--- /dev/null
+#!/usr/bin/env perl
+#Version 2.01 (25/02/03)
+use Cwd;
+use Env;
+use File::Path;
+use FileHandle;
+use strict;
+
+
+our (%MODE, %PG, %ENV_SET, %SUPPORTED_OS);
+
+
+our $EXIT_SUCCESS=0;
+our $EXIT_FAILURE=1;
+our $INTERNET=0;
+
+#our $CP="cp -d ";
+our $CP="cp "; #was causing a crash on MacOSX
+our $SILENT=">/dev/null 2>/dev/null";
+our $WEB_BASE="http://www.tcoffee.org";
+our $TCLINKDB_ADDRESS="$WEB_BASE/Resources/tclinkdb.txt";
+our $OS=get_os();
+our $ROOT=&get_root();
+our $CD=cwd();
+our $CDIR=$CD;
+our $HOME=$ENV{'HOME'};
+
+our $OSNAME=$ENV{'OSNAME'};
+our $OSARCH=$ENV{'OSARCH'};
+our $REPO_ROOT="";
+
+our $TCDIR;
+our $TCCACHE;
+our $TCTMP;
+our $TCM;
+our $TCMETHODS;
+our $TCPLUGINS;
+our $PLUGINS_DIR="";
+our $INSTALL_DIR="";
+
+########### DEFINITIONS ##############################
+#
+#
+our $CXX="g++";
+our $CXXFLAGS="";
+
+our $CPP="g++";
+our $CPPFLAGS="";
+
+our $CC="gcc";
+our $CFLAGS="";
+
+our $FC="f77";
+our $FFLAGS="";
+
+my $install="all";
+my $default_update_action="no_update";
+########################################################
+my @required_applications=("wget_OR_curl");
+########### Mode Definitions ##############################
+#
+#
+my @smode=("all", "clean", "install");
+
+########################################################
+&initialize_PG();
+
+#Parse The Command Line
+my $cl=join( " ", @ARGV);
+if ($#ARGV==-1 || ($cl=~/-h/) ||($cl=~/-H/) )
+ {
+ print "\n!!!!!!! ./install t_coffee --> installs t_coffee only";
+ print "\n!!!!!!! ./install all --> installs all the modes [mcoffee, expresso, psicoffee,rcoffee..]";
+ print "\n!!!!!!! ./install [mcoffee|rcoffee|..] --> installs the specified mode";
+ print "\n!!!!!!! ./install -h --> print usage\n\n";
+ if ( $#ARGV==-1){exit ($EXIT_FAILURE);}
+ }
+
+if (($cl=~/-h/) ||($cl=~/-H/) )
+ {
+ my $m;
+ print "\n\n!!!!!!! advanced mode\n";
+ foreach $m ((keys (%MODE)),@smode)
+ {
+ print "!!!!!!! ./install $m\n";
+ }
+
+ print "!!!!!!! ./install [target:package|mode|] [-update|-force|-exec=dir|-dis=dir|-root|-tclinkdb=file|-] [CC=|FCC=|CXX=|CFLAGS=|CXXFLAGS=]\n";
+ print "!!!!!!! ./install clean [removes all executables]\n";
+ print "!!!!!!! ./install [optional:target] -update [updates package already installed]\n";
+ print "!!!!!!! ./install [optional:target] -force [Forces recompilation over everything]\n";
+
+ print "!!!!!!! ./install [optional:target] -root [You are running as root]\n";
+ print "!!!!!!! ./install [optional:target] -exec=/foo/bar/ [address for the T-Coffee executable]\n";
+ print "!!!!!!! ./install [optional:target] -dis=/foo/bar/ [Address where distributions should be stored]\n";
+ print "!!!!!!! ./install [optional:target] -tclinkdb=foo|update [file containing all the packages to be installed]\n";
+ print "!!!!!!! ./install [optional:target] -clean [clean everything]\n";
+ print "!!!!!!! ./install [optional:target] -plugins [plugins directory]\n";
+ print "!!!!!!! ./install [optional:target] -tcdir=/foor/bar [base path where T-Coffee will be installed]\n";
+ print "!!!!!!! ./install [optional:target] -repo=/path/to/repo [binaries repository root directory]\n";
+ print "!!!!!!! mode:";
+ foreach $m (keys(%MODE)){print "$m ";}
+ print "\n";
+ print "!!!!!!! Packages:";
+ foreach $m (keys (%PG)){print "$m ";}
+ print "\n";
+
+ print "\n\n";
+ exit ($EXIT_FAILURE);
