binaries/src/tcoffee/install

   1 #!/usr/bin/env perl
   2 #Version 2.01 (25/02/03)
   3 use Cwd;
   4 use File::Path;
   5 use FileHandle;
   6 use strict;
   7
   8
   9 our (%MODE, %PG, %ENV_SET, %SUPPORTED_OS);
  10
  11
  12 our $EXIT_SUCCESS=0;
  13 our $EXIT_FAILURE=1;
  14 our $INTERNET=0;
  15
  16 #our $CP="cp -d ";
  17 our $CP="cp "; #was causing a crash on MacOSX
  18 our $SILENT=">/dev/null 2>/dev/null";
  19 our $WEB_BASE="http://www.tcoffee.org";
  20 our $TCLINKDB_ADDRESS="$WEB_BASE/Resources/tclinkdb.txt";
  21 our $OS=get_os();
  22 our $ROOT=&get_root();
  23 our $CD=cwd();
  24 our $CDIR=$CD;
  25 our $HOME=$ENV{'HOME'};
  26 ###########   DEFINITIONS ##############################
  27 #
  28 #
  29 our $CXX="g++";
  30 our $CXXFLAGS="";
  31
  32 our $CPP="g++";
  33 our $CPPFLAGS="";
  34
  35 our $CC="gcc";
  36 our $CFLAGS="";
  37
  38 our $FC="f77";
  39 our $FFLAGS="";
  40
  41 my $install="all";
  42 my $default_update_action="no_update";
  43 ########################################################
  44 my @required_applications=("wget_OR_curl");
  45 ########### Mode Definitions ##############################
  46 #
  47 #
  48 my @smode=("all", "clean", "install");
  49
  50 ########################################################
  51 &initialize_PG();
  52
  53 #Parse The Command Line
  54 my $cl=join( " ", @ARGV);
  55 if ($#ARGV==-1 || ($cl=~/-h/) ||($cl=~/-H/) )
  56   {
  57      print "\n!!!!!!! ./install  t_coffee             --> installs t_coffee only";
  58      print "\n!!!!!!! ./install  all                  --> installs all the modes [mcoffee, expresso, psicoffee,rcoffee..]";
  59      print "\n!!!!!!! ./install  [mcoffee|rcoffee|..] --> installs the specified mode";
  60      print "\n!!!!!!! ./install  -h                   --> print usage\n\n";
  61      if ( $#ARGV==-1){exit ($EXIT_FAILURE);}
  62    }
  63
  64 if (($cl=~/-h/) ||($cl=~/-H/) )
  65   {
  66     my $m;
  67     print "\n\n!!!!!!! advanced mode\n";
  68     foreach $m ((keys (%MODE)),@smode)
  69       {
  70         print "!!!!!!!       ./install $m\n";
  71       }
  72
  73     print "!!!!!!! ./install [target:package|mode|] [-update|-force|-exec=dir|-dis=dir|-root|-tclinkdb=file|-] [CC=|FCC=|CXX=|CFLAGS=|CXXFLAGS=]\n";
  74     print "!!!!!!! ./install clean    [removes all executables]\n";
  75     print "!!!!!!! ./install [optional:target] -update               [updates package already installed]\n";
  76     print "!!!!!!! ./install [optional:target] -force                [Forces recompilation over everything]\n";
  77
  78     print "!!!!!!! ./install [optional:target] -root                 [You are running as root]\n";
  79     print "!!!!!!! ./install [optional:target] -exec=/foo/bar/       [address for the T-Coffee executable]\n";
  80     print "!!!!!!! ./install [optional:target] -dis=/foo/bar/        [Address where distributions should be stored]\n";
  81     print "!!!!!!! ./install [optional:target] -tclinkdb=foo|update  [file containing all the packages to be installed]\n";
  82     print "!!!!!!! ./install [optional:target] -tclinkdb=foo|update  [file containing all the packages to be installed]\n";
  83     print "!!!!!!! ./install [optional:target] -clean                [clean everything]\n";
  84     print "!!!!!!! ./install [optional:target] -plugins              [plugins directory]\n";
  85     print "!!!!!!! mode:";
  86     foreach $m (keys(%MODE)){print "$m ";}
  87     print "\n";
  88     print "!!!!!!! Packages:";
  89     foreach $m (keys (%PG)){print "$m ";}
  90     print "\n";
  91
  92     print "\n\n";
  93     exit ($EXIT_FAILURE);
  94   }
  95
  96
  97
  98 # parse compiler flags
  99 my (@argl)=($cl=~/(\S+=[^=]+)\s\w+=/g);
 100 push (@argl, ($cl=~/(\S+=[^=]+\S)\s*$/g));
 101
 102 foreach $a (@argl)
 103   {
 104     if ( ($cl=~/CXX=(.*)/)){$CXX=$1;}
 105     if ( ($cl=~/-CC=(.*)/    )){$CC=$1;}
 106     if ( ($cl=~/-FC=(.*)/    )){$FC=$1;}
 107     if ( ($cl=~/-CFLAGS=(.*)/)){$CFLAGS=$1;}
 108     if ( ($cl=~/-CXXFLAGS=(.*)/)){$CXXFLAGS=$1;}
 109   }
 110 #parse install flags
 111 our ($ROOT_INSTALL, $NO_QUESTION, $default_update_action,$BINARIES_ONLY,$force, $default_update_action, $INSTALL_DIR, $PLUGINS_DIR, $DISTRIBUTIONS,$tclinkdb, $proxy, $clean);
 112 if ( ($cl=~/-root/)){$ROOT_INSTALL=1;}
 113 if ( ($cl=~/-no_question/)){$NO_QUESTION=1;}
 114 if ( ($cl=~/-update/)){$default_update_action="update";}
 115 if ( ($cl=~/-binaries/)){$BINARIES_ONLY=1;}
 116 if ( ($cl=~/-force/)){$force=1;$default_update_action="update"}
 117 if ( ($cl=~/-exec=\s*(\S+)/)){$INSTALL_DIR=$1;}
 118 if ( ($cl=~/-plugins=\s*(\S+)/)){$PLUGINS_DIR=$1;}
 119 if ( ($cl=~/-dis=\s*(\S+)/)){$DISTRIBUTIONS=$1;}
 120
 121 if ( ($cl=~/-tclinkdb=\s*(\S+)/)){$tclinkdb=$1;}
 122 if ( ($cl=~/-proxy=\s*(\S+)/)){$proxy=$1;}
 123 if ( ($cl=~/-clean/)){$clean=1;}
 124 #automated update
 125 if ($tclinkdb){&update_tclinkdb ($tclinkdb);}
 126
 127 #Prepare the T-Coffee directory structure
 128 our $TCDIR=$ENV{DIR_4_TCOFFEE};
 129 our $TCCACHE=$ENV{CACHE_4_TCOFFEE};
 130 our $TCTMP=$ENV{CACHE_4_TCOFFEE};
 131 our $TCM=$ENV{MCOFFEE_4_TCOFFEE};
 132 our $TCMETHODS=$ENV{METHODS_4_TCOFFEE};
 133 our $TCPLUGINS=$ENV{PLUGINS_4_TCOFFEE};
 134 our $PLUGINS_DIR="";
 135 our $INSTALL_DIR="";
 136
 137 &add_dir ($TCDIR="$HOME/.t_coffee");
 138 &add_dir ($TCCACHE="$TCDIR/cache");
 139 &add_dir ($TCTMP="$CDIR/tmp");
 140 &add_dir ($TCM="$TCDIR/mcoffee");
 141 &add_dir ($TCMETHODS="$TCDIR/methods");
 142 &add_dir ($TCPLUGINS="$TCDIR/plugins/$OS");
 143
 144 #Prepare the Installation Structure
 145
 146 our $BASE="$CD/bin";
 147 our $BIN="$BASE/binaries/$OS";
 148 our $DOWNLOAD_DIR="$BASE/download";
 149 our $DOWNLOAD_FILE="$DOWNLOAD_DIR/files";
 150 our $TMP="$BASE/tmp";
 151
 152 &add_dir($BASE);
 153 &add_dir($BIN);
 154 &add_dir($DOWNLOAD_DIR);
 155 &add_dir($DOWNLOAD_FILE);
 156 if (!$DISTRIBUTIONS){$DISTRIBUTIONS="$DOWNLOAD_DIR/distributions";}
 157 &add_dir ($DISTRIBUTIONS);
 158 &add_dir ($TMP);
 159
 160
 161 #set the directory for the plugins
 162 if    (!$PLUGINS_DIR && !$ROOT_INSTALL){$PLUGINS_DIR=$TCPLUGINS;}
 163 elsif (!$PLUGINS_DIR &&  $ROOT_INSTALL){$PLUGINS_DIR="/usr/local/bin/";}
 164
 165 #set the directory for t_coffee
 166 if    (!$INSTALL_DIR && !$ROOT_INSTALL){$INSTALL_DIR="$HOME/bin/";mkpath ($INSTALL_DIR);}
 167 elsif (!$INSTALL_DIR &&  $ROOT_INSTALL){$INSTALL_DIR="/usr/local/bin/";}
 168
 169 #prepare mcoffee files [Only if vanilla installation]
 170 if (-d "mcoffee"){`cp mcoffee/* $TCM`;}
 171
 172
 173 #prepare the environement
 174 our $ENV_FILE="$TCDIR/t_coffee_env";
 175 &env_file2putenv ($ENV_FILE);
 176 &set_proxy($proxy);
 177 my ($target, $p, $r);
 178 $target=$p;
 179
 180 foreach $p (  ((keys (%PG)),(keys(%MODE)),(@smode)) )
 181   {
 182     if ($ARGV[0] eq $p && $target eq ""){$target=$p;}
 183   }
 184 if ($target eq ""){exit ($EXIT_FAILURE);}
 185
 186
 187 # Check the basic requirements are met
 188 foreach $r (@required_applications)
 189   {
