 \r
 710 # Item # 12 -- alignment --\r
 711 ./alignment.o : alignment.cpp\r
 712         $(CC) $(CC_OPTIONS) alignment.cpp -c $(INCLUDE) -o ./alignment.o\r
 713 \r
 714 \r
 715 # Item # 13 -- alignmentcell --\r
 716 ./alignmentcell.o : alignmentcell.cpp\r
 717         $(CC) $(CC_OPTIONS) alignmentcell.cpp -c $(INCLUDE) -o ./alignmentcell.o\r
 718 \r
 719 \r
 720 # Item # 14 -- gotohoverlap --\r
 721 ./gotohoverlap.o : gotohoverlap.cpp\r
 722         $(CC) $(CC_OPTIONS) gotohoverlap.cpp -c $(INCLUDE) -o ./gotohoverlap.o\r
 723 \r
 724 \r
 725 # Item # 15 -- overlap --\r
 726 ./overlap.o : overlap.cpp\r
 727         $(CC) $(CC_OPTIONS) overlap.cpp -c $(INCLUDE) -o ./overlap.o\r
 728 \r
 729 \r
 730 # Item # 16 -- needlemanoverlap --\r
 731 ./needlemanoverlap.o : needlemanoverlap.cpp\r
 732         $(CC) $(CC_OPTIONS) needlemanoverlap.cpp -c $(INCLUDE) -o ./needlemanoverlap.o\r
 733 \r
 734 \r
 735 # Item # 17 -- blastalign --\r
 736 ./blastalign.o : blastalign.cpp\r
 737         $(CC) $(CC_OPTIONS) blastalign.cpp -c $(INCLUDE) -o ./blastalign.o\r
 738 \r
 739 \r
 740 # Item # 18 -- noalign --\r
 741 ./noalign.o : noalign.cpp\r
 742         $(CC) $(CC_OPTIONS) noalign.cpp -c $(INCLUDE) -o ./noalign.o\r
 743 \r
 744 \r
 745 # Item # 19 -- suffixdb --\r
 746 ./suffixdb.o : suffixdb.cpp\r
 747         $(CC) $(CC_OPTIONS) suffixdb.cpp -c $(INCLUDE) -o ./suffixdb.o\r
 748 \r
 749 \r
 750 # Item # 20 -- suffixnodes --\r
 751 ./suffixnodes.o : suffixnodes.cpp\r
 752         $(CC) $(CC_OPTIONS) suffixnodes.cpp -c $(INCLUDE) -o ./suffixnodes.o\r
 753 \r
 754 \r
 755 # Item # 21 -- suffixtree --\r
 756 ./suffixtree.o : suffixtree.cpp\r
 757         $(CC) $(CC_OPTIONS) suffixtree.cpp -c $(INCLUDE) -o ./suffixtree.o\r
 758 \r
 759 \r
 760 # Item # 22 -- blastdb --\r
 761 ./blastdb.o : blastdb.cpp\r
 762         $(CC) $(CC_OPTIONS) blastdb.cpp -c $(INCLUDE) -o ./blastdb.o\r
 763 \r
 764 \r
 765 # Item # 23 -- nast --\r
 766 ./nast.o : nast.cpp\r
 767         $(CC) $(CC_OPTIONS) nast.cpp -c $(INCLUDE) -o ./nast.o\r
 768 \r
 769 \r
 770 # Item # 24 -- nastreport --\r
 771 ./nastreport.o : nastreport.cpp\r
 772         $(CC) $(CC_OPTIONS) nastreport.cpp -c $(INCLUDE) -o ./nastreport.o\r
 773 \r
 774 \r
 775 # Item # 25 -- boneh --\r
 776 ./boneh.o : boneh.cpp\r
 777         $(CC) $(CC_OPTIONS) boneh.cpp -c $(INCLUDE) -o ./boneh.o\r
 778 \r
 779 \r
 780 # Item # 26 -- efron --\r
 781 ./efron.o : efron.cpp\r
 782         $(CC) $(CC_OPTIONS) efron.cpp -c $(INCLUDE) -o ./efron.o\r
 783 \r
 784 \r
 785 # Item # 27 -- solow --\r
 786 ./solow.o : solow.cpp\r
 787         $(CC) $(CC_OPTIONS) solow.cpp -c $(INCLUDE) -o ./solow.o\r
 788 \r
 789 \r
 790 # Item # 28 -- unifracweightedcommand --\r
 791 ./unifracweightedcommand.o : unifracweightedcommand.cpp\r
 792         $(CC) $(CC_OPTIONS) unifracweightedcommand.cpp -c $(INCLUDE) -o ./unifracweightedcommand.o\r
 793 \r
 794 \r
 795 # Item # 29 -- weighted --\r
 796 ./weighted.o : weighted.cpp\r
 797         $(CC) $(CC_OPTIONS) weighted.cpp -c $(INCLUDE) -o ./weighted.o\r
 798 \r
 799 \r
 800 # Item # 30 -- unweighted --\r
 801 ./unweighted.o : unweighted.cpp\r
 802         $(CC) $(CC_OPTIONS) unweighted.cpp -c $(INCLUDE) -o ./unweighted.o\r
 803 \r
 804 \r
 805 # Item # 31 -- unifracunweightedcommand --\r
 806 ./unifracunweightedcommand.o : unifracunweightedcommand.cpp\r
 807         $(CC) $(CC_OPTIONS) unifracunweightedcommand.cpp -c $(INCLUDE) -o ./unifracunweightedcommand.o\r
 808 \r
 809 \r
 810 # Item # 32 -- getsabundcommand --\r
 811 ./getsabundcommand.o : getsabundcommand.cpp\r
 812         $(CC) $(CC_OPTIONS) getsabundcommand.cpp -c $(INCLUDE) -o ./getsabundcommand.o\r
 813 \r
 814 \r
 815 # Item # 33 -- getrabundcommand --\r
 816 ./getrabundcommand.o : getrabundcommand.cpp\r
 817         $(CC) $(CC_OPTIONS) getrabundcommand.cpp -c $(INCLUDE) -o ./getrabundcommand.o\r
 818 \r
 819 \r
 820 # Item # 34 -- bellerophon --\r
 821 ./bellerophon.o : bellerophon.cpp\r
 822         $(CC) $(CC_OPTIONS) bellerophon.cpp -c $(INCLUDE) -o ./bellerophon.o\r
 823 \r
 824 \r
 825 # Item # 35 -- pintail --\r
 826 ./pintail.o : pintail.cpp\r
 827         $(CC) $(CC_OPTIONS) pintail.cpp -c $(INCLUDE) -o ./pintail.o\r
 828 \r
 829 \r
 830 # Item # 36 -- sharedanderbergs --\r
 831 ./sharedanderbergs.o : sharedanderbergs.cpp\r
