2 #Version 2.01 (25/02/03)
9 our (%MODE, %PG, %ENV_SET, %SUPPORTED_OS);
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";
22 our $ROOT=&get_root();
25 our $HOME=$ENV{'HOME'};
26 ########### DEFINITIONS ##############################
42 my $default_update_action="no_update";
43 ########################################################
44 my @required_applications=("wget_OR_curl");
45 ########### Mode Definitions ##############################
48 my @smode=("all", "clean", "install");
50 ########################################################
53 #Parse The Command Line
54 my $cl=join( " ", @ARGV);
55 if ($#ARGV==-1 || ($cl=~/-h/) ||($cl=~/-H/) )
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);}
64 if (($cl=~/-h/) ||($cl=~/-H/) )
67 print "\n\n!!!!!!! advanced mode\n";
68 foreach $m ((keys (%MODE)),@smode)
70 print "!!!!!!! ./install $m\n";
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";
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 ";}
88 print "!!!!!!! Packages:";
89 foreach $m (keys (%PG)){print "$m ";}
98 # parse compiler flags
99 my (@argl)=($cl=~/(\S+=[^=]+)\s\w+=/g);
100 push (@argl, ($cl=~/(\S+=[^=]+\S)\s*$/g));
104 if ( ($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=$1;}
111 our ($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=$1;}
121 if ( ($cl=~/-tclinkdb=\s*(\S+)/)){$tclinkdb=$1;}
122 if ( ($cl=~/-proxy=\s*(\S+)/)){$proxy=$1;}
123 if ( ($cl=~/-clean/)){$clean=1;}
125 if ($tclinkdb){&update_tclinkdb ($tclinkdb);}
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};
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");
144 #Prepare the Installation Structure
147 our $BIN="$BASE/binaries/$OS";
148 our $DOWNLOAD_DIR="$BASE/download";
149 our $DOWNLOAD_FILE="$DOWNLOAD_DIR/files";
150 our $TMP="$BASE/tmp";
154 &add_dir($DOWNLOAD_DIR);
155 &add_dir($DOWNLOAD_FILE);
156 if (!$DISTRIBUTIONS){$DISTRIBUTIONS="$DOWNLOAD_DIR/distributions";}
157 &add_dir ($DISTRIBUTIONS);
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/";}
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/";}
169 #prepare mcoffee files [Only if vanilla installation]
170 if (-d "mcoffee"){`cp mcoffee/* $TCM`;}
173 #prepare the environement
174 our $ENV_FILE="$TCDIR/t_coffee_env";
175 &env_file2putenv ($ENV_FILE);
177 my ($target, $p, $r);
180 foreach $p ( ((keys (%PG)),(keys(%MODE)),(@smode)) )
182 if ($ARGV[0] eq $p && $target eq ""){$target=$p;}
184 if ($target eq ""){exit ($EXIT_FAILURE);}
187 # Check the basic requirements are met
188 foreach $r (@required_applications)
194 @app_list=split (/_OR_/, $r);
195 foreach my $pg (@app_list)
197 $i+=&pg_is_installed ($pg);
201 print "One of the following packages must be installed to proceed: ";
202 foreach my $pg (@app_list)
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
218 #Directory structure of the installation WITHIN the distribution dir
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 $c (keys(%PG))
235 if ($PG{$c}{compiler})
237 $arguments="$PG{$c}{compiler_flag}=$PG{$c}{compiler} ";
238 if ($PG{$c}{options})
240 $arguments.="$PG{$c}{options_flag}=$PG{$c}{options} ";
242 $PG{$c}{arguments}=$arguments;
246 # select the list of packages to update
247 if ($PG{$target}){$PG{$target}{install}=1;}
250 foreach my $pg (keys(%PG))