 190     my @app_list;
 191     my $i;
 192     $i=0;
 193
 194     @app_list=split (/_OR_/, $r);
 195     foreach my $pg (@app_list)
 196       {
 197         $i+=&pg_is_installed ($pg);
 198       }
 199     if ($i==0)
 200       {
 201       print "One of the following packages must be installed to proceed: ";
 202       foreach my $pg (@app_list)
 203         {
 204           print ("$pg ");
 205         }
 206       die;
 207     }
 208   }
 209
 210
 211 # Set the mains paths and create directories
 212 # distrib_dir/install/bin
 213 # distrib_dir/install/Downloads
 214 # distrib_dir/install/Downloads/Files
 215 # distrib_dir/install/Downloads/Distributions
 216 # distrib_dir/tmp
 217
 218 #Directory structure of the installation WITHIN the distribution dir
 219
 220
 221
 222 #sign the license
 223 &sign_license_ni();
 224
 225
 226 #Configure the copilers and their optins
 227 $PG{C}{compiler}=get_C_compiler($CC);
 228 $PG{Fortran}{compiler}=get_F_compiler($FC);
 229 $PG{CXX}{compiler}=$PG{CPP}{compiler}=$PG{GPP}{compiler}=get_CXX_compiler($CXX);
 230 if ($CXXFLAGS){$PG{CPP}{options}=$PG{GPP}{options}=$PG{CXX}{options}=$CXXFLAGS;}
 231 if ($CFLAGS){$PG{C}{options}=$CFLAGS;}
 232 foreach my $c (keys(%PG))
 233   {
 234     my $arguments;
 235     if ($PG{$c}{compiler})
 236       {
 237         $arguments="$PG{$c}{compiler_flag}=$PG{$c}{compiler} ";
 238         if ($PG{$c}{options})
 239           {
 240             $arguments.="$PG{$c}{options_flag}=$PG{$c}{options} ";
 241           }
 242         $PG{$c}{arguments}=$arguments;
 243       }
 244   }
 245
 246 # select the list of packages to update
 247 if ($PG{$target}){$PG{$target}{install}=1;}
 248 else
 249   {
 250     foreach my $pg (keys(%PG))
 251       {
 252         if ( $target eq "all" || ($PG{$pg}{mode}=~/$target/))
 253           {
 254             $PG{$pg} {install}=1;
 255           }
 256       }
 257   }
 258
 259 foreach my $pg (keys(%PG))
 260   {
 261     if (!$PG{$pg}{update_action}){$PG{$pg}{update_action}=$default_update_action;}
 262     elsif ($PG{$pg}{update_action} eq "never"){$PG{$pg}{install}=0;}
 263     if ( $force && $PG{$pg}{install})
 264       {
 265         `rm $BIN/$pg $BIN/$pg.exe $SILENT`;
 266       }
 267     if ($PG{$pg}{update_action} eq "update" && $PG{$pg}{install}){$PG{$pg}{update}=1;}
 268   }
 269
 270 #Execute the target: install/remove all the selected components
 271 if (($target=~/clean/))
 272   {
 273     print "------- cleaning executables -----\n";
 274     `rm bin/* $SILENT`;
 275     exit ($EXIT_SUCCESS);
 276   }
 277
 278 if ( !$PG{$target}){print "------- Installing T-Coffee Modes\n";}
 279
 280 #1 - Installing various modes
 281 foreach my $m (keys(%MODE))
 282   {
 283     if ( $target eq "all" || $target eq $m)
 284       {
 285         print "\n------- The installer will now install the $m components $MODE{$m}{description}\n";
 286         foreach my $pg (keys(%PG))
 287           {
 288             if ( $PG{$pg}{mode} =~/$m/ && $PG{$pg}{install})
 289               {
 290                 if ($PG{$pg}{touched}){print "------- $PG{$pg}{dname}: already processed\n";}
 291                 else {$PG{$pg}{success}=&install_pg($pg);$PG{$pg}{touched}=1;}
 292               }
 293           }
 294       }
 295   }
 296
 297 #2 - Installing Various Packages
 298 if ( $PG{$target}){print "------- Installing Individual Package\n";}
 299 foreach my $pg (keys (%PG))
 300   {
 301
 302     if ( $PG{$pg}{install} && !$PG{$pg}{touched})
 303       {
 304         print "\n------- Install $pg\n";
 305         $PG{$pg}{success}=&install_pg($pg);$PG{$pg}{touched}=1;
 306       }
 307   }
 308 print "------- Finishing The installation\n";
 309 my $final_report=&install ($INSTALL_DIR);
 310
 311 print "\n";
 312 print "*********************************************************************\n";
 313 print "********              INSTALLATION SUMMARY          *****************\n";
 314 print "*********************************************************************\n";
 315 print "------- SUMMARY package Installation:\n";
 316 foreach my $pg (keys(%PG))
 317   {
 318     if ( $PG{$pg}{install})
 319       {
 320         my $bin_status=($PG{$pg}{from_binary} && $PG{$pg}{success})?"[from binary]":"";
 321         if     ( $PG{$pg}{new} && !$PG{$pg}{old})                     {print "*------        $PG{$pg}{dname}: installed $bin_status\n"; $PG{$pg}{status}=1;}
 322         elsif  ( $PG{$pg}{new} &&  $PG{$pg}{old})                     {print "*------        $PG{$pg}{dname}: updated $bin_status\n"  ; $PG{$pg}{status}=1;}
 323         elsif  (!$PG{$pg}{new} &&  $PG{$pg}{old} && !$PG{$pg}{update}){print "*------        $PG{$pg}{dname}: previous\n" ; $PG{$pg}{status}=1;}
 324         elsif  (!$PG{$pg}{new} &&  $PG{$pg}{old} &&  $PG{$pg}{update}){print "*------        $PG{$pg}{dname}: failed update (previous installation available)\n";$PG{$pg}{status}=0;}
 325         else                                                          {print "*------        $PG{$pg}{dname}: failed installation";$PG{$pg}{status}=0;}
 326       }
 327   }
 328
 329 if ( !$PG{$target}){print "*------ SUMMARY mode Installation:\n";}
 330 foreach my $m (keys(%MODE))
 331   {
 332     if ( $target eq "all" || $target eq $m)
 333       {
 334         my $succesful=1;
 335         foreach my $pg (keys(%PG))
 336           {
 337             if (($PG{$pg}{mode}=~/$m/) && $PG{$pg}{install} && $PG{$pg}{status}==0)
 338               {
 339                 $succesful=0;
 340                 print "*!!!!!!       $PG{$pg}{dname}: Missing\n";
 341               }
 342           }
 343         if ( $succesful)
 344           {
 345             $MODE{$m}{status}=1;
 346             print "*------       MODE $MODE{$m}{dname} SUCCESFULY installed\n";
 347           }
 348         else
 349           {
 350             $MODE{$m}{status}=0;
 351             print "*!!!!!!       MODE $MODE{$m}{dname} UNSUCCESFULY installed\n";
 352           }
 353       }
 354   }
 355
 356 if ($clean==1 && ($BASE=~/install4tcoffee/) ){print "*------ Clean Installation Directory: $BASE\n";`rm -rf $BASE`;}
 357 #failure if one program was not well installed
 358 foreach my $pg (keys(%PG)){if ($PG{$pg}{install} && $PG{$pg}{status}==0){exit ($EXIT_FAILURE);}}
 359 exit ($EXIT_SUCCESS);
 360
 361 #################################################################################
 362 #                                                                               #
 363 #                                                                               #
 364 #                                                                               #
 365 #                   GENERIC INSTALLATION                                        #
 366 #                                                                               #
 367 #                                                                               #
 368 #                                                                               #