 832         $(CC) $(CC_OPTIONS) sharedanderbergs.cpp -c $(INCLUDE) -o ./sharedanderbergs.o\r
 833 \r
 834 \r
 835 # Item # 37 -- venncommand --\r
 836 ./venncommand.o : venncommand.cpp\r
 837         $(CC) $(CC_OPTIONS) venncommand.cpp -c $(INCLUDE) -o ./venncommand.o\r
 838 \r
 839 \r
 840 # Item # 38 -- venn --\r
 841 ./venn.o : venn.cpp\r
 842         $(CC) $(CC_OPTIONS) venn.cpp -c $(INCLUDE) -o ./venn.o\r
 843 \r
 844 \r
 845 # Item # 39 -- fullmatrix --\r
 846 ./fullmatrix.o : fullmatrix.cpp\r
 847         $(CC) $(CC_OPTIONS) fullmatrix.cpp -c $(INCLUDE) -o ./fullmatrix.o\r
 848 \r
 849 \r
 850 # Item # 40 -- heatmap --\r
 851 ./heatmap.o : heatmap.cpp\r
 852         $(CC) $(CC_OPTIONS) heatmap.cpp -c $(INCLUDE) -o ./heatmap.o\r
 853 \r
 854 \r
 855 # Item # 41 -- heatmapcommand --\r
 856 ./heatmapcommand.o : heatmapcommand.cpp\r
 857         $(CC) $(CC_OPTIONS) heatmapcommand.cpp -c $(INCLUDE) -o ./heatmapcommand.o\r
 858 \r
 859 \r
 860 # Item # 42 -- libshuffcommand --\r
 861 ./libshuffcommand.o : libshuffcommand.cpp\r
 862         $(CC) $(CC_OPTIONS) libshuffcommand.cpp -c $(INCLUDE) -o ./libshuffcommand.o\r
 863 \r
 864 \r
 865 # Item # 43 -- nocommands --\r
 866 ./nocommands.o : nocommands.cpp\r
 867         $(CC) $(CC_OPTIONS) nocommands.cpp -c $(INCLUDE) -o ./nocommands.o\r
 868 \r
 869 \r
 870 # Item # 44 -- sharedbraycurtis --\r
 871 ./sharedbraycurtis.o : sharedbraycurtis.cpp\r
 872         $(CC) $(CC_OPTIONS) sharedbraycurtis.cpp -c $(INCLUDE) -o ./sharedbraycurtis.o\r
 873 \r
 874 \r
 875 # Item # 45 -- sharedkulczynski --\r
 876 ./sharedkulczynski.o : sharedkulczynski.cpp\r
 877         $(CC) $(CC_OPTIONS) sharedkulczynski.cpp -c $(INCLUDE) -o ./sharedkulczynski.o\r
 878 \r
 879 \r
 880 # Item # 46 -- sharedlennon --\r
 881 ./sharedlennon.o : sharedlennon.cpp\r
 882         $(CC) $(CC_OPTIONS) sharedlennon.cpp -c $(INCLUDE) -o ./sharedlennon.o\r
 883 \r
 884 \r
 885 # Item # 47 -- sharedkulczynskicody --\r
 886 ./sharedkulczynskicody.o : sharedkulczynskicody.cpp\r
 887         $(CC) $(CC_OPTIONS) sharedkulczynskicody.cpp -c $(INCLUDE) -o ./sharedkulczynskicody.o\r
 888 \r
 889 \r
 890 # Item # 48 -- sharedmorisitahorn --\r
 891 ./sharedmorisitahorn.o : sharedmorisitahorn.cpp\r
 892         $(CC) $(CC_OPTIONS) sharedmorisitahorn.cpp -c $(INCLUDE) -o ./sharedmorisitahorn.o\r
 893 \r
 894 \r
 895 # Item # 49 -- sharedochiai --\r
 896 ./sharedochiai.o : sharedochiai.cpp\r
 897         $(CC) $(CC_OPTIONS) sharedochiai.cpp -c $(INCLUDE) -o ./sharedochiai.o\r
 898 \r
 899 \r
 900 # Item # 50 -- readcolumn --\r
 901 ./readcolumn.o : readcolumn.cpp\r
 902         $(CC) $(CC_OPTIONS) readcolumn.cpp -c $(INCLUDE) -o ./readcolumn.o\r
 903 \r
 904 \r
 905 # Item # 51 -- readotu --\r
 906 ./readotu.o : readotu.cpp\r
 907         $(CC) $(CC_OPTIONS) readotu.cpp -c $(INCLUDE) -o ./readotu.o\r
 908 \r
 909 \r
 910 # Item # 52 -- readphylip --\r
 911 ./readphylip.o : readphylip.cpp\r
 912         $(CC) $(CC_OPTIONS) readphylip.cpp -c $(INCLUDE) -o ./readphylip.o\r
 913 \r
 914 \r
 915 # Item # 53 -- consensuscommand --\r
 916 ./consensuscommand.o : consensuscommand.cpp\r
 917         $(CC) $(CC_OPTIONS) consensuscommand.cpp -c $(INCLUDE) -o ./consensuscommand.o\r
 918 \r
 919 \r
 920 # Item # 54 -- heatmapsimcommand --\r
 921 ./heatmapsimcommand.o : heatmapsimcommand.cpp\r
 922         $(CC) $(CC_OPTIONS) heatmapsimcommand.cpp -c $(INCLUDE) -o ./heatmapsimcommand.o\r
 923 \r
 924 \r
 925 # Item # 55 -- heatmapsim --\r
 926 ./heatmapsim.o : heatmapsim.cpp\r
 927         $(CC) $(CC_OPTIONS) heatmapsim.cpp -c $(INCLUDE) -o ./heatmapsim.o\r
 928 \r
 929 \r
 930 # Item # 56 -- optionparser --\r
 931 ./optionparser.o : optionparser.cpp\r
 932         $(CC) $(CC_OPTIONS) optionparser.cpp -c $(INCLUDE) -o ./optionparser.o\r
 933 \r
 934 \r
 935 # Item # 57 -- filterseqscommand --\r
 936 ./filterseqscommand.o : filterseqscommand.cpp\r
 937         $(CC) $(CC_OPTIONS) filterseqscommand.cpp -c $(INCLUDE) -o ./filterseqscommand.o\r
 938 \r
 939 \r
 940 # Item # 58 -- goodscoverage --\r
 941 ./goodscoverage.o : goodscoverage.cpp\r
 942         $(CC) $(CC_OPTIONS) goodscoverage.cpp -c $(INCLUDE) -o ./goodscoverage.o\r
 943 \r
 944 \r
 945 # Item # 59 -- sequencedb --\r
 946 ./sequencedb.o : sequencedb.cpp\r