252 if ( $target eq "all" || ($PG{$pg}{mode}=~/$target/))
254 $PG{$pg} {install}=1;
259 foreach my $pg (keys(%PG))
261 if (!$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})
265 `rm $BIN/$pg $BIN/$pg.exe $SILENT`;
267 if ($PG{$pg}{update_action} eq "update" && $PG{$pg}{install}){$PG{$pg}{update}=1;}
270 #Execute the target: install/remove all the selected components
271 if (($target=~/clean/))
273 print "------- cleaning executables -----\n";
275 exit ($EXIT_SUCCESS);
278 if ( !$PG{$target}){print "------- Installing T-Coffee Modes\n";}
280 #1 - Installing various modes
281 foreach my $m (keys(%MODE))
283 if ( $target eq "all" || $target eq $m)
285 print "\n------- The installer will now install the $m components $MODE{$m}{description}\n";
286 foreach my $pg (keys(%PG))
288 if ( $PG{$pg}{mode} =~/$m/ && $PG{$pg}{install})
290 if ($PG{$pg}{touched}){print "------- $PG{$pg}{dname}: already processed\n";}
291 else {$PG{$pg}{success}=&install_pg($pg);$PG{$pg}{touched}=1;}
297 #2 - Installing Various Packages
298 if ( $PG{$target}){print "------- Installing Individual Package\n";}
299 foreach my $pg (keys (%PG))
302 if ( $PG{$pg}{install} && !$PG{$pg}{touched})
304 print "\n------- Install $pg\n";
305 $PG{$pg}{success}=&install_pg($pg);$PG{$pg}{touched}=1;
308 print "------- Finishing The installation\n";
309 my $final_report=&install ($INSTALL_DIR);
312 print "*********************************************************************\n";
313 print "******** INSTALLATION SUMMARY *****************\n";
314 print "*********************************************************************\n";
315 print "------- SUMMARY package Installation:\n";
316 foreach my $pg (keys(%PG))
318 if ( $PG{$pg}{install})
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;}
329 if ( !$PG{$target}){print "*------ SUMMARY mode Installation:\n";}
330 foreach my $m (keys(%MODE))
332 if ( $target eq "all" || $target eq $m)
335 foreach my $pg (keys(%PG))
337 if (($PG{$pg}{mode}=~/$m/) && $PG{$pg}{install} && $PG{$pg}{status}==0)
340 print "*!!!!!! $PG{$pg}{dname}: Missing\n";
346 print "*------ MODE $MODE{$m}{dname} SUCCESFULY installed\n";
351 print "*!!!!!! MODE $MODE{$m}{dname} UNSUCCESFULY installed\n";
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);
361 #################################################################################
365 # GENERIC INSTALLATION #
369 #################################################################################
375 return get_compil ($c, @clist);
380 my (@clist)=("gcc", "cc", "icc");
382 return get_compil ($c, @clist);
388 my @clist=("f77", "g77", "gfortran", "ifort");
389 return get_compil ($c, @clist);
394 my ($fav,@clist)=(@_);
396 #return the first compiler found installed in the system. Check first the favorite
397 foreach my $c ($fav,@clist)
399 if (&pg_is_installed ($c)){return $c;}
403 sub exit_if_pg_not_installed
409 if ( !&pg_is_installed ($p))
411 print "!!!!!!!! The $p utility must be installed for this installation to proceed [FATAL]\n";
422 @list= ("HTTP_proxy", "http_proxy", "HTTP_PROXY", "ALL_proxy", "all_proxy","HTTP_proxy_4_TCOFFEE","http_proxy_4_TCOFFEE");
426 foreach my $p (@list)
428 if ( ($ENV_SET{$p}) || $ENV{$p}){$proxy=$ENV{$p};}
431 foreach my $p(@list){$ENV{$p}=$proxy;}
434 sub check_internet_connection