 369 #################################################################################
 370 sub get_CXX_compiler
 371   {
 372     my $c=@_[0];
 373     my (@clist)=("g++");
 374
 375     return get_compil ($c, @clist);
 376  }
 377 sub get_C_compiler
 378   {
 379     my $c=@_[0];
 380     my (@clist)=("gcc", "cc", "icc");
 381
 382     return get_compil ($c, @clist);
 383  }
 384
 385 sub get_F_compiler
 386   {
 387     my ($c)=@_[0];
 388     my @clist=("f77", "g77", "gfortran", "ifort");
 389     return get_compil ($c, @clist);
 390   }
 391
 392 sub get_compil
 393   {
 394     my ($fav,@clist)=(@_);
 395
 396     #return the first compiler found installed in the system. Check first the favorite
 397     foreach my $c ($fav,@clist)
 398       {
 399         if  (&pg_is_installed ($c)){return $c;}
 400       }
 401     return "";
 402   }
 403 sub exit_if_pg_not_installed
 404   {
 405     my (@arg)=(@_);
 406
 407     foreach my $p (@arg)
 408       {
 409         if ( !&pg_is_installed ($p))
 410           {
 411             print "!!!!!!!! The $p utility must be installed for this installation to proceed [FATAL]\n";
 412             die;
 413           }
 414       }
 415     return 1;
 416   }
 417 sub set_proxy
 418   {
 419     my ($proxy)=(@_);
 420     my (@list,$p);
 421
 422     @list= ("HTTP_proxy", "http_proxy", "HTTP_PROXY", "ALL_proxy", "all_proxy","HTTP_proxy_4_TCOFFEE","http_proxy_4_TCOFFEE");
 423
 424     if (!$proxy)
 425       {
 426         foreach my $p (@list)
 427           {
 428             if ( ($ENV_SET{$p}) || $ENV{$p}){$proxy=$ENV{$p};}
 429           }
 430       }
 431     foreach my $p(@list){$ENV{$p}=$proxy;}
 432   }
 433
 434 sub check_internet_connection
 435   {
 436     my $internet;
 437
 438     if ( -e "x"){unlink ("x");}
 439     if     (&pg_is_installed    ("wget")){`wget www.google.com -Ox >/dev/null 2>/dev/null`;}
 440     elsif  (&pg_is_installed    ("curl")){`curl www.google.com -ox >/dev/null 2>/dev/null`;}
 441     else
 442       {
 443         printf stderr "\nERROR: No pg for remote file fetching [wget or curl][FATAL]\n";
 444         exit ($EXIT_FAILURE);
 445       }
 446
 447     if ( !-e "x" || -s "x" < 10){$internet=0;}
 448     else {$internet=1;}
 449     if (-e "x"){unlink "x";}
 450     return $internet;
 451   }
 452 sub url2file
 453   {
 454     my ($cmd, $file,$wget_arg, $curl_arg)=(@_);
 455     my ($exit,$flag, $pg, $arg);
 456
 457     if ($INTERNET || check_internet_connection ()){$INTERNET=1;}
 458     else
 459       {
 460         print STDERR "ERROR: No Internet Connection [FATAL:install.pl]\n";
 461         exit ($EXIT_FAILURE);
 462       }
 463
 464     if     (&pg_is_installed    ("wget")){$pg="wget"; $flag="-O";$arg=$wget_arg;}
 465     elsif  (&pg_is_installed    ("curl")){$pg="curl"; $flag="-o";$arg=$curl_arg;}
 466     else
 467       {
 468         printf stderr "\nERROR: No pg for remote file fetching [wget or curl][FATAL]\n";
 469         exit ($EXIT_FAILURE);
 470       }
 471
 472
 473     if (-e $file){unlink($file);}
 474     $exit=system "$pg $cmd $flag$file $arg";
 475     return $exit;
 476   }
 477
 478 sub pg_is_installed
 479   {
 480     my ($p, $dir)=(@_);
 481     my ($r,$m);
 482     my ($supported, $language, $compil);
 483
 484     if ( $PG{$p})
 485       {
 486         $language=$PG{$p}{language2};
 487         $compil=$PG{$language}{compiler};
 488       }
 489
 490     if ( $compil eq "CPAN")
 491       {
 492         if ( system ("perl -M$p -e 1")==$EXIT_SUCCESS){return 1;}
 493         else {return 0;}
 494       }
 495     elsif ($dir)
 496       {
 497         if (-e "$dir/$p" || -e "$dir/$p\.exe"){return 1;}
 498         else {return 0;}
 499       }
 500     elsif (-e "$PLUGINS_DIR/$p" || -e "$PLUGINS_DIR/$p.exe"){return 1;}
 501     else
 502       {
 503         $r=`which $p 2>/dev/null`;
 504         if ($r eq ""){return 0;}
 505         else {return 1;}
 506       }
 507     return 0;
 508   }
 509 sub install
 510   {
 511     my ($new_bin)=(@_);
 512     my ($copied, $report);
 513
 514
 515     if (!$ROOT_INSTALL)
 516       {
 517
 518         if (-e "$BIN/t_coffee"){`$CP $BIN/t_coffee $INSTALL_DIR`};
 519         `cp $BIN/* $PLUGINS_DIR`;
 520         $copied=1;
 521       }
 522     else
 523       {
 524         $copied=&root_run ("You must be root to finalize the installation", "$CP $BIN/* $INSTALL_DIR $SILENT");
 525       }
 526
 527
 528   if ( !$copied)
 529     {
 530       $report="*!!!!!! Installation unsuccesful. The executables have been left in $BASE/bin\n";
 531     }
 532   elsif ( $copied && $ROOT)
 533     {
 534       $report="*------ Installation succesful. Your executables have been copied in $new_bin and are on your PATH\n";
 535     }
 536   elsif ( $copied && !$ROOT)
 537     {
 538       $report= "*!!!!!! T-Coffee and associated packages have been copied in: $new_bin\n";
 539       $report.="*!!!!!! This address is NOT in your PATH sytem variable\n";
 540       $report.="*!!!!!! You can do so by adding the following line in your ~/.bashrc file:\n";
 541       $report.="*!!!!!! export PATH=$new_bin:\$PATH\n";
 542     }
 543   return $report;
 544 }
 545
 546 sub sign_license_ni
 547   {
 548     my $F=new FileHandle;
 549     open ($F, "license.txt");
 550     while (<$F>)
 551       {
 552         print "$_";
 553       }
 554     close ($F);
 555
 556     return;
 557   }
 558 #################################################################################
 559 #                                                                               #
 560 #                                                                               #
 561 #                                                                               #
 562 #                   INDIVIDUAL MULTIPLE SEQUENCE ALIGNMNT PACKAGES INSTALLATION #
 563 #                                                                               #
 564 #                                                                               #
 565 #                                                                               #
 566 #################################################################################
 567
 568 sub install_pg
 569   {
 570     my ($pg)=(@_);
 571     my ($report, $previous, $language, $compiler, $return);
 572
 573     if (!$PG{$pg}{install}){return 1;}
 574
 575     $previous=&pg_is_installed ($pg);
 576
 577     if ($PG{$pg}{update_action} eq "no_update" && $previous)
 578       {
 579         $PG{$pg}{old}=1;
 580         $PG{$pg}{new}=0;
 581         $return=1;
 582       }
 583     else
 584       {
 585         $PG{$pg}{old}=$previous;
 586
 587         if ($PG{$pg} {language2} eq "Perl"){&install_perl_package ($pg);}
 588         elsif ($BINARIES_ONLY && &install_binary_package ($pg)){$PG{$pg}{from_binary}=1;}
 589         elsif (&install_source_package ($pg)){;}
 590         else
 591           {
 592
 593             if (!&supported_os($OS))
 594               {