 947         $(CC) $(CC_OPTIONS) sequencedb.cpp -c $(INCLUDE) -o ./sequencedb.o\r
 948 \r
 949 \r
 950 # Item # 60 -- sharedjackknife --\r
 951 ./sharedjackknife.o : sharedjackknife.cpp\r
 952         $(CC) $(CC_OPTIONS) sharedjackknife.cpp -c $(INCLUDE) -o ./sharedjackknife.o\r
 953 \r
 954 \r
 955 # Item # 61 -- sharedmarczewski --\r
 956 ./sharedmarczewski.o : sharedmarczewski.cpp\r
 957         $(CC) $(CC_OPTIONS) sharedmarczewski.cpp -c $(INCLUDE) -o ./sharedmarczewski.o\r
 958 \r
 959 \r
 960 # Item # 62 -- aligncommand --\r
 961 ./aligncommand.o : aligncommand.cpp\r
 962         $(CC) $(CC_OPTIONS) aligncommand.cpp -c $(INCLUDE) -o ./aligncommand.o\r
 963 \r
 964 \r
 965 # Item # 63 -- treemap --\r
 966 ./treemap.o : treemap.cpp\r
 967         $(CC) $(CC_OPTIONS) treemap.cpp -c $(INCLUDE) -o ./treemap.o\r
 968 \r
 969 \r
 970 # Item # 64 -- parsimonycommand --\r
 971 ./parsimonycommand.o : parsimonycommand.cpp\r
 972         $(CC) $(CC_OPTIONS) parsimonycommand.cpp -c $(INCLUDE) -o ./parsimonycommand.o\r
 973 \r
 974 \r
 975 # Item # 65 -- parsimony --\r
 976 ./parsimony.o : parsimony.cpp\r
 977         $(CC) $(CC_OPTIONS) parsimony.cpp -c $(INCLUDE) -o ./parsimony.o\r
 978 \r
 979 \r
 980 # Item # 66 -- seqsummarycommand --\r
 981 ./seqsummarycommand.o : seqsummarycommand.cpp\r
 982         $(CC) $(CC_OPTIONS) seqsummarycommand.cpp -c $(INCLUDE) -o ./seqsummarycommand.o\r
 983 \r
 984 \r
 985 # Item # 67 -- chimeraseqscommand --\r
 986 ./chimeraseqscommand.o : chimeraseqscommand.cpp\r
 987         $(CC) $(CC_OPTIONS) chimeraseqscommand.cpp -c $(INCLUDE) -o ./chimeraseqscommand.o\r
 988 \r
 989 \r
 990 # Item # 68 -- sharedlistvector --\r
 991 ./sharedlistvector.o : sharedlistvector.cpp\r
 992         $(CC) $(CC_OPTIONS) sharedlistvector.cpp -c $(INCLUDE) -o ./sharedlistvector.o\r
 993 \r
 994 \r
 995 # Item # 69 -- tree --\r
 996 ./tree.o : tree.cpp\r
 997         $(CC) $(CC_OPTIONS) tree.cpp -c $(INCLUDE) -o ./tree.o\r
 998 \r
 999 \r
1000 # Item # 70 -- readtree --\r
1001 ./readtree.o : readtree.cpp\r
1002         $(CC) $(CC_OPTIONS) readtree.cpp -c $(INCLUDE) -o ./readtree.o\r
1003 \r
1004 \r
1005 # Item # 71 -- sharedsobscollectsummary --\r
1006 ./sharedsobscollectsummary.o : sharedsobscollectsummary.cpp\r
1007         $(CC) $(CC_OPTIONS) sharedsobscollectsummary.cpp -c $(INCLUDE) -o ./sharedsobscollectsummary.o\r
1008 \r
1009 \r
1010 # Item # 72 -- deconvolutecommand --\r
1011 ./deconvolutecommand.o : deconvolutecommand.cpp\r
1012         $(CC) $(CC_OPTIONS) deconvolutecommand.cpp -c $(INCLUDE) -o ./deconvolutecommand.o\r
1013 \r
1014 \r
1015 # Item # 73 -- listseqscommand --\r
1016 ./listseqscommand.o : listseqscommand.cpp\r
1017         $(CC) $(CC_OPTIONS) listseqscommand.cpp -c $(INCLUDE) -o ./listseqscommand.o\r
1018 \r
1019 \r
1020 # Item # 74 -- getseqscommand --\r
1021 ./getseqscommand.o : getseqscommand.cpp\r
1022         $(CC) $(CC_OPTIONS) getseqscommand.cpp -c $(INCLUDE) -o ./getseqscommand.o\r
1023 \r
1024 \r
1025 # Item # 75 -- removeseqscommand --\r
1026 ./removeseqscommand.o : removeseqscommand.cpp\r
1027         $(CC) $(CC_OPTIONS) removeseqscommand.cpp -c $(INCLUDE) -o ./removeseqscommand.o\r
1028 \r
1029 \r
1030 # Item # 76 -- systemcommand --\r
1031 ./systemcommand.o : systemcommand.cpp\r
1032         $(CC) $(CC_OPTIONS) systemcommand.cpp -c $(INCLUDE) -o ./systemcommand.o\r
1033 \r
1034 \r
1035 # Item # 77 -- binsequencecommand --\r
1036 ./binsequencecommand.o : binsequencecommand.cpp\r
1037         $(CC) $(CC_OPTIONS) binsequencecommand.cpp -c $(INCLUDE) -o ./binsequencecommand.o\r
1038 \r
1039 \r
1040 # Item # 78 -- distancecommand --\r
1041 ./distancecommand.o : distancecommand.cpp\r
1042         $(CC) $(CC_OPTIONS) distancecommand.cpp -c $(INCLUDE) -o ./distancecommand.o\r
1043 \r
1044 \r
1045 # Item # 79 -- ace --\r
1046 ./ace.o : ace.cpp\r
1047         $(CC) $(CC_OPTIONS) ace.cpp -c $(INCLUDE) -o ./ace.o\r
1048 \r
1049 \r
1050 # Item # 80 -- averagelinkage --\r
1051 ./averagelinkage.o : averagelinkage.cpp\r
1052         $(CC) $(CC_OPTIONS) averagelinkage.cpp -c $(INCLUDE) -o ./averagelinkage.o\r
1053 \r
1054 \r
1055 # Item # 81 -- bootstrap --\r
1056 ./bootstrap.o : bootstrap.cpp\r
1057         $(CC) $(CC_OPTIONS) bootstrap.cpp -c $(INCLUDE) -o ./bootstrap.o\r
1058 \r