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`;}
443 printf stderr "\nERROR: No pg for remote file fetching [wget or curl][FATAL]\n";
444 exit ($EXIT_FAILURE);
447 if ( !-e "x" || -s "x" < 10){$internet=0;}
449 if (-e "x"){unlink "x";}
454 my ($cmd, $file,$wget_arg, $curl_arg)=(@_);
455 my ($exit,$flag, $pg, $arg);
457 if ($INTERNET || check_internet_connection ()){$INTERNET=1;}
460 print STDERR "ERROR: No Internet Connection [FATAL:install.pl]\n";
461 exit ($EXIT_FAILURE);
464 if (&pg_is_installed ("wget")){$pg="wget"; $flag="-O";$arg=$wget_arg;}
465 elsif (&pg_is_installed ("curl")){$pg="curl"; $flag="-o";$arg=$curl_arg;}
468 printf stderr "\nERROR: No pg for remote file fetching [wget or curl][FATAL]\n";
469 exit ($EXIT_FAILURE);
473 if (-e $file){unlink($file);}
474 $exit=system "$pg $cmd $flag$file $arg";
482 my ($supported, $language, $compil);
486 $language=$PG{$p}{language2};
487 $compil=$PG{$language}{compiler};
490 if ( $compil eq "CPAN")
492 if ( system ("perl -M$p -e 1")==$EXIT_SUCCESS){return 1;}
497 if (-e "$dir/$p" || -e "$dir/$p\.exe"){return 1;}
500 elsif (-e "$PLUGINS_DIR/$p" || -e "$PLUGINS_DIR/$p.exe"){return 1;}
503 $r=`which $p 2>/dev/null`;
504 if ($r eq ""){return 0;}
512 my ($copied, $report);
518 if (-e "$BIN/t_coffee"){`$CP $BIN/t_coffee $INSTALL_DIR`};
519 `cp $BIN/* $PLUGINS_DIR`;
524 $copied=&root_run ("You must be root to finalize the installation", "$CP $BIN/* $INSTALL_DIR $SILENT");
530 $report="*!!!!!! Installation unsuccesful. The executables have been left in $BASE/bin\n";
532 elsif ( $copied && $ROOT)
534 $report="*------ Installation succesful. Your executables have been copied in $new_bin and are on your PATH\n";
536 elsif ( $copied && !$ROOT)
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";
548 my $F=new FileHandle;
549 open ($F, "license.txt");
558 #################################################################################
562 # INDIVIDUAL MULTIPLE SEQUENCE ALIGNMNT PACKAGES INSTALLATION #
566 #################################################################################
571 my ($report, $previous, $language, $compiler, $return);
573 if (!$PG{$pg}{install}){return 1;}
575 $previous=&pg_is_installed ($pg);
577 if ($PG{$pg}{update_action} eq "no_update" && $previous)
585 $PG{$pg}{old}=$previous;
587 if ($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 ($pg)){;}
593 if (!&supported_os($OS))
595 print "!!!!!!!! $pg compilation failed, binary unsupported for $OS\n";
597 elsif (!($PG{$pg}{from_binary}=&install_binary_package ($pg)))
599 print "!!!!!!!! $pg compilation and binary installation failed\n";
602 $PG{$pg}{new}=$return=&pg_is_installed ($pg,$BIN);
608 sub install_perl_package
611 my ($report, $language, $compiler);
613 $language=$PG{$pg} {language2};
614 $compiler=$PG{$language}{compiler};
616 if (!&pg_is_installed ($pg))
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 $pg'");}
622 return &pg_is_installed ($pg);
627 sub install_source_package
630 my ($report, $download, $arguments, $language, $address, $name, $ext, $main_dir, $distrib);
631 my $wget_tmp="$TMP/wget.tmp";
633 if ( -e "$BIN/$pg" || -e "$BIN/$pg.exe"){return 1;}
635 if ($pg eq "t_coffee") {return &install_t_coffee ($pg);}
636 elsif ($pg eq "TMalign"){return &install_TMalign ($pg);}
638 chdir $DISTRIBUTIONS;