 595                 print "!!!!!!!! $pg compilation failed, binary unsupported for $OS\n";
 596               }
 597             elsif (!($PG{$pg}{from_binary}=&install_binary_package ($pg)))
 598               {
 599                 print "!!!!!!!! $pg compilation and  binary installation failed\n";
 600               }
 601           }
 602         $PG{$pg}{new}=$return=&pg_is_installed ($pg,$BIN);
 603       }
 604
 605
 606     return $return;
 607   }
 608 sub install_perl_package
 609   {
 610     my ($pg)=(@_);
 611     my ($report, $language, $compiler);
 612
 613     $language=$PG{$pg} {language2};
 614     $compiler=$PG{$language}{compiler};
 615
 616     if (!&pg_is_installed ($pg))
 617       {
 618         if ( $OS eq "windows"){`perl -M$compiler -e 'install $pg'`;}
 619         elsif ( $ROOT eq "sudo"){system ("sudo perl -M$compiler -e 'install $pg'");}
 620         else {system ("su root -c perl -M$compiler -e 'install $pg'");}
 621       }
 622     return &pg_is_installed ($pg);
 623   }
 624
 625
 626
 627 sub install_source_package
 628   {
 629     my ($pg)=(@_);
 630     my ($report, $download, $arguments, $language, $address, $name, $ext, $main_dir, $distrib);
 631     my $wget_tmp="$TMP/wget.tmp";
 632     my (@fl);
 633     if ( -e "$BIN/$pg" || -e "$BIN/$pg.exe"){return 1;}
 634
 635     if ($pg eq "t_coffee")  {return   &install_t_coffee ($pg);}
 636     elsif ($pg eq "TMalign"){return   &install_TMalign ($pg);}
 637
 638     chdir $DISTRIBUTIONS;
 639
 640     $download=$PG{$pg}{source};
 641
 642     if (($download =~/tgz/))
 643       {
 644         ($address,$name,$ext)=($download=~/(.+\/)([^\/]+)(\.tgz)/);
 645       }
 646     elsif (($download=~/tar\.gz/))
 647       {
 648         ($address,$name,$ext)=($download=~/(.+\/)([^\/]+)(\.tar\.gz)/);
 649       }
 650     elsif (($download=~/tar/))
 651       {
 652         ($address,$name,$ext)=($download=~/(.+\/)([^\/]+)(\.tar)/);
 653       }
 654     else
 655       {
 656         ($address,$name)=($download=~/(.+\/)([^\/]+)/);
 657         $ext="";
 658       }
 659     $distrib="$name$ext";
 660
 661     if ( !-d $pg){mkdir $pg;}
 662     chdir $pg;
 663
 664     #get the distribution if available
 665     if ( -e "$DOWNLOAD_DIR/$distrib")
 666       {
 667         `$CP $DOWNLOAD_DIR/$distrib .`;
 668       }
 669     #UNTAR and Prepare everything
 670     if (!-e "$name.tar" && !-e "$name")
 671       {
 672         &check_rm ($wget_tmp);
 673         print "\n------- Downloading/Installing $pg\n";
 674         if (!-e $distrib && &url2file ("$download", "$wget_tmp")==$EXIT_SUCCESS)
 675           {
 676
 677             `mv $wget_tmp $distrib`;
 678             `$CP $distrib $DOWNLOAD_DIR/`;
 679           }
 680
 681         if (!-e $distrib)
 682           {
 683             print "!!!!!!! Download of $pg distribution failed\n";
 684             print "!!!!!!! Check Address: $PG{$pg}{source}\n";
 685             return 0;
 686           }
 687         print "\n------- unzipping/untaring $name\n";
 688         if (($ext =~/z/))
 689           {
 690             &flush_command ("gunzip $name$ext");
 691
 692           }
 693         if (($ext =~/tar/) || ($ext =~/tgz/))
 694           {
 695             &flush_command("tar -xvf $name.tar");
 696           }
 697       }
 698     #Guess and enter the distribution directory
 699     @fl=ls($p);
 700     foreach my $f (@fl)
 701       {
 702         if (-d $f)
 703           {
 704             $main_dir=$f;
 705           }
 706       }
 707     if (-d $main_dir)
 708           {chdir $main_dir;}
 709
 710     print "\n------- Compiling/Installing $pg\n";
 711     `make clean $SILENT`;
 712     #sap
 713     if ($pg eq "sap")
 714       {
 715         `rm *.o sap  sap.exe ./util/aa/*.o  ./util/wt/.o $SILENT`;
 716         &flush_command ("make $arguments sap");
 717         &check_cp ($pg, "$BIN");
 718       }
 719     elsif ($pg eq "clustalw2")
 720       {
 721         &flush_command("./configure");
 722         &flush_command("make $arguments");
 723         &check_cp ("./src/$pg", "$BIN");
 724
 725       }
 726     elsif ($pg eq "clustalw")
 727       {
 728         &flush_command("make $arguments clustalw");
 729         `$CP $pg $BIN $SILENT`;
 730       }
 731
 732     elsif ($pg eq "mafft")
 733       {
 734         my $base=cwd();
 735         my $c;
 736
 737         #compile core
 738         mkpath ("./mafft/bin");
 739         mkpath ("./mafft/lib");
 740         chdir "$base/core";
 741         `make clean $SILENT`;
 742         &flush_command ("make $arguments");
 743         &flush_command ("make install LIBDIR=../mafft/lib BINDIR=../mafft/bin");
 744
 745         #compile extension
 746         chdir "$base/extensions";
 747         `make clean $SILENT`;
 748         &flush_command ("make $arguments");
 749         &flush_command ("make install LIBDIR=../mafft/lib BINDIR=../mafft/bin");
 750
 751         #put everything in mafft and copy the coompiled stuff in bin
 752         chdir "$base";
 753         if ($ROOT_INSTALL)
 754           {
 755             &root_run ("You Must be Roor to Install MAFFT\n", "mkdir /usr/local/mafft/;$CP mafft/lib/* /usr/local/mafft;$CP mafft/lib/mafft* /usr/local/bin ;$CP mafft/bin/mafft /usr/local/bin/; ");
 756           }
 757         else
 758           {
 759             `$CP mafft/lib/*  $BIN`;
 760             `$CP mafft/bin/mafft  $BIN`;
 761           }
 762         `tar -cvf mafft.tar mafft`;
 763         `gzip mafft.tar`;
 764         `mv mafft.tar.gz $BIN`;
 765       }
 766     elsif ( $pg eq "dialign-tx")
 767       {
 768         my $f;
 769         my $base=cwd();
 770
 771         chdir "./source";
 772         &flush_command (" make CPPFLAGS='-O3 -funroll-loops' all");
 773
 774         chdir "..";
 775         &check_cp ("./source/$pg", "$BIN");
 776         &check_cp ("./source/$pg", "$BIN/dialign-t");
 777       }
 778     elsif ($pg eq "poa")
 779       {
 780         &flush_command ("make $arguments poa");
 781         &check_cp ("$pg", "$BIN");
 782       }
 783     elsif ( $pg eq "probcons")
 784       {
 785         `rm *.exe $SILENT`;
 786         &flush_command ("make $arguments probcons");
 787         &check_cp("$pg", "$BIN/$pg");
 788       }
 789     elsif ( $pg eq "probcons" || $pg eq "probconsRNA")
 790       {
 791         `rm *.exe $SILENT`;
 792         &flush_command ("make $arguments probcons");
 793         &check_cp("probcons", "$BIN/$pg");
 794       }
 795
 796     elsif (  $pg eq "muscle")
 797       {
 798         `rm *.o muscle muscle.exe $SILENT`;
 799         &flush_command ("make $arguments all");
 800         &check_cp("$pg", "$BIN");
 801       }
 802     elsif ( $pg eq "pcma")
 803       {
 804         &flush_command ("make $arguments pcma");
 805         &check_cp("$pg", "$BIN");
 806       }
 807     elsif ($pg eq "kalign")
 808       {
 809         &flush_command ("./configure");
 810         &flush_command("make $arguments");
 811         &check_cp ("$pg",$BIN);
 812       }