1059 \r
1060 # Item # 82 -- calculator --\r
1061 ./calculator.o : calculator.cpp\r
1062         $(CC) $(CC_OPTIONS) calculator.cpp -c $(INCLUDE) -o ./calculator.o\r
1063 \r
1064 \r
1065 # Item # 83 -- chao1 --\r
1066 ./chao1.o : chao1.cpp\r
1067         $(CC) $(CC_OPTIONS) chao1.cpp -c $(INCLUDE) -o ./chao1.o\r
1068 \r
1069 \r
1070 # Item # 84 -- cluster --\r
1071 ./cluster.o : cluster.cpp\r
1072         $(CC) $(CC_OPTIONS) cluster.cpp -c $(INCLUDE) -o ./cluster.o\r
1073 \r
1074 \r
1075 # Item # 85 -- clustercommand --\r
1076 ./clustercommand.o : clustercommand.cpp\r
1077         $(CC) $(CC_OPTIONS) clustercommand.cpp -c $(INCLUDE) -o ./clustercommand.o\r
1078 \r
1079 \r
1080 # Item # 86 -- collect --\r
1081 ./collect.o : collect.cpp\r
1082         $(CC) $(CC_OPTIONS) collect.cpp -c $(INCLUDE) -o ./collect.o\r
1083 \r
1084 \r
1085 # Item # 87 -- collectcommand --\r
1086 ./collectcommand.o : collectcommand.cpp\r
1087         $(CC) $(CC_OPTIONS) collectcommand.cpp -c $(INCLUDE) -o ./collectcommand.o\r
1088 \r
1089 \r
1090 # Item # 88 -- collectsharedcommand --\r
1091 ./collectsharedcommand.o : collectsharedcommand.cpp\r
1092         $(CC) $(CC_OPTIONS) collectsharedcommand.cpp -c $(INCLUDE) -o ./collectsharedcommand.o\r
1093 \r
1094 \r
1095 # Item # 89 -- commandoptionparser --\r
1096 ./commandoptionparser.o : commandoptionparser.cpp\r
1097         $(CC) $(CC_OPTIONS) commandoptionparser.cpp -c $(INCLUDE) -o ./commandoptionparser.o\r
1098 \r
1099 \r
1100 # Item # 90 -- completelinkage --\r
1101 ./completelinkage.o : completelinkage.cpp\r
1102         $(CC) $(CC_OPTIONS) completelinkage.cpp -c $(INCLUDE) -o ./completelinkage.o\r
1103 \r
1104 \r
1105 # Item # 91 -- database --\r
1106 ./database.o : database.cpp\r
1107         $(CC) $(CC_OPTIONS) database.cpp -c $(INCLUDE) -o ./database.o\r
1108 \r
1109 \r
1110 # Item # 92 -- engine --\r
1111 ./engine.o : engine.cpp\r
1112         $(CC) $(CC_OPTIONS) engine.cpp -c $(INCLUDE) -o ./engine.o\r
1113 \r
1114 \r
1115 # Item # 93 -- fastamap --\r
1116 ./fastamap.o : fastamap.cpp\r
1117         $(CC) $(CC_OPTIONS) fastamap.cpp -c $(INCLUDE) -o ./fastamap.o\r
1118 \r
1119 \r
1120 # Item # 94 -- fileoutput --\r
1121 ./fileoutput.o : fileoutput.cpp\r
1122         $(CC) $(CC_OPTIONS) fileoutput.cpp -c $(INCLUDE) -o ./fileoutput.o\r
1123 \r
1124 \r
1125 # Item # 95 -- globaldata --\r
1126 ./globaldata.o : globaldata.cpp\r
1127         $(CC) $(CC_OPTIONS) globaldata.cpp -c $(INCLUDE) -o ./globaldata.o\r
1128 \r
1129 \r
1130 # Item # 96 -- groupmap --\r
1131 ./groupmap.o : groupmap.cpp\r
1132         $(CC) $(CC_OPTIONS) groupmap.cpp -c $(INCLUDE) -o ./groupmap.o\r
1133 \r
1134 \r
1135 # Item # 97 -- helpcommand --\r
1136 ./helpcommand.o : helpcommand.cpp\r
1137         $(CC) $(CC_OPTIONS) helpcommand.cpp -c $(INCLUDE) -o ./helpcommand.o\r
1138 \r
1139 \r
1140 # Item # 98 -- inputdata --\r
1141 ./inputdata.o : inputdata.cpp\r
1142         $(CC) $(CC_OPTIONS) inputdata.cpp -c $(INCLUDE) -o ./inputdata.o\r
1143 \r
1144 \r
1145 # Item # 99 -- jackknife --\r
1146 ./jackknife.o : jackknife.cpp\r
1147         $(CC) $(CC_OPTIONS) jackknife.cpp -c $(INCLUDE) -o ./jackknife.o\r
1148 \r
1149 \r
1150 # Item # 100 -- kmer --\r
1151 ./kmer.o : kmer.cpp\r
1152         $(CC) $(CC_OPTIONS) kmer.cpp -c $(INCLUDE) -o ./kmer.o\r
1153 \r
1154 \r
1155 # Item # 101 -- kmerdb --\r
1156 ./kmerdb.o : kmerdb.cpp\r
1157         $(CC) $(CC_OPTIONS) kmerdb.cpp -c $(INCLUDE) -o ./kmerdb.o\r
1158 \r
1159 \r
1160 # Item # 102 -- listvector --\r
1161 ./listvector.o : listvector.cpp\r
1162         $(CC) $(CC_OPTIONS) listvector.cpp -c $(INCLUDE) -o ./listvector.o\r
1163 \r
1164 \r
1165 # Item # 103 -- mothur --\r
1166 ./mothur.o : mothur.cpp\r
1167         $(CC) $(CC_OPTIONS) mothur.cpp -c $(INCLUDE) -o ./mothur.o\r
1168 \r
1169 \r
1170 # Item # 104 -- nameassignment --\r
1171 ./nameassignment.o : nameassignment.cpp\r
1172         $(CC) $(CC_OPTIONS) nameassignment.cpp -c $(INCLUDE) -o ./nameassignment.o\r
1173 \r
1174 \r
1175 # Item # 105 -- npshannon --\r
1176 ./npshannon.o : npshannon.cpp\r
1177         $(CC) $(CC_OPTIONS) npshannon.cpp -c $(INCLUDE) -o ./npshannon.o\r
1178 \r
1179 \r
1180 # Item # 106 -- ordervector --\r
1181 ./ordervector.o : ordervector.cpp\r
1182         $(CC) $(CC_OPTIONS) ordervector.cpp -c $(INCLUDE) -o ./ordervector.o\r