640 $download=$PG{$pg}{source};
642 if (($download =~/tgz/))
644 ($address,$name,$ext)=($download=~/(.+\/)([^\/]+)(\.tgz)/);
646 elsif (($download=~/tar\.gz/))
648 ($address,$name,$ext)=($download=~/(.+\/)([^\/]+)(\.tar\.gz)/);
650 elsif (($download=~/tar/))
652 ($address,$name,$ext)=($download=~/(.+\/)([^\/]+)(\.tar)/);
656 ($address,$name)=($download=~/(.+\/)([^\/]+)/);
659 $distrib="$name$ext";
661 if ( !-d $pg){mkdir $pg;}
664 #get the distribution if available
665 if ( -e "$DOWNLOAD_DIR/$distrib")
667 `$CP $DOWNLOAD_DIR/$distrib .`;
669 #UNTAR and Prepare everything
670 if (!-e "$name.tar" && !-e "$name")
672 &check_rm ($wget_tmp);
673 print "\n------- Downloading/Installing $pg\n";
674 if (!-e $distrib && &url2file ("$download", "$wget_tmp")==$EXIT_SUCCESS)
677 `mv $wget_tmp $distrib`;
678 `$CP $distrib $DOWNLOAD_DIR/`;
683 print "!!!!!!! Download of $pg distribution failed\n";
684 print "!!!!!!! Check Address: $PG{$pg}{source}\n";
687 print "\n------- unzipping/untaring $name\n";
690 &flush_command ("gunzip $name$ext");
693 if (($ext =~/tar/) || ($ext =~/tgz/))
695 &flush_command("tar -xvf $name.tar");
698 #Guess and enter the distribution directory
710 print "\n------- Compiling/Installing $pg\n";
711 `make clean $SILENT`;
715 `rm *.o sap sap.exe ./util/aa/*.o ./util/wt/.o $SILENT`;
716 &flush_command ("make $arguments sap");
717 &check_cp ($pg, "$BIN");
719 elsif ($pg eq "clustalw2")
721 &flush_command("./configure");
722 &flush_command("make $arguments");
723 &check_cp ("./src/$pg", "$BIN");
726 elsif ($pg eq "clustalw")
728 &flush_command("make $arguments clustalw");
729 `$CP $pg $BIN $SILENT`;
732 elsif ($pg eq "mafft")
738 mkpath ("./mafft/bin");
739 mkpath ("./mafft/lib");
741 `make clean $SILENT`;
742 &flush_command ("make $arguments");
743 &flush_command ("make install LIBDIR=../mafft/lib BINDIR=../mafft/bin");
746 chdir "$base/extensions";
747 `make clean $SILENT`;
748 &flush_command ("make $arguments");
749 &flush_command ("make install LIBDIR=../mafft/lib BINDIR=../mafft/bin");
751 #put everything in mafft and copy the coompiled stuff in bin
755 &root_run ("You Must be Roor to Install MAFFT\n", "mkdir /usr/local/mafft/;$CP mafft/lib/* /usr/local/mafft;$CP mafft/lib/mafft* /usr/local/bin ;$CP mafft/bin/mafft /usr/local/bin/; ");
759 `$CP mafft/lib/* $BIN`;
760 `$CP mafft/bin/mafft $BIN`;
762 `tar -cvf mafft.tar mafft`;
764 `mv mafft.tar.gz $BIN`;
766 elsif ( $pg eq "dialign-tx")
772 &flush_command (" make CPPFLAGS='-O3 -funroll-loops' all");
775 &check_cp ("./source/$pg", "$BIN");
776 &check_cp ("./source/$pg", "$BIN/dialign-t");
780 &flush_command ("make $arguments poa");
781 &check_cp ("$pg", "$BIN");
783 elsif ( $pg eq "probcons")
786 &flush_command ("make $arguments probcons");
787 &check_cp("$pg", "$BIN/$pg");
789 elsif ( $pg eq "probcons" || $pg eq "probconsRNA")
792 &flush_command ("make $arguments probcons");
793 &check_cp("probcons", "$BIN/$pg");
796 elsif ( $pg eq "muscle")
798 `rm *.o muscle muscle.exe $SILENT`;
799 &flush_command ("make $arguments all");
800 &check_cp("$pg", "$BIN");
802 elsif ( $pg eq "pcma")
804 &flush_command ("make $arguments pcma");
805 &check_cp("$pg", "$BIN");
807 elsif ($pg eq "kalign")
809 &flush_command ("./configure");
810 &flush_command("make $arguments");