 813     elsif ( $pg eq "amap")
 814       {
 815         chdir "align";
 816         `make clean $SILENT`;
 817         &flush_command ("make $arguments all");
 818         &check_cp ("$pg", $BIN);
 819       }
 820     elsif ( $pg eq "proda")
 821       {
 822         &flush_command ("make $arguments all");
 823         &check_cp ("$pg", $BIN);
 824       }
 825     elsif ( $pg eq "prank")
 826       {
 827         &flush_command ("make $arguments all");
 828         &check_cp ("$pg", $BIN);
 829       }
 830     elsif ( $pg eq "mustang")
 831       {
 832         &flush_command ("make $arguments all");
 833         if ( $OS=~/windows/){&check_cp("./bin/MUSTANG_v.3", "$BIN/mustang.exe");}
 834         else {&check_cp("./bin/MUSTANG_v.3", "$BIN/mustang");}
 835       }
 836     elsif ( $pg eq "RNAplfold")
 837       {
 838         &flush_command("./configure");
 839         &flush_command ("make $arguments all");
 840         &check_cp("./Progs/RNAplfold", "$BIN");
 841       }
 842     chdir $CDIR;
 843     return &pg_is_installed ($pg, $BIN);
 844   }
 845
 846 sub install_t_coffee
 847   {
 848     my ($pg)=(@_);
 849     my ($report,$cflags, $arguments, $language, $compiler) ;
 850     #1-Install T-Coffee
 851     chdir "t_coffee_source";
 852     &flush_command ("make clean");
 853     print "\n------- Compiling T-Coffee\n";
 854     $language=$PG{$pg} {language2};
 855     $arguments=$PG{$language}{arguments};
 856     if (!($arguments =~/CFLAGS/)){$arguments .= " CFLAGS=-O2 ";}
 857
 858     if ( $CC ne ""){&flush_command ("make -i $arguments t_coffee");}
 859     &check_cp ($pg, $BIN);
 860
 861     chdir $CDIR;
 862     return &pg_is_installed ($pg, $BIN);
 863   }
 864 sub install_TMalign
 865   {
 866     my ($pg)=(@_);
 867     my $report;
 868     chdir "t_coffee_source";
 869     print "\n------- Compiling TMalign\n";
 870     `rm TMalign TMalign.exe $SILENT`;
 871     if ( $FC ne ""){&flush_command ("make -i $PG{Fortran}{arguments} TMalign");}
 872     &check_cp ($pg, $BIN);
 873     if ( !-e "$BIN/$pg" && pg_has_binary_distrib ($pg))
 874       {
 875         print "!!!!!!! Compilation of $pg impossible. Will try to install from binary\n";
 876         return &install_binary_package ($pg);
 877       }
 878     chdir $CDIR;
 879     return &pg_is_installed ($pg, $BIN);
 880   }
 881
 882 sub pg_has_binary_distrib
 883   {
 884     my ($pg)=(@_);
 885     if ($PG{$pg}{windows}){return 1;}
 886     elsif ($PG{$pg}{osx}){return 1;}
 887     elsif ($PG{$pg}{linux}){return 1;}
 888     return 0;
 889   }
 890 sub install_binary_package
 891   {
 892     my ($pg)=(@_);
 893     my ($base,$report,$name, $download, $arguments, $language, $dir);
 894     my $isdir;
 895     &input_os();
 896
 897     if (!&supported_os($OS)){return 0;}
 898     if ( $PG{$pg}{binary}){$name=$PG{$pg}{binary};}
 899     else
 900       {
 901         $name=$pg;
 902         if ( $OS eq "windows"){$name.=".exe";}
 903       }
 904
 905     $download="$WEB_BASE/Packages/Binaries/$OS/$name";
 906
 907     $base=cwd();
 908     chdir $TMP;
 909
 910     if (!-e $name)
 911       {
 912         `rm x $SILENT`;
 913         if ( url2file("$download","x")==$EXIT_SUCCESS)
 914           {
 915             `mv x $name`;
 916           }
 917       }
 918
 919     if (!-e $name)
 920       {
 921         print "!!!!!!! $PG{$pg}{dname}: Download of $pg binary failed\n";
 922         print "!!!!!!! $PG{$pg}{dname}: Check Address: $download\n";
 923         return 0;
 924       }
 925     print "\n------- Installing $pg\n";
 926
 927     if ($name =~/tar\.gz/)
 928       {
 929         `gunzip  $name`;
 930         `tar -xvf $pg.tar`;
 931         chdir $pg;
 932         if ( $pg eq "mafft")
 933           {
 934             if ($ROOT_INSTALL)
 935               {
 936                 &root_run ("You Must be Roor to Install MAFFT\n", "$CP mafft/bin/* /usr/local/mafft;mkdir /usr/local/mafft/; $CP mafft/lib/* /usr/local/bin/");
 937               }
 938             else
 939               {
 940                 `$CP $TMP/$pg/bin/* $BIN $SILENT`;
 941                 `$CP $TMP/$pg/lib/* $BIN $SILENT`;
 942               }
 943           }
 944         else
 945           {
 946             if (-e "$TMP/$pg/data"){`$CP $TMP/$pg/data/* $TCM $SILENT`;}
 947             if (!($pg=~/\*/)){`rm -rf $pg`;}
 948           }
 949       }
 950     else
 951       {
 952         &check_cp ("$pg", "$BIN");
 953         `chmod u+x $BIN/$pg`;
 954         unlink ($pg);
 955       }
 956     chdir $base;
 957     $PG{$pg}{from_binary}=1;
 958     return &pg_is_installed ($pg, $BIN);
 959   }
 960
 961 ################################################################################
 962 #                                                                               #
 963 #                                                                               #
 964 #                                                                               #
 965 #                   Simple Utilities                                            #
 966 #                                                                               #
 967 #                                                                               #
 968 #                                                                               #
 969 #################################################################################
 970 sub add_dir
 971   {
 972     my $dir=@_[0];
 973
 974     if (!-e $dir && !-d $dir)
 975       {
 976         return mkpath ($dir);
 977       }
 978     else
 979       {
 980         return 0;
 981       }
 982   }
 983 sub check_rm
 984   {
 985     my ($file)=(@_);
 986
 987     if ( -e $file)
 988       {
 989         return unlink($file);
 990       }
 991     return 0;
 992   }
 993 sub check_cp
 994   {
 995     my ($from, $to)=(@_);
 996     if ( !-e $from && -e "$from\.exe"){$from="$from\.exe";}
 997     if ( !-e $from){return 0;}
 998
 999     `$CP $from $to`;
1000     return 1;
1001   }
1002 sub check_file_list_exists
1003   {
1004     my ($base, @flist)=(@_);
1005     my $f;
1006
1007     foreach $f (@flist)
1008       {
1009         if ( !-e "$base/$f"){return 0;}
1010       }
1011     return 1;
1012   }
1013 sub ls
1014   {
1015     my $f=@_[0];
1016     my @fl;
1017     chomp(@fl=`ls -1 $f`);
1018     return @fl;
1019   }
1020 sub flush_command
1021   {
1022     my $command=@_[0];
1023     my $F=new FileHandle;
1024     open ($F, "$command|");
1025     while (<$F>){print "    --- $_";}
1026     close ($F);
1027   }
1028
1029 sub input_installation_directory
1030   {
1031     my $dir=@_[0];
1032     my $new;
1033
1034     print "------- The current installation directory is: [$dir]\n";
1035     print "??????? Return to keep the default or new value:";
1036
1037     if ($NO_QUESTION==0)
1038       {
1039         chomp ($new=<stdin>);
1040         while ( $new ne "" && !input_yes ("You have entered $new. Is this correct? ([y]/n):"))
1041           {