1183 \r
1184 \r
1185 # Item # 107 -- progress --\r
1186 ./progress.o : progress.cpp\r
1187         $(CC) $(CC_OPTIONS) progress.cpp -c $(INCLUDE) -o ./progress.o\r
1188 \r
1189 \r
1190 # Item # 108 -- quitcommand --\r
1191 ./quitcommand.o : quitcommand.cpp\r
1192         $(CC) $(CC_OPTIONS) quitcommand.cpp -c $(INCLUDE) -o ./quitcommand.o\r
1193 \r
1194 \r
1195 # Item # 109 -- rabundvector --\r
1196 ./rabundvector.o : rabundvector.cpp\r
1197         $(CC) $(CC_OPTIONS) rabundvector.cpp -c $(INCLUDE) -o ./rabundvector.o\r
1198 \r
1199 \r
1200 # Item # 110 -- rarecalc --\r
1201 ./rarecalc.o : rarecalc.cpp\r
1202         $(CC) $(CC_OPTIONS) rarecalc.cpp -c $(INCLUDE) -o ./rarecalc.o\r
1203 \r
1204 \r
1205 # Item # 111 -- raredisplay --\r
1206 ./raredisplay.o : raredisplay.cpp\r
1207         $(CC) $(CC_OPTIONS) raredisplay.cpp -c $(INCLUDE) -o ./raredisplay.o\r
1208 \r
1209 \r
1210 # Item # 112 -- rarefact --\r
1211 ./rarefact.o : rarefact.cpp\r
1212         $(CC) $(CC_OPTIONS) rarefact.cpp -c $(INCLUDE) -o ./rarefact.o\r
1213 \r
1214 \r
1215 # Item # 113 -- rarefactcommand --\r
1216 ./rarefactcommand.o : rarefactcommand.cpp\r
1217         $(CC) $(CC_OPTIONS) rarefactcommand.cpp -c $(INCLUDE) -o ./rarefactcommand.o\r
1218 \r
1219 \r
1220 # Item # 114 -- rarefactsharedcommand --\r
1221 ./rarefactsharedcommand.o : rarefactsharedcommand.cpp\r
1222         $(CC) $(CC_OPTIONS) rarefactsharedcommand.cpp -c $(INCLUDE) -o ./rarefactsharedcommand.o\r
1223 \r
1224 \r
1225 # Item # 115 -- sabundvector --\r
1226 ./sabundvector.o : sabundvector.cpp\r
1227         $(CC) $(CC_OPTIONS) sabundvector.cpp -c $(INCLUDE) -o ./sabundvector.o\r
1228 \r
1229 \r
1230 # Item # 116 -- sequence --\r
1231 ./sequence.o : sequence.cpp\r
1232         $(CC) $(CC_OPTIONS) sequence.cpp -c $(INCLUDE) -o ./sequence.o\r
1233 \r
1234 \r
1235 # Item # 117 -- shannon --\r
1236 ./shannon.o : shannon.cpp\r
1237         $(CC) $(CC_OPTIONS) shannon.cpp -c $(INCLUDE) -o ./shannon.o\r
1238 \r
1239 \r
1240 # Item # 118 -- sharedace --\r
1241 ./sharedace.o : sharedace.cpp\r
1242         $(CC) $(CC_OPTIONS) sharedace.cpp -c $(INCLUDE) -o ./sharedace.o\r
1243 \r
1244 \r
1245 # Item # 119 -- sharedchao1 --\r
1246 ./sharedchao1.o : sharedchao1.cpp\r
1247         $(CC) $(CC_OPTIONS) sharedchao1.cpp -c $(INCLUDE) -o ./sharedchao1.o\r
1248 \r
1249 \r
1250 # Item # 120 -- sharedcommand --\r
1251 ./sharedcommand.o : sharedcommand.cpp\r
1252         $(CC) $(CC_OPTIONS) sharedcommand.cpp -c $(INCLUDE) -o ./sharedcommand.o\r
1253 \r
1254 \r
1255 # Item # 121 -- sharedjabund --\r
1256 ./sharedjabund.o : sharedjabund.cpp\r
1257         $(CC) $(CC_OPTIONS) sharedjabund.cpp -c $(INCLUDE) -o ./sharedjabund.o\r
1258 \r
1259 \r
1260 # Item # 122 -- sharedjclass --\r
1261 ./sharedjclass.o : sharedjclass.cpp\r
1262         $(CC) $(CC_OPTIONS) sharedjclass.cpp -c $(INCLUDE) -o ./sharedjclass.o\r
1263 \r
1264 \r
1265 # Item # 123 -- sharedjest --\r
1266 ./sharedjest.o : sharedjest.cpp\r
1267         $(CC) $(CC_OPTIONS) sharedjest.cpp -c $(INCLUDE) -o ./sharedjest.o\r
1268 \r
1269 \r
1270 # Item # 124 -- sharedordervector --\r
1271 ./sharedordervector.o : sharedordervector.cpp\r
1272         $(CC) $(CC_OPTIONS) sharedordervector.cpp -c $(INCLUDE) -o ./sharedordervector.o\r
1273 \r
1274 \r
1275 # Item # 125 -- sharedrabundvector --\r
1276 ./sharedrabundvector.o : sharedrabundvector.cpp\r
1277         $(CC) $(CC_OPTIONS) sharedrabundvector.cpp -c $(INCLUDE) -o ./sharedrabundvector.o\r
1278 \r
1279 \r
1280 # Item # 126 -- sharedsabundvector --\r
1281 ./sharedsabundvector.o : sharedsabundvector.cpp\r
1282         $(CC) $(CC_OPTIONS) sharedsabundvector.cpp -c $(INCLUDE) -o ./sharedsabundvector.o\r
1283 \r
1284 \r
1285 # Item # 127 -- sharedsobs --\r
1286 ./sharedsobs.o : sharedsobs.cpp\r
1287         $(CC) $(CC_OPTIONS) sharedsobs.cpp -c $(INCLUDE) -o ./sharedsobs.o\r
1288 \r
1289 \r
1290 # Item # 128 -- sharedsorabund --\r
1291 ./sharedsorabund.o : sharedsorabund.cpp\r
1292         $(CC) $(CC_OPTIONS) sharedsorabund.cpp -c $(INCLUDE) -o ./sharedsorabund.o\r
1293 \r
1294 \r
1295 # Item # 129 -- sharedsorclass --\r
1296 ./sharedsorclass.o : sharedsorclass.cpp\r
1297         $(CC) $(CC_OPTIONS) sharedsorclass.cpp -c $(INCLUDE) -o ./sharedsorclass.o\r
1298 \r
1299 \r