+ }
+
+
+
+# parse compiler flags
+my (@argl)=($cl=~/(\S+=[^=]+)\s\w+=/g);
+push (@argl, ($cl=~/(\S+=[^=]+\S)\s*$/g));
+
+foreach $a (@argl)
+ {
+ if ( ($cl=~/CXX=(.*)/)){$CXX=$1;}
+ if ( ($cl=~/-CC=(.*)/ )){$CC=$1;}
+ if ( ($cl=~/-FC=(.*)/ )){$FC=$1;}
+ if ( ($cl=~/-CFLAGS=(.*)/)){$CFLAGS=$1;}
+ if ( ($cl=~/-CXXFLAGS=(.*)/)){$CXXFLAGS=$1;}
+ }
+#parse install flags
+our ($ROOT_INSTALL, $NO_QUESTION, $default_update_action,$BINARIES_ONLY,$force, $default_update_action, $INSTALL_DIR, $PLUGINS_DIR, $DISTRIBUTIONS,$tclinkdb, $proxy, $clean);
+if ( ($cl=~/-root/)){$ROOT_INSTALL=1;}
+if ( ($cl=~/-no_question/)){$NO_QUESTION=1;}
+if ( ($cl=~/-update/)){$default_update_action="update";}
+if ( ($cl=~/-binaries/)){$BINARIES_ONLY=1;}
+if ( ($cl=~/-force/)){$force=1;$default_update_action="update"}
+if ( ($cl=~/-exec=\s*(\S+)/)){$INSTALL_DIR=$1;}
+if ( ($cl=~/-plugins=\s*(\S+)/)){$PLUGINS_DIR=$1;}
+if ( ($cl=~/-dis=\s*(\S+)/)){$DISTRIBUTIONS=$1;}
+
+if ( ($cl=~/-tclinkdb=\s*(\S+)/)){$tclinkdb=$1;}
+if ( ($cl=~/-proxy=\s*(\S+)/)){$proxy=$1;}
+if ( ($cl=~/-clean/)){$clean=1;}
+if ( ($cl=~/-repo=\s*(\S+)/)){ $REPO_ROOT=$1; }
+if ( ($cl=~/-tcdir=\s*(\S+)/)){ $TCDIR=$1; }
+#automated update
+if ($tclinkdb){&update_tclinkdb ($tclinkdb);}
+
+
+if( $REPO_ROOT ne "" ) {
+ if( $OSNAME eq "" ) { print "You have specified the repository folder but the required \"OSNAME\" enviroment variable is missing. \n"; exit 1; }
+ if( $OSARCH eq "" ) { print "You have specified the repository folder but the required \"OSARCH\" enviroment variable is missing. \n"; exit 1; }
+}
+
+#Prepare the T-Coffee directory structure
+
+if(!$TCDIR) { $TCDIR="$HOME/.t_coffee"; }
+&add_dir ($TCDIR);
+&add_dir ($TCCACHE="$TCDIR/cache");
+&add_dir ($TCTMP="$CDIR/tmp");
+&add_dir ($TCM="$TCDIR/mcoffee");
+&add_dir ($TCMETHODS="$TCDIR/methods");
+&add_dir ($TCPLUGINS="$TCDIR/plugins/$OS");
+
+#Prepare the Installation Structure
+
+our $BASE="$CD/bin";
+our $BIN="$BASE/binaries/$OS";
+our $DOWNLOAD_DIR="$BASE/download";
+our $DOWNLOAD_FILE="$DOWNLOAD_DIR/files";
+our $TMP="$BASE/tmp";
+
+&add_dir($BASE);
+&add_dir($BIN);
+&add_dir($DOWNLOAD_DIR);
+&add_dir($DOWNLOAD_FILE);
+if (!$DISTRIBUTIONS){$DISTRIBUTIONS="$DOWNLOAD_DIR/distributions";}
+&add_dir ($DISTRIBUTIONS);
+&add_dir ($TMP);
+
+
+#set the directory for the plugins
+if (!$PLUGINS_DIR && !$ROOT_INSTALL){$PLUGINS_DIR=$TCPLUGINS;}
+elsif (!$PLUGINS_DIR && $ROOT_INSTALL){$PLUGINS_DIR="/usr/local/bin/";}
+
+#set the directory for t_coffee
+if (!$INSTALL_DIR && !$ROOT_INSTALL){$INSTALL_DIR="$HOME/bin/";mkpath ($INSTALL_DIR);}
+elsif (!$INSTALL_DIR && $ROOT_INSTALL){$INSTALL_DIR="/usr/local/bin/";}
+
+#prepare mcoffee files [Only if vanilla installation]
+if (-d "mcoffee"){`cp mcoffee/* $TCM`;}
+
+
+#prepare the environement
+our $ENV_FILE="$TCDIR/t_coffee_env";
+&env_file2putenv ($ENV_FILE);
+&set_proxy($proxy);
+my ($target, $p, $r);
+$target=$p;
+
+foreach $p ( ((keys (%PG)),(keys(%MODE)),(@smode)) )
+ {
+ if ($ARGV[0] eq $p && $target eq ""){$target=$p;}
+ }
+if ($target eq ""){exit ($EXIT_FAILURE);}
+
+
+# Check the basic requirements are met
+foreach $r (@required_applications)
+ {
+ my @app_list;
+ my $i;
+ $i=0;
+
+ @app_list=split (/_OR_/, $r);
+ foreach my $pg (@app_list)
+ {
+ $i+=&pg_is_installed ($pg);
+ }
+ if ($i==0)
+ {
+ print "One of the following packages must be installed to proceed: ";
+ foreach my $pg (@app_list)
+ {
+ print ("$pg ");
+ }
+ die;
+ }
+ }
+
+
+# Set the mains paths and create directories
+# distrib_dir/install/bin
+# distrib_dir/install/Downloads
+# distrib_dir/install/Downloads/Files
+# distrib_dir/install/Downloads/Distributions
+# distrib_dir/tmp
+
+#Directory structure of the installation WITHIN the distribution dir
+
+
+
+#sign the license
+&sign_license_ni();
+
+
+#Configure the copilers and their optins
+$PG{C}{compiler}=get_C_compiler($CC);
+$PG{Fortran}{compiler}=get_F_compiler($FC);
+$PG{CXX}{compiler}=$PG{CPP}{compiler}=$PG{GPP}{compiler}=get_CXX_compiler($CXX);
+if ($CXXFLAGS){$PG{CPP}{options}=$PG{GPP}{options}=$PG{CXX}{options}=$CXXFLAGS;}
+if ($CFLAGS){$PG{C}{options}=$CFLAGS;}
+foreach my $c (keys(%PG))
+ {
+ my $arguments;
+ if ($PG{$c}{compiler})
+ {
+ $arguments="$PG{$c}{compiler_flag}=$PG{$c}{compiler} ";
+ if ($PG{$c}{options})
+ {
+ $arguments.="$PG{$c}{options_flag}=$PG{$c}{options} ";
+ }
+ $PG{$c}{arguments}=$arguments;
+ }
+ }
+
+# select the list of packages to update
+if ($PG{$target}){$PG{$target}{install}=1;}
+else
+ {
+ foreach my $pg (keys(%PG))
+ {
+ if ( $target eq "all" || ($PG{$pg}{mode}=~/$target/))
+ {
+ $PG{$pg} {install}=1;
+ }
+ }
+ }
+
+foreach my $pg (keys(%PG))
+ {
+ if (!$PG{$pg}{update_action}){$PG{$pg}{update_action}=$default_update_action;}
+ elsif ($PG{$pg}{update_action} eq "never"){$PG{$pg}{install}=0;}
+ if ( $force && $PG{$pg}{install})
+ {
+ `rm $BIN/$pg $BIN/$pg.exe $SILENT`;
+ }
+ if ($PG{$pg}{update_action} eq "update" && $PG{$pg}{install}){$PG{$pg}{update}=1;}
+ }
+
+#Execute the target: install/remove all the selected components
+if (($target=~/clean/))
+ {
+ print "------- cleaning executables -----\n";
+ `rm bin/* $SILENT`;
+ exit ($EXIT_SUCCESS);
+ }
+
+if ( !$PG{$target}){print "------- Installing T-Coffee Modes\n";}
+
+#1 - Installing various modes
+foreach my $m (keys(%MODE))
+ {
+ if ( $target eq "all" || $target eq $m)
+ {
+ print "\n------- The installer will now install the $m components $MODE{$m}{description}\n";
+ foreach my $pg (keys(%PG))
+ {
+ if ( $PG{$pg}{mode} =~/$m/ && $PG{$pg}{install})
+ {
+ if ($PG{$pg}{touched}){print "------- $PG{$pg}{dname}: already processed\n";}
+ else {$PG{$pg}{success}=&install_pg($pg);$PG{$pg}{touched}=1;}
+ }
+ }
+ }
+ }
+
+#2 - Installing Various Packages
+if ( $PG{$target}){print "------- Installing Individual Package\n";}
+foreach my $pg (keys (%PG))
+ {
+
+ if ( $PG{$pg}{install} && !$PG{$pg}{touched})
+ {
+ print "\n------- Install $pg\n";
+ $PG{$pg}{success}=&install_pg($pg);$PG{$pg}{touched}=1;
+ }
+ }
+print "------- Finishing The installation\n";
+my $final_report=&install ($INSTALL_DIR);
+
+print "\n";
+print "*********************************************************************\n";
+print "******** INSTALLATION SUMMARY *****************\n";
+print "*********************************************************************\n";
+print "------- SUMMARY package Installation:\n";
+print "------- Executable Installed in: $PLUGINS_DIR\n";
+
+foreach my $pg (keys(%PG))
+ {
+ if ( $PG{$pg}{install})
+ {
+ my $bin_status=($PG{$pg}{from_binary} && $PG{$pg}{success})?"[from binary]":"";
+ if ( $PG{$pg}{new} && !$PG{$pg}{old}) {print "*------ $PG{$pg}{dname}: installed $bin_status\n"; $PG{$pg}{status}=1;}
+ elsif