1042             print "???????New installation directory:";
1043             chomp ($new=<stdin>);
1044           }
1045         $dir=($new eq "")?$dir:$new;
1046         $dir=~s/\/$//;
1047       }
1048
1049     if ( -d $dir){return $dir;}
1050     elsif (&root_run ("You must be root to create $dir","mkdir $dir")==$EXIT_SUCCESS){return $dir;}
1051     else
1052       {
1053         print "!!!!!!! $dir could not be created\n";
1054         if ( $NO_QUESTION)
1055           {
1056             return "";
1057           }
1058         elsif ( &input_yes ("??????? Do you want to provide a new directory([y]/n)?:"))
1059           {
1060             return input_installation_directory ($dir);
1061           }
1062         else
1063           {
1064             return "";
1065           }
1066       }
1067
1068   }
1069 sub input_yes
1070   {
1071     my $question =@_[0];
1072     my $answer;
1073
1074     if ($NO_QUESTION==1){return 1;}
1075
1076     if ($question eq ""){$question="??????? Do you wish to proceed ([y]/n)?:";}
1077     print $question;
1078     chomp($answer=lc(<STDIN>));
1079     if (($answer=~/^y/) || $answer eq ""){return 1;}
1080     elsif ( ($answer=~/^n/)){return 0;}
1081     else
1082       {
1083         return input_yes($question);
1084       }
1085   }
1086 sub root_run
1087   {
1088     my ($txt, $cmd)=(@_);
1089
1090     if ( system ($cmd)==$EXIT_SUCCESS){return $EXIT_SUCCESS;}
1091     else
1092       {
1093         print "------- $txt\n";
1094         if ( $ROOT eq "sudo"){return system ("sudo $cmd");}
1095         else {return system ("su root -c \"$cmd\"");}
1096       }
1097   }
1098 #analyze environement
1099 sub get_root
1100   {
1101     if (&pg_is_installed ("sudo")){return "sudo";}
1102     else {return "su";}
1103   }
1104
1105 sub get_os
1106   {
1107     my $raw_os=`uname`;
1108     my $os;
1109
1110     $raw_os=lc ($raw_os);
1111
1112     if ($raw_os =~/cygwin/){$os="windows";}
1113     elsif ($raw_os =~/linux/){$os="linux";}
1114     elsif ($raw_os =~/osx/){$os="macosx";}
1115     elsif ($raw_os =~/darwin/){$os="macosx";}
1116     else
1117       {
1118         $os=$raw_os;
1119       }
1120     return $os;
1121   }
1122 sub input_os
1123   {
1124     my $answer;
1125     if ($OS) {return $OS;}
1126
1127     print "??????? which os do you use: [w]indows, [l]inux, [m]acosx:?";
1128     $answer=lc(<STDIN>);
1129
1130     if (($answer=~/^m/)){$OS="macosx";}
1131     elsif ( ($answer=~/^w/)){$OS="windows";}
1132     elsif ( ($answer=~/^linux/)){$OS="linux";}
1133
1134     else
1135       {
1136         return &input_os();
1137       }
1138     return $OS;
1139   }
1140
1141 sub supported_os
1142   {
1143     my ($os)=(@_[0]);
1144     return $SUPPORTED_OS{$os};
1145   }
1146
1147
1148 ################################################################################
1149 #                                                                               #
1150 #                                                                               #
1151 #                                                                               #
1152 #                  update/initialize links                                      #
1153 #                                                                               #
1154 #                                                                               #
1155 #                                                                               #
1156 #################################################################################
1157
1158
1159 sub update_tclinkdb
1160   {
1161     my $file =@_[0];
1162     my $name;
1163     my $F=new FileHandle;
1164     my ($download, $address, $name, $l, $db);
1165
1166     if ( $file eq "update"){$file=$TCLINKDB_ADDRESS;}
1167
1168     if ( $file =~/http:\/\// || $file =~/ftp:\/\//)
1169       {
1170         ($address, $name)=($download=~/(.*)\/([^\/]+)$/);
1171         `rm x $SILENT`;
1172         if (&url2file ($file,"x")==$EXIT_SUCCESS)
1173           {
1174             print "------- Susscessful upload of $name";
1175             `mv x $name`;
1176             $file=$name;
1177           }
1178       }
1179     open ($F, "$file");
1180     while (<$F>)
1181       {
1182         my $l=$_;
1183         if (($l =~/^\/\//) || ($db=~/^#/)){;}
1184         elsif ( !($l =~/\w/)){;}
1185         else
1186           {
1187             my @v=split (/\s+/, $l);
1188             if ( $l=~/^MODE/)
1189               {
1190                 $MODE{$v[1]}{$v[2]}=$v[3];
1191               }
1192             elsif ($l=~/^PG/)
1193               {
1194                 $PG{$v[1]}{$v[2]}=$v[3];
1195               }
1196           }
1197       }
1198     close ($F);
1199     &post_process_PG();
1200     return;
1201   }
1202
1203
1204
1205 sub initialize_PG
1206   {
1207
1208 $PG{"t_coffee"}{"4_TCOFFEE"}="TCOFFEE";
1209 $PG{"t_coffee"}{"type"}="sequence_multiple_aligner";
1210 $PG{"t_coffee"}{"ADDRESS"}="http://www.tcoffee.org";
1211 $PG{"t_coffee"}{"language"}="C";
1212 $PG{"t_coffee"}{"language2"}="C";
1213 $PG{"t_coffee"}{"source"}="http://www.tcoffee.org/Packages/T-COFFEE_distribution.tar.gz";
1214 $PG{"t_coffee"}{"update_action"}="always";
1215 $PG{"t_coffee"}{"mode"}="tcoffee,mcoffee,rcoffee,expresso,3dcoffee";
1216 $PG{"clustalw2"}{"4_TCOFFEE"}="CLUSTALW2";
1217 $PG{"clustalw2"}{"type"}="sequence_multiple_aligner";
1218 $PG{"clustalw2"}{"ADDRESS"}="http://www.clustal.org";
1219 $PG{"clustalw2"}{"language"}="C++";
1220 $PG{"clustalw2"}{"language2"}="CXX";
1221 $PG{"clustalw2"}{"source"}="http://www.clustal.org/download/2.0.10/clustalw-2.0.10-src.tar.gz";
1222 $PG{"clustalw2"}{"mode"}="mcoffee,rcoffee";
1223 $PG{"clustalw"}{"4_TCOFFEE"}="CLUSTALW";
1224 $PG{"clustalw"}{"type"}="sequence_multiple_aligner";
1225 $PG{"clustalw"}{"ADDRESS"}="http://www.clustal.org";
1226 $PG{"clustalw"}{"language"}="C";
1227 $PG{"clustalw"}{"language2"}="C";
1228 $PG{"clustalw"}{"source"}="http://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/ClustalW/clustalw1.82.UNIX.tar.gz";
1229 $PG{"clustalw"}{"mode"}="mcoffee,rcoffee";
1230 $PG{"dialign-t"}{"4_TCOFFEE"}="DIALIGNT";
1231 $PG{"dialign-t"}{"type"}="sequence_multiple_aligner";
1232 $PG{"dialign-t"}{"ADDRESS"}="http://dialign-tx.gobics.de/";
1233 $PG{"dialign-t"}{"DIR"}="/usr/share/dialign-tx/";
1234 $PG{"dialign-t"}{"language"}="C";
1235 $PG{"dialign-t"}{"language2"}="C";
1236 $PG{"dialign-t"}{"source"}="http://dialign-tx.gobics.de/DIALIGN-TX_1.0.1.tar.gz";
1237 $PG{"dialign-t"}{"mode"}="mcoffee";
1238 $PG{"dialign-t"}{"binary"}="dialign-t";
1239 $PG{"dialign-tx"}{"4_TCOFFEE"}="DIALIGNTX";
1240 $PG{"dialign-tx"}{"type"}="sequence_multiple_aligner";
1241 $PG{"dialign-tx"}{"ADDRESS"}="http://dialign-tx.gobics.de/";
1242 $PG{"dialign-tx"}{"DIR"}="/usr/share/dialign-tx/";
1243 $PG{"dialign-tx"}{"language"}="C";
1244 $PG{"dialign-tx"}{"language2"}="C";
1245 $PG{"dialign-tx"}{"source"}="http://dialign-tx.gobics.de/DIALIGN-TX_1.0.1.tar.gz";
1246 $PG{"dialign-tx"}{"mode"}="mcoffee";