1300 # Item # 130 -- sharedsorest --\r
1301 ./sharedsorest.o : sharedsorest.cpp\r
1302         $(CC) $(CC_OPTIONS) sharedsorest.cpp -c $(INCLUDE) -o ./sharedsorest.o\r
1303 \r
1304 \r
1305 # Item # 131 -- sharedthetan --\r
1306 ./sharedthetan.o : sharedthetan.cpp\r
1307         $(CC) $(CC_OPTIONS) sharedthetan.cpp -c $(INCLUDE) -o ./sharedthetan.o\r
1308 \r
1309 \r
1310 # Item # 132 -- sharedthetayc --\r
1311 ./sharedthetayc.o : sharedthetayc.cpp\r
1312         $(CC) $(CC_OPTIONS) sharedthetayc.cpp -c $(INCLUDE) -o ./sharedthetayc.o\r
1313 \r
1314 \r
1315 # Item # 133 -- simpson --\r
1316 ./simpson.o : simpson.cpp\r
1317         $(CC) $(CC_OPTIONS) simpson.cpp -c $(INCLUDE) -o ./simpson.o\r
1318 \r
1319 \r
1320 # Item # 134 -- singlelinkage --\r
1321 ./singlelinkage.o : singlelinkage.cpp\r
1322         $(CC) $(CC_OPTIONS) singlelinkage.cpp -c $(INCLUDE) -o ./singlelinkage.o\r
1323 \r
1324 \r
1325 # Item # 135 -- sparsematrix --\r
1326 ./sparsematrix.o : sparsematrix.cpp\r
1327         $(CC) $(CC_OPTIONS) sparsematrix.cpp -c $(INCLUDE) -o ./sparsematrix.o\r
1328 \r
1329 \r
1330 # Item # 136 -- summarycommand --\r
1331 ./summarycommand.o : summarycommand.cpp\r
1332         $(CC) $(CC_OPTIONS) summarycommand.cpp -c $(INCLUDE) -o ./summarycommand.o\r
1333 \r
1334 \r
1335 # Item # 137 -- summarysharedcommand --\r
1336 ./summarysharedcommand.o : summarysharedcommand.cpp\r
1337         $(CC) $(CC_OPTIONS) summarysharedcommand.cpp -c $(INCLUDE) -o ./summarysharedcommand.o\r
1338 \r
1339 \r
1340 # Item # 138 -- uvest --\r
1341 ./uvest.o : uvest.cpp\r
1342         $(CC) $(CC_OPTIONS) uvest.cpp -c $(INCLUDE) -o ./uvest.o\r
1343 \r
1344 \r
1345 # Item # 139 -- validcalculator --\r
1346 ./validcalculator.o : validcalculator.cpp\r
1347         $(CC) $(CC_OPTIONS) validcalculator.cpp -c $(INCLUDE) -o ./validcalculator.o\r
1348 \r
1349 \r
1350 # Item # 140 -- validparameter --\r
1351 ./validparameter.o : validparameter.cpp\r
1352         $(CC) $(CC_OPTIONS) validparameter.cpp -c $(INCLUDE) -o ./validparameter.o\r
1353 \r
1354 \r
1355 # Item # 141 -- treenode --\r
1356 ./treenode.o : treenode.cpp\r
1357         $(CC) $(CC_OPTIONS) treenode.cpp -c $(INCLUDE) -o ./treenode.o\r
1358 \r
1359 \r
1360 # Item # 142 -- readtreecommand --\r
1361 ./readtreecommand.o : readtreecommand.cpp\r
1362         $(CC) $(CC_OPTIONS) readtreecommand.cpp -c $(INCLUDE) -o ./readtreecommand.o\r
1363 \r
1364 \r
1365 # Item # 143 -- reversecommand --\r
1366 ./reversecommand.o : reversecommand.cpp\r
1367         $(CC) $(CC_OPTIONS) reversecommand.cpp -c $(INCLUDE) -o ./reversecommand.o\r
1368 \r
1369 \r
1370 # Item # 144 -- trimseqscommand --\r
1371 ./trimseqscommand.o : trimseqscommand.cpp\r
1372         $(CC) $(CC_OPTIONS) trimseqscommand.cpp -c $(INCLUDE) -o ./trimseqscommand.o\r
1373 \r
1374 \r
1375 # Item # 145 -- slibshuff --\r
1376 ./slibshuff.o : slibshuff.cpp\r
1377         $(CC) $(CC_OPTIONS) slibshuff.cpp -c $(INCLUDE) -o ./slibshuff.o\r
1378 \r
1379 \r
1380 # Item # 146 -- libshuff --\r
1381 ./libshuff.o : libshuff.cpp\r
1382         $(CC) $(CC_OPTIONS) libshuff.cpp -c $(INCLUDE) -o ./libshuff.o\r
1383 \r
1384 \r
1385 # Item # 147 -- dlibshuff --\r
1386 ./dlibshuff.o : dlibshuff.cpp\r
1387         $(CC) $(CC_OPTIONS) dlibshuff.cpp -c $(INCLUDE) -o ./dlibshuff.o\r
1388 \r
1389 \r
1390 # Item # 148 -- mergefilecommand --\r
1391 ./mergefilecommand.o : mergefilecommand.cpp\r
1392         $(CC) $(CC_OPTIONS) mergefilecommand.cpp -c $(INCLUDE) -o ./mergefilecommand.o\r
1393 \r
1394 \r
1395 # Item # 149 -- coverage --\r
1396 ./coverage.o : coverage.cpp\r
1397         $(CC) $(CC_OPTIONS) coverage.cpp -c $(INCLUDE) -o ./coverage.o\r
1398 \r
1399 \r
1400 # Item # 150 -- whittaker --\r
1401 ./whittaker.o : whittaker.cpp\r
1402         $(CC) $(CC_OPTIONS) whittaker.cpp -c $(INCLUDE) -o ./whittaker.o\r
1403 \r
1404 \r
1405 # Item # 151 -- preclustercommand --\r
1406 ./preclustercommand.o : preclustercommand.cpp\r
1407         $(CC) $(CC_OPTIONS) preclustercommand.cpp -c $(INCLUDE) -o ./preclustercommand.o\r
1408 \r
1409 \r
1410 # Item # 152 -- otuhierarchycommand --\r
1411 ./otuhierarchycommand.o : otuhierarchycommand.cpp\r
1412         $(CC) $(CC_OPTIONS) otuhierarchycommand.cpp -c $(INCLUDE) -o ./otuhierarchycommand.o\r
1413 \r
1414 \r