811 &check_cp ("$pg",$BIN);
813 elsif ( $pg eq "amap")
816 `make clean $SILENT`;
817 &flush_command ("make $arguments all");
818 &check_cp ("$pg", $BIN);
820 elsif ( $pg eq "proda")
822 &flush_command ("make $arguments all");
823 &check_cp ("$pg", $BIN);
825 elsif ( $pg eq "prank")
827 &flush_command ("make $arguments all");
828 &check_cp ("$pg", $BIN);
830 elsif ( $pg eq "mustang")
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");}
836 elsif ( $pg eq "RNAplfold")
838 &flush_command("./configure");
839 &flush_command ("make $arguments all");
840 &check_cp("./Progs/RNAplfold", "$BIN");
843 return &pg_is_installed ($pg, $BIN);
849 my ($report,$cflags, $arguments, $language, $compiler) ;
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 ";}
858 if ( $CC ne ""){&flush_command ("make -i $arguments t_coffee");}
859 &check_cp ($pg, $BIN);
862 return &pg_is_installed ($pg, $BIN);
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))
875 print "!!!!!!! Compilation of $pg impossible. Will try to install from binary\n";
876 return &install_binary_package ($pg);
879 return &pg_is_installed ($pg, $BIN);
882 sub pg_has_binary_distrib
885 if ($PG{$pg}{windows}){return 1;}
886 elsif ($PG{$pg}{osx}){return 1;}
887 elsif ($PG{$pg}{linux}){return 1;}
890 sub install_binary_package
893 my ($base,$report,$name, $download, $arguments, $language, $dir);
897 if (!&supported_os($OS)){return 0;}
898 if ( $PG{$pg}{binary}){$name=$PG{$pg}{binary};}
902 if ( $OS eq "windows"){$name.=".exe";}
905 $download="$WEB_BASE/Packages/Binaries/$OS/$name";
913 if ( url2file("$download","x")==$EXIT_SUCCESS)
921 print "!!!!!!! $PG{$pg}{dname}: Download of $pg binary failed\n";
922 print "!!!!!!! $PG{$pg}{dname}: Check Address: $download\n";
925 print "\n------- Installing $pg\n";
927 if ($name =~/tar\.gz/)
936 &root_run ("You Must be Roor to Install MAFFT\n", "$CP mafft/bin/* /usr/local/mafft;mkdir /usr/local/mafft/; $CP mafft/lib/* /usr/local/bin/");
940 `$CP $TMP/$pg/bin/* $BIN $SILENT`;
941 `$CP $TMP/$pg/lib/* $BIN $SILENT`;
946 if (-e "$TMP/$pg/data"){`$CP $TMP/$pg/data/* $TCM $SILENT`;}
947 if (!($pg=~/\*/)){`rm -rf $pg`;}
952 &check_cp ("$pg", "$BIN");
953 `chmod u+x $BIN/$pg`;
957 $PG{$pg}{from_binary}=1;
958 return &pg_is_installed ($pg, $BIN);
961 ################################################################################
969 #################################################################################
974 if (!-e $dir && !-d $dir)
976 return mkpath ($dir);
989 return unlink($file);
995 my ($from, $to)=(@_);
996 if ( !-e $from && -e "$from\.exe"){$from="$from\.exe";}
997 if ( !-e $from){return 0;}
1002 sub check_file_list_exists
1004 my ($base, @flist)=(@_);
1009 if ( !-e "$base/$f"){return 0;}
1017 chomp(@fl=`ls -1 $f`);
1023 my $F=new FileHandle;
1024 open ($F, "$command|");
1025 while (<$F>){print " --- $_";}
1029 sub input_installation_directory
1034 print "------- The current installation directory is: [$dir]\n";
1035 print "??????? Return to keep the default or new value:";
1037 if ($NO_QUESTION==0)
1039 chomp ($new=<stdin>);
1040 while ( $new ne "" && !input_yes ("You have entered $new. Is this correct? ([y]/n):"))
1042 print "???????New installation directory:";
1043 chomp ($new=<stdin>);
1045 $dir=($new eq "")?$dir:$new;
1049 if ( -d $dir){return $dir;}