1247 $PG{"dialign-tx"}{"binary"}="dialign-tx";
1248 $PG{"poa"}{"4_TCOFFEE"}="POA";
1249 $PG{"poa"}{"type"}="sequence_multiple_aligner";
1250 $PG{"poa"}{"ADDRESS"}="http://www.bioinformatics.ucla.edu/poa/";
1251 $PG{"poa"}{"language"}="C";
1252 $PG{"poa"}{"language2"}="C";
1253 $PG{"poa"}{"source"}="http://downloads.sourceforge.net/poamsa/poaV2.tar.gz";
1254 $PG{"poa"}{"DIR"}="/usr/share/";
1255 $PG{"poa"}{"FILE1"}="blosum80.mat";
1256 $PG{"poa"}{"mode"}="mcoffee";
1257 $PG{"poa"}{"binary"}="poa";
1258 $PG{"probcons"}{"4_TCOFFEE"}="PROBCONS";
1259 $PG{"probcons"}{"type"}="sequence_multiple_aligner";
1260 $PG{"probcons"}{"ADDRESS"}="http://probcons.stanford.edu/";
1261 $PG{"probcons"}{"language2"}="CXX";
1262 $PG{"probcons"}{"language"}="C++";
1263 $PG{"probcons"}{"source"}="http://probcons.stanford.edu/probcons_v1_12.tar.gz";
1264 $PG{"probcons"}{"mode"}="mcoffee";
1265 $PG{"probcons"}{"binary"}="probcons";
1266 $PG{"mafft"}{"4_TCOFFEE"}="MAFFT";
1267 $PG{"mafft"}{"type"}="sequence_multiple_aligner";
1268 $PG{"mafft"}{"ADDRESS"}="http://align.bmr.kyushu-u.ac.jp/mafft/online/server/";
1269 $PG{"mafft"}{"language"}="C";
1270 $PG{"mafft"}{"language"}="C";
1271 $PG{"mafft"}{"source"}="http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-with-extensions-src.tgz";
1272 $PG{"mafft"}{"windows"}="http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-mingw.tar";
1273 $PG{"mafft"}{"mode"}="mcoffee,rcoffee";
1274 $PG{"mafft"}{"binary"}="mafft.tar.gz";
1275 $PG{"muscle"}{"4_TCOFFEE"}="MUSCLE";
1276 $PG{"muscle"}{"type"}="sequence_multiple_aligner";
1277 $PG{"muscle"}{"ADDRESS"}="http://www.drive5.com/muscle/";
1278 $PG{"muscle"}{"language"}="C++";
1279 $PG{"muscle"}{"language2"}="GPP";
1280 $PG{"muscle"}{"source"}="http://www.drive5.com/muscle/downloads3.6/muscle3.6_src.tar.gz";
1281 $PG{"muscle"}{"windows"}="http://www.drive5.com/muscle/downloads3.6/muscle3.6_win32.zip";
1282 $PG{"muscle"}{"linux"}="http://www.drive5.com/muscle/downloads3.6/muscle3.6_linux_ia32.tar.gz";
1283 $PG{"muscle"}{"mode"}="mcoffee,rcoffee";
1284 $PG{"pcma"}{"4_TCOFFEE"}="PCMA";
1285 $PG{"pcma"}{"type"}="sequence_multiple_aligner";
1286 $PG{"pcma"}{"ADDRESS"}="ftp://iole.swmed.edu/pub/PCMA/";
1287 $PG{"pcma"}{"language"}="C";
1288 $PG{"pcma"}{"language2"}="C";
1289 $PG{"pcma"}{"source"}="ftp://iole.swmed.edu/pub/PCMA/pcma.tar.gz";
1290 $PG{"pcma"}{"mode"}="mcoffee";
1291 $PG{"kalign"}{"4_TCOFFEE"}="KALIGN";
1292 $PG{"kalign"}{"type"}="sequence_multiple_aligner";
1293 $PG{"kalign"}{"ADDRESS"}="http://msa.cgb.ki.se";
1294 $PG{"kalign"}{"language"}="C";
1295 $PG{"kalign"}{"language2"}="C";
1296 $PG{"kalign"}{"source"}="http://msa.cgb.ki.se/downloads/kalign/current.tar.gz";
1297 $PG{"kalign"}{"mode"}="mcoffee";
1298 $PG{"amap"}{"4_TCOFFEE"}="AMAP";
1299 $PG{"amap"}{"type"}="sequence_multiple_aligner";
1300 $PG{"amap"}{"ADDRESS"}="http://bio.math.berkeley.edu/amap/";
1301 $PG{"amap"}{"language"}="C++";
1302 $PG{"amap"}{"language2"}="CXX";
1303 $PG{"amap"}{"source"}="http://baboon.math.berkeley.edu/amap/download/amap.2.2.tar.gz";
1304 $PG{"amap"}{"mode"}="mcoffee";
1305 $PG{"proda"}{"4_TCOFFEE"}="PRODA";
1306 $PG{"proda"}{"type"}="sequence_multiple_aligner";
1307 $PG{"proda"}{"ADDRESS"}="http://proda.stanford.edu";
1308 $PG{"proda"}{"language"}="C++";
1309 $PG{"proda"}{"language2"}="CXX";
1310 $PG{"proda"}{"source"}="http://proda.stanford.edu/proda_1_0.tar.gz";
1311 $PG{"proda"}{"mode"}="mcoffee";
1312 $PG{"prank"}{"4_TCOFFEE"}="PRANK";
1313 $PG{"prank"}{"type"}="sequence_multiple_aligner";
1314 $PG{"prank"}{"ADDRESS"}="http://www.ebi.ac.uk/goldman-srv/prank/";
1315 $PG{"prank"}{"language"}="C++";
1316 $PG{"prank"}{"language2"}="CXX";
1317 $PG{"prank"}{"source"}="http://www.ebi.ac.uk/goldman-srv/prank/src/old/prank.src.081202.tgz";
1318 $PG{"prank"}{"mode"}="mcoffee";
1319 $PG{"sap"}{"4_TCOFFEE"}="SAP";
1320 $PG{"sap"}{"type"}="structure_pairwise_aligner";
1321 $PG{"sap"}{"ADDRESS"}="http://mathbio.nimr.mrc.ac.uk/wiki/Software";
1322 $PG{"sap"}{"language"}="C";
1323 $PG{"sap"}{"language2"}="C";
1324 $PG{"sap"}{"source"}="http://www.tcoffee.org/Packages/sap_distribution_TCC_0.6.tar.gz";
1325 $PG{"sap"}{"mode"}="expresso,3dcoffee";
1326 $PG{"TMalign"}{"4_TCOFFEE"}="TMALIGN";
1327 $PG{"TMalign"}{"type"}="structure_pairwise_aligner";
1328 $PG{"TMalign"}{"ADDRESS"}="http://zhang.bioinformatics.ku.edu/TM-align/TMalign.f";
1329 $PG{"TMalign"}{"language"}="Fortran";
1330 $PG{"TMalign"}{"language2"}="Fortran";
1331 $PG{"TMalign"}{"source"}="http://zhang.bioinformatics.ku.edu/TM-align/TMalign.f";
1332 $PG{"TMalign"}{"linux"}="http://zhang.bioinformatics.ku.edu/TM-align/TMalign_32.gz";
1333 $PG{"TMalign"}{"mode"}="expresso,3dcoffee";
1334 $PG{"mustang"}{"4_TCOFFEE"}="MUSTANG";
1335 $PG{"mustang"}{"type"}="structure_pairwise_aligner";
1336 $PG{"mustang"}{"ADDRESS"}="http://www.cs.mu.oz.au/~arun/mustang";
1337 $PG{"mustang"}{"language"}="C++";
1338 $PG{"mustang"}{"language2"}="CXX";
1339 $PG{"mustang"}{"source"}="http://www.cs.mu.oz.au/~arun/mustang/mustang_v.3.tgz";
1340 $PG{"mustang"}{"mode"}="expresso,3dcoffee";
1341 $PG{"lsqman"}{"4_TCOFFEE"}="LSQMAN";
1342 $PG{"lsqman"}{"type"}="structure_pairwise_aligner";
1343 $PG{"lsqman"}{"ADDRESS"}="empty";
1344 $PG{"lsqman"}{"language"}="empty";
1345 $PG{"lsqman"}{"language2"}="empty";
1346 $PG{"lsqman"}{"source"}="empty";
1347 $PG{"lsqman"}{"update_action"}="never";
1348 $PG{"lsqman"}{"mode"}="expresso,3dcoffee";
1349 $PG{"align_pdb"}{"4_TCOFFEE"}="ALIGN_PDB";
1350 $PG{"align_pdb"}{"type"}="structure_pairwise_aligner";
1351 $PG{"align_pdb"}{"ADDRESS"}="empty";
1352 $PG{"align_pdb"}{"language"}="empty";
1353 $PG{"align_pdb"}{"language2"}="empty";
1354 $PG{"align_pdb"}{"source"}="empty";
1355 $PG{"align_pdb"}{"update_action"}="never";
1356 $PG{"align_pdb"}{"mode"}="expresso,3dcoffee";
1357 $PG{"fugueali"}{"4_TCOFFEE"}="FUGUE";
1358 $PG{"fugueali"}{"type"}="structure_pairwise_aligner";
1359 $PG{"fugueali"}{"ADDRESS"}="http://www-cryst.bioc.cam.ac.uk/fugue/download.html";
1360 $PG{"fugueali"}{"language"}="empty";
1361 $PG{"fugueali"}{"language2"}="empty";
1362 $PG{"fugueali"}{"source"}="empty";
1363 $PG{"fugueali"}{"update_action"}="never";
1364 $PG{"fugueali"}{"mode"}="expresso,3dcoffee";
1365 $PG{"dalilite.pl"}{"4_TCOFFEE"}="DALILITEc";
1366 $PG{"dalilite.pl"}{"type"}="structure_pairwise_aligner";
1367 $PG{"dalilite.pl"}{"ADDRESS"}="built_in";
1368 $PG{"dalilite.pl"}{"ADDRESS2"}="http://www.ebi.ac.uk/Tools/webservices/services/dalilite";
1369 $PG{"dalilite.pl"}{"language"}="Perl";
1370 $PG{"dalilite.pl"}{"language2"}="Perl";
1371 $PG{"dalilite.pl"}{"source"}="empty";
1372 $PG{"dalilite.pl"}{"update_action"}="never";
1373 $PG{"dalilite.pl"}{"mode"}="expresso,3dcoffee";
1374 $PG{"probconsRNA"}{"4_TCOFFEE"}="PROBCONSRNA";
1375 $PG{"probconsRNA"}{"type"}="RNA_multiple_aligner";
1376 $PG{"probconsRNA"}{"ADDRESS"}="http://probcons.stanford.edu/";
1377 $PG{"probconsRNA"}{"language"}="C++";
1378 $PG{"probconsRNA"}{"language2"}="CXX";
1379 $PG{"probconsRNA"}{"source"}="http://probcons.stanford.edu/probconsRNA.tar.gz";