1415 # Item # 153 -- setdircommand --\r
1416 ./setdircommand.o : setdircommand.cpp\r
1417         $(CC) $(CC_OPTIONS) setdircommand.cpp -c $(INCLUDE) -o ./setdircommand.o\r
1418 \r
1419 \r
1420 # Item # 154 -- getgroupcommand --\r
1421 ./getgroupcommand.o : getgroupcommand.cpp\r
1422         $(CC) $(CC_OPTIONS) getgroupcommand.cpp -c $(INCLUDE) -o ./getgroupcommand.o\r
1423 \r
1424 \r
1425 # Item # 155 -- getlabelcommand --\r
1426 ./getlabelcommand.o : getlabelcommand.cpp\r
1427         $(CC) $(CC_OPTIONS) getlabelcommand.cpp -c $(INCLUDE) -o ./getlabelcommand.o\r
1428 \r
1429 \r
1430 # Item # 156 -- secondarystructurecommand --\r
1431 ./secondarystructurecommand.o : secondarystructurecommand.cpp\r
1432         $(CC) $(CC_OPTIONS) secondarystructurecommand.cpp -c $(INCLUDE) -o ./secondarystructurecommand.o\r
1433 \r
1434 \r
1435 # Item # 157 -- mothurout --\r
1436 ./mothurout.o : mothurout.cpp\r
1437         $(CC) $(CC_OPTIONS) mothurout.cpp -c $(INCLUDE) -o ./mothurout.o\r
1438 \r
1439 \r
1440 # Item # 158 -- parselistscommand --\r
1441 ./parselistscommand.o : parselistscommand.cpp\r
1442         $(CC) $(CC_OPTIONS) parselistscommand.cpp -c $(INCLUDE) -o ./parselistscommand.o\r
1443 \r
1444 \r
1445 # Item # 159 -- readblast --\r
1446 ./readblast.o : readblast.cpp\r
1447         $(CC) $(CC_OPTIONS) readblast.cpp -c $(INCLUDE) -o ./readblast.o\r
1448 \r
1449 \r
1450 # Item # 160 -- chimeracheckrdp --\r
1451 ./chimeracheckrdp.o : chimeracheckrdp.cpp\r
1452         $(CC) $(CC_OPTIONS) chimeracheckrdp.cpp -c $(INCLUDE) -o ./chimeracheckrdp.o\r
1453 \r
1454 \r
1455 # Item # 161 -- hclustercommand --\r
1456 ./hclustercommand.o : hclustercommand.cpp\r
1457         $(CC) $(CC_OPTIONS) hclustercommand.cpp -c $(INCLUDE) -o ./hclustercommand.o\r
1458 \r
1459 \r
1460 # Item # 162 -- hcluster --\r
1461 ./hcluster.o : hcluster.cpp\r
1462         $(CC) $(CC_OPTIONS) hcluster.cpp -c $(INCLUDE) -o ./hcluster.o\r
1463 \r
1464 \r
1465 # Item # 163 -- getlistcountcommand --\r
1466 ./getlistcountcommand.o : getlistcountcommand.cpp\r
1467         $(CC) $(CC_OPTIONS) getlistcountcommand.cpp -c $(INCLUDE) -o ./getlistcountcommand.o\r
1468 \r
1469 \r
1470 # Item # 164 -- readcluster --\r
1471 ./readcluster.o : readcluster.cpp\r
1472         $(CC) $(CC_OPTIONS) readcluster.cpp -c $(INCLUDE) -o ./readcluster.o\r
1473 \r
1474 \r
1475 # Item # 165 -- ccode --\r
1476 ./ccode.o : ccode.cpp\r
1477         $(CC) $(CC_OPTIONS) ccode.cpp -c $(INCLUDE) -o ./ccode.o\r
1478 \r
1479 \r
1480 # Item # 166 -- taxonomyequalizer --\r
1481 ./taxonomyequalizer.o : taxonomyequalizer.cpp\r
1482         $(CC) $(CC_OPTIONS) taxonomyequalizer.cpp -c $(INCLUDE) -o ./taxonomyequalizer.o\r
1483 \r
1484 \r
1485 # Item # 167 -- phylotypecommand --\r
1486 ./phylotypecommand.o : phylotypecommand.cpp\r
1487         $(CC) $(CC_OPTIONS) phylotypecommand.cpp -c $(INCLUDE) -o ./phylotypecommand.o\r
1488 \r
1489 \r
1490 # Item # 168 -- classifyseqscommand --\r
1491 ./classifyseqscommand.o : classifyseqscommand.cpp\r
1492         $(CC) $(CC_OPTIONS) classifyseqscommand.cpp -c $(INCLUDE) -o ./classifyseqscommand.o\r
1493 \r
1494 \r
1495 # Item # 169 -- classify --\r
1496 ./classify.o : classify.cpp\r
1497         $(CC) $(CC_OPTIONS) classify.cpp -c $(INCLUDE) -o ./classify.o\r
1498 \r
1499 \r
1500 # Item # 170 -- phylotree --\r
1501 ./phylotree.o : phylotree.cpp\r
1502         $(CC) $(CC_OPTIONS) phylotree.cpp -c $(INCLUDE) -o ./phylotree.o\r
1503 \r
1504 \r
1505 # Item # 171 -- bayesian --\r
1506 ./bayesian.o : bayesian.cpp\r
1507         $(CC) $(CC_OPTIONS) bayesian.cpp -c $(INCLUDE) -o ./bayesian.o\r
1508 \r
1509 \r
1510 # Item # 172 -- alignmentdb --\r
1511 ./alignmentdb.o : alignmentdb.cpp\r
1512         $(CC) $(CC_OPTIONS) alignmentdb.cpp -c $(INCLUDE) -o ./alignmentdb.o\r
1513 \r
1514 \r
1515 # Item # 173 -- knn --\r
1516 ./knn.o : knn.cpp\r
1517         $(CC) $(CC_OPTIONS) knn.cpp -c $(INCLUDE) -o ./knn.o\r
1518 \r
1519 \r
1520 # Item # 174 -- distancedb --\r
1521 ./distancedb.o : distancedb.cpp\r
1522         $(CC) $(CC_OPTIONS) distancedb.cpp -c $(INCLUDE) -o ./distancedb.o\r
1523 \r
1524 \r
1525 # Item # 175 -- chimeraslayer --\r
1526 ./chimeraslayer.o : chimeraslayer.cpp\r
1527         $(CC) $(CC_OPTIONS) chimeraslayer.cpp -c $(INCLUDE) -o ./chimeraslayer.o\r
1528 \r
1529 \r
1530 # Item # 176 -- slayer --\r
1531 ./slayer.o : slayer.cpp\r
1532         $(CC) $(CC_OPTIONS) slayer.cpp -c $(INCLUDE) -o ./slayer.o\r
1533 \r
1534 \r
1535 # Item # 177 -- pcacommand --\r
1536 ./pcacommand.o : pcacommand.cpp\r
1537         $(CC) $(CC_OPTIONS) pcacommand.cpp -c $(INCLUDE) -o ./pcacommand.o\r
1538 \r
1539 \r
1540 # Item # 178 -- formatcolumn --\r
1541 ./formatcolumn.o : formatcolumn.cpp\r
1542         $(CC) $(CC_OPTIONS) formatcolumn.cpp -c $(INCLUDE) -o ./formatcolumn.o\r
1543 \r
1544 \r
1545 # Item # 179 -- formatphylip --\r
1546 ./formatphylip.o : formatphylip.cpp\r
1547         $(CC) $(CC_OPTIONS) formatphylip.cpp -c $(INCLUDE) -o ./formatphylip.o\r
1548 \r
1549 \r
1550 # Item # 180 -- mgclustercommand --\r
1551 ./mgclustercommand.o : mgclustercommand.cpp\r
1552         $(CC) $(CC_OPTIONS) mgclustercommand.cpp -c $(INCLUDE) -o ./mgclustercommand.o\r
1553 \r
1554 \r
1555 # Item # 181 -- getsharedotucommand --\r
1556 ./getsharedotucommand.o : getsharedotucommand.cpp\r
1557         $(CC) $(CC_OPTIONS) getsharedotucommand.cpp -c $(INCLUDE) -o ./getsharedotucommand.o\r
1558 \r
1559 \r
1560 # Item # 182 -- maligner --\r
1561 ./maligner.o : maligner.cpp\r
1562         $(CC) $(CC_OPTIONS) maligner.cpp -c $(INCLUDE) -o ./maligner.o\r
1563 \r
1564 \r
1565 # Item # 183 -- chimerarealigner --\r
1566 ./chimerarealigner.o : chimerarealigner.cpp\r
1567         $(CC) $(CC_OPTIONS) chimerarealigner.cpp -c $(INCLUDE) -o ./chimerarealigner.o\r
1568 \r
1569 \r
1570 # Item # 184 -- bergerparker --\r
1571 ./bergerparker.o : bergerparker.cpp\r
1572         $(CC) $(CC_OPTIONS) bergerparker.cpp -c $(INCLUDE) -o ./bergerparker.o\r
1573 \r
1574 \r
1575 # Item # 185 -- bstick --\r
1576 ./bstick.o : bstick.cpp\r
1577         $(CC) $(CC_OPTIONS) bstick.cpp -c $(INCLUDE) -o ./bstick.o\r
1578 \r
1579 \r
1580 # Item # 186 -- sharedkstest --\r
1581 ./sharedkstest.o : sharedkstest.cpp\r
1582         $(CC) $(CC_OPTIONS) sharedkstest.cpp -c $(INCLUDE) -o ./sharedkstest.o\r
1583 \r
1584 \r
1585 # Item # 187 -- qstat --\r
1586 ./qstat.o : qstat.cpp\r
1587         $(CC) $(CC_OPTIONS) qstat.cpp -c $(INCLUDE) -o ./qstat.o\r
1588 \r
1589 \r
1590 # Item # 188 -- shen --\r
1591 ./shen.o : shen.cpp\r
1592         $(CC) $(CC_OPTIONS) shen.cpp -c $(INCLUDE) -o ./shen.o\r
1593 \r
1594 \r
1595 # Item # 189 -- logsd --\r
1596 ./logsd.o : logsd.cpp\r
1597         $(CC) $(CC_OPTIONS) logsd.cpp -c $(INCLUDE) -o ./logsd.o\r
1598 \r
1599 \r
1600 # Item # 190 -- geom --\r
1601 ./geom.o : geom.cpp\r
1602         $(CC) $(CC_OPTIONS) geom.cpp -c $(INCLUDE) -o ./geom.o\r
1603 \r
1604 # Item # 191 -- parsesffcommand --\r
1605 ./parsesffcommand.o : parsesffcommand.cpp\r
1606         $(CC) $(CC_OPTIONS) parsesffcommand.cpp -c $(INCLUDE) -o ./parsesffcommand.o\r
1607 \r
1608 # Item # 192 -- chimeraccodecommand --\r
1609 ./chimeraccodecommand.o : chimeraccodecommand.cpp\r
1610         $(CC) $(CC_OPTIONS) chimeraccodecommand.cpp -c $(INCLUDE) -o ./chimeraccodecommand.o\r
1611 \r
1612 # Item # 193 -- chimeracheckcommand --\r
1613 ./chimeracheckcommand.o : chimeracheckcommand.cpp\r
1614         $(CC) $(CC_OPTIONS) chimeracheckcommand.cpp -c $(INCLUDE) -o ./chimeracheckcommand.o\r
1615 \r
1616 \r
1617 # Item # 194 -- chimeraslayercommand --\r
1618 ./chimeraslayercommand.o : chimeraslayercommand.cpp\r
1619         $(CC) $(CC_OPTIONS) chimeraslayercommand.cpp -c $(INCLUDE) -o ./chimeraslayercommand.o\r
1620 \r
1621 # Item # 195 -- chimerapintailcommand --\r
1622 ./chimerapintailcommand.o : chimerapintailcommand.cpp\r
1623         $(CC) $(CC_OPTIONS) chimerapintailcommand.cpp -c $(INCLUDE) -o ./chimerapintailcommand.o\r
1624 \r
1625 # Item # 196 -- chimerabellerophoncommand --\r
1626 ./chimerabellerophoncommand.o : chimerabellerophoncommand.cpp\r
1627         $(CC) $(CC_OPTIONS) chimerabellerophoncommand.cpp -c $(INCLUDE) -o ./chimerabellerophoncommand.o\r
1628
1629 # Item # 197 -- phylosummary --\r
1630 ./phylosummary.o : phylosummary.cpp\r
1631         $(CC) $(CC_OPTIONS) phylosummary.cpp -c $(INCLUDE) -o ./phylosummary.o\r
1632
1633 # Item # 198 -- setlogfilecommand --\r
1634 ./setlogfilecommand.o : setlogfilecommand.cpp\r
1635         $(CC) $(CC_OPTIONS) setlogfilecommand.cpp -c $(INCLUDE) -o ./setlogfilecommand.o\r
1636 \r
1637 \r
1638 \r
1639 ##### END RUN ####\r