1050 elsif (&root_run ("You must be root to create $dir","mkdir $dir")==$EXIT_SUCCESS){return $dir;}
1053 print "!!!!!!! $dir could not be created\n";
1058 elsif ( &input_yes ("??????? Do you want to provide a new directory([y]/n)?:"))
1060 return input_installation_directory ($dir);
1071 my $question =@_[0];
1074 if ($NO_QUESTION==1){return 1;}
1076 if ($question eq ""){$question="??????? Do you wish to proceed ([y]/n)?:";}
1078 chomp($answer=lc(<STDIN>));
1079 if (($answer=~/^y/) || $answer eq ""){return 1;}
1080 elsif ( ($answer=~/^n/)){return 0;}
1083 return input_yes($question);
1088 my ($txt, $cmd)=(@_);
1090 if ( system ($cmd)==$EXIT_SUCCESS){return $EXIT_SUCCESS;}
1093 print "------- $txt\n";
1094 if ( $ROOT eq "sudo"){return system ("sudo $cmd");}
1095 else {return system ("su root -c \"$cmd\"");}
1098 #analyze environement
1101 if (&pg_is_installed ("sudo")){return "sudo";}
1110 $raw_os=lc ($raw_os);
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";}
1125 if ($OS) {return $OS;}
1127 print "??????? which os do you use: [w]indows, [l]inux, [m]acosx:?";
1128 $answer=lc(<STDIN>);
1130 if (($answer=~/^m/)){$OS="macosx";}
1131 elsif ( ($answer=~/^w/)){$OS="windows";}
1132 elsif ( ($answer=~/^linux/)){$OS="linux";}
1144 return $SUPPORTED_OS{$os};
1148 ################################################################################
1152 # update/initialize links #
1156 #################################################################################
1163 my $F=new FileHandle;
1164 my ($download, $address, $name, $l, $db);
1166 if ( $file eq "update"){$file=$TCLINKDB_ADDRESS;}
1168 if ( $file =~/http:\/\// || $file =~/ftp:\/\//)
1170 ($address, $name)=($download=~/(.*)\/([^\/]+)$/);
1172 if (&url2file ($file,"x")==$EXIT_SUCCESS)
1174 print "------- Susscessful upload of $name";
1183 if (($l =~/^\/\//) || ($db=~/^#/)){;}
1184 elsif ( !($l =~/\w/)){;}
1187 my @v=split (/\s+/, $l);
1190 $MODE{$v[1]}{$v[2]}=$v[3];
1194 $PG{$v[1]}{$v[2]}=$v[3];
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
1460 ########### Compilers ##############################
1464 $PG{C}{compiler}="gcc";
1465 $PG{C}{compiler_flag}="CC";
1467 $PG{C}{options_flag}="CFLAGS";
1468 $PG{C}{type}="compiler";
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";
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";
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";
1488 $PG{Fortran}{compiler}="g77";
1489 $PG{Fortran}{compiler_flag}="FCC";
1490 $PG{Fortran}{type}="compiler";
1492 $PG{Perl}{compiler}="CPAN";
1493 $PG{Perl}{type}="compiler";
1495 $SUPPORTED_OS{macox}="Macintosh";
1496 $SUPPORTED_OS{linux}="Linux";
1497 $SUPPORTED_OS{windows}="Cygwin";
1501 $MODE{t_coffee}{description}=" for regular multiple sequence alignments";
1502 $MODE{rcoffee} {description}=" for RNA multiple sequence alignments";
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
1519 %PG=&name2dname (%PG);
1520 %MODE=&name2dname(%MODE);
1521 foreach $p (keys(%PG)){if ( $PG{$p}{type} eq "compiler"){$PG{$p}{update_action}="never";}}
1530 foreach my $pg (keys(%L))
1533 if ( $l>$ml){$ml=$l;}
1536 foreach my $pg (keys(%L))
1539 $l=$ml-length ($pg);
1541 for ( $b=0; $b<$l; $b++)
1545 $L{$pg}{dname}=$name;
1553 my $F=new FileHandle;
1560 my($var, $value)=($_=~/(\S+)\=(\S*)/);