1380 $PG{"probconsRNA"}{"mode"}="mcoffee,rcoffee";
1381 $PG{"sfold"}{"4_TCOFFEE"}="CONSAN";
1382 $PG{"sfold"}{"type"}="RNA_pairwise_aligner";
1383 $PG{"sfold"}{"ADDRESS"}="http://selab.janelia.org/software/consan/";
1384 $PG{"sfold"}{"language"}="empty";
1385 $PG{"sfold"}{"language2"}="empty";
1386 $PG{"sfold"}{"source"}="empty";
1387 $PG{"sfold"}{"update_action"}="never";
1388 $PG{"sfold"}{"mode"}="rcoffee";
1389 $PG{"RNAplfold"}{"4_TCOFFEE"}="RNAPLFOLD";
1390 $PG{"RNAplfold"}{"type"}="RNA_secondarystructure_predictor";
1391 $PG{"RNAplfold"}{"ADDRESS"}="http://www.tbi.univie.ac.at/~ivo/RNA/";
1392 $PG{"RNAplfold"}{"language"}="C";
1393 $PG{"RNAplfold"}{"language2"}="C";
1394 $PG{"RNAplfold"}{"source"}="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-1.7.2.tar.gz";
1395 $PG{"RNAplfold"}{"mode"}="rcoffee";
1396 $PG{"hmmtop"}{"4_TCOFFEE"}="HMMTOP";
1397 $PG{"hmmtop"}{"type"}="protein_secondarystructure_predictor";
1398 $PG{"hmmtop"}{"ADDRESS"}="www.enzim.hu/hmmtop/";
1399 $PG{"hmmtop"}{"language"}="C";
1400 $PG{"hmmtop"}{"language2"}="C";
1401 $PG{"hmmtop"}{"source"}="empty";
1402 $PG{"hmmtop"}{"update_action"}="never";
1403 $PG{"hmmtop"}{"mode"}="tcoffee";
1404 $PG{"gorIV"}{"4_TCOFFEE"}="GOR4";
1405 $PG{"gorIV"}{"type"}="protein_secondarystructure_predictor";
1406 $PG{"gorIV"}{"ADDRESS"}="http://mig.jouy.inra.fr/logiciels/gorIV/";
1407 $PG{"gorIV"}{"language"}="C";
1408 $PG{"gorIV"}{"language2"}="C";
1409 $PG{"gorIV"}{"source"}="http://mig.jouy.inra.fr/logiciels/gorIV/GOR_IV.tar.gz";
1410 $PG{"gorIV"}{"update_action"}="never";
1411 $PG{"gorIV"}{"mode"}="tcoffee";
1412 $PG{"wublast.pl"}{"4_TCOFFEE"}="EBIWUBLASTc";
1413 $PG{"wublast.pl"}{"type"}="protein_homology_predictor";
1414 $PG{"wublast.pl"}{"ADDRESS"}="built_in";
1415 $PG{"wublast.pl"}{"ADDRESS2"}="http://www.ebi.ac.uk/Tools/webservices/services/wublast";
1416 $PG{"wublast.pl"}{"language"}="Perl";
1417 $PG{"wublast.pl"}{"language2"}="Perl";
1418 $PG{"wublast.pl"}{"source"}="empty";
1419 $PG{"wublast.pl"}{"update_action"}="never";
1420 $PG{"wublast.pl"}{"mode"}="psicoffee,expresso,3dcoffee";
1421 $PG{"blastpgp.pl"}{"4_TCOFFEE"}="EBIBLASTPGPc";
1422 $PG{"blastpgp.pl"}{"type"}="protein_homology_predictor";
1423 $PG{"blastpgp.pl"}{"ADDRESS"}="built_in";
1424 $PG{"blastpgp.pl"}{"ADDRESS2"}="http://www.ebi.ac.uk/Tools/webservices/services/blastpgp";
1425 $PG{"blastpgp.pl"}{"language"}="Perl";
1426 $PG{"blastpgp.pl"}{"language2"}="Perl";
1427 $PG{"blastpgp.pl"}{"source"}="empty";
1428 $PG{"blastpgp.pl"}{"update_action"}="never";
1429 $PG{"blastpgp.pl"}{"mode"}="psicoffee,expresso,3dcoffee";
1430 $PG{"blastcl3"}{"4_TCOFFEE"}="NCBIWEBBLAST";
1431 $PG{"blastcl3"}{"type"}="protein_homology_predictor";
1432 $PG{"blastcl3"}{"ADDRESS"}="ftp://ftp.ncbi.nih.gov/blast/executables/LATEST";
1433 $PG{"blastcl3"}{"language"}="C";
1434 $PG{"blastcl3"}{"language2"}="C";
1435 $PG{"blastcl3"}{"source"}="empty";
1436 $PG{"blastcl3"}{"update_action"}="never";
1437 $PG{"blastcl3"}{"mode"}="psicoffee,expresso,3dcoffee";
1438 $PG{"blastpgp"}{"4_TCOFFEE"}="NCBIBLAST";
1439 $PG{"blastpgp"}{"type"}="protein_homology_predictor";
1440 $PG{"blastpgp"}{"ADDRESS"}="ftp://ftp.ncbi.nih.gov/blast/executables/LATEST";
1441 $PG{"blastpgp"}{"language"}="C";
1442 $PG{"blastpgp"}{"language2"}="C";
1443 $PG{"blastpgp"}{"source"}="empty";
1444 $PG{"blastpgp"}{"update_action"}="never";
1445 $PG{"blastpgp"}{"mode"}="psicoffee,expresso,3dcoffee";
1446 $PG{"SOAP::Lite"}{"4_TCOFFEE"}="SOAPLITE";
1447 $PG{"SOAP::Lite"}{"type"}="library";
1448 $PG{"SOAP::Lite"}{"ADDRESS"}="http://cpansearch.perl.org/src/MKUTTER/SOAP-Lite-0.710.08/Makefile.PL";
1449 $PG{"SOAP::Lite"}{"language"}="Perl";
1450 $PG{"SOAP::Lite"}{"language2"}="Perl";
1451 $PG{"SOAP::Lite"}{"source"}="empty";
1452 $PG{"SOAP::Lite"}{"mode"}="psicoffee,expresso,3dcoffee";
1453 $MODE{"tcoffee"}{"name"}="tcoffee";
1454 $MODE{"rcoffee"}{"name"}="rcoffee";
1455 $MODE{"3dcoffee"}{"name"}="3dcoffee";
1456 $MODE{"mcoffee"}{"name"}="mcoffee";
1457 $MODE{"expresso"}{"name"}="expresso";
1458 #TclinkdbEnd End tag for the list updating
1459
1460 ########### Compilers ##############################
1461 #
1462 #
1463
1464 $PG{C}{compiler}="gcc";
1465 $PG{C}{compiler_flag}="CC";
1466 $PG{C}{options}="";
1467 $PG{C}{options_flag}="CFLAGS";
1468 $PG{C}{type}="compiler";
1469
1470 $PG{"CXX"}{compiler}="g++";
1471 $PG{"CXX"}{compiler_flag}="CXX";
1472 $PG{"CXX"}{options}="";
1473 $PG{"CXX"}{options_flag}="CXXFLAGS";
1474 $PG{CXX}{type}="compiler";
1475
1476 $PG{"CPP"}{compiler}="g++";
1477 $PG{"CPP"}{compiler_flag}="CPP";
1478 $PG{"CPP"}{options}="";
1479 $PG{"CPP"}{options_flag}="CPPFLAGS";
1480 $PG{CPP}{type}="compiler";
1481
1482 $PG{"GPP"}{compiler}="g++";
1483 $PG{"GPP"}{compiler_flag}="GPP";
1484 $PG{"GPP"}{options}="";
1485 $PG{"GPP"}{options_flag}="CFLAGS";
1486 $PG{GPP}{type}="compiler";
1487
1488 $PG{Fortran}{compiler}="g77";
1489 $PG{Fortran}{compiler_flag}="FCC";
1490 $PG{Fortran}{type}="compiler";
1491
1492 $PG{Perl}{compiler}="CPAN";
1493 $PG{Perl}{type}="compiler";
1494
1495 $SUPPORTED_OS{macox}="Macintosh";
1496 $SUPPORTED_OS{linux}="Linux";
1497 $SUPPORTED_OS{windows}="Cygwin";
1498
1499
1500
1501 $MODE{t_coffee}{description}=" for regular multiple sequence alignments";
1502 $MODE{rcoffee} {description}=" for RNA multiple sequence alignments";
1503
1504 $MODE{psicoffee} {description}=" for Homology Extended multiple sequence alignments";
1505 $MODE{expresso}{description}=" for very accurate structure based multiple sequence alignments";
1506 $MODE{"3dcoffee"}{description}=" for multiple structure alignments";
1507 $MODE{mcoffee} {description}=" for combining alternative multiple sequence alignment packages\n------- into a unique meta-package. The installer will upload several MSA packages and compile them\n
1508 ";
1509
1510
1511 &post_process_PG();
1512 return;
1513 }
1514
1515 sub post_process_PG
1516   {
1517     my $p;
1518
1519     %PG=&name2dname (%PG);
1520     %MODE=&name2dname(%MODE);
1521     foreach $p (keys(%PG)){if ( $PG{$p}{type} eq "compiler"){$PG{$p}{update_action}="never";}}
1522
1523   }
1524
1525 sub name2dname
1526   {
1527     my (%L)=(@_);
1528     my ($l, $ml);
1529
1530     foreach my $pg (keys(%L))
1531       {
1532         $l=length ($pg);
1533         if ( $l>$ml){$ml=$l;}
1534       }
1535     $ml+=1;
1536     foreach my $pg (keys(%L))
1537       {
1538         my $name;
1539         $l=$ml-length ($pg);
1540         $name=$pg;
1541         for ( $b=0; $b<$l; $b++)
1542           {
1543             $name .=" ";
1544           }
1545         $L{$pg}{dname}=$name;
1546       }
1547     return %L;
1548   }
1549
1550 sub env_file2putenv
1551   {
1552     my $f=@_[0];
1553     my $F=new FileHandle;
1554     my $n;
1555
1556     open ($F, "$f");
1557     while (<$F>)
1558       {
1559         my $line=$_;
1560         my($var, $value)=($_=~/(\S+)\=(\S*)/);
1561         $ENV{$var}=$value;
1562         $ENV_SET{$var}=1;
1563         $n++;
1564       }
1565     close ($F);
1566     return $n;
1567   }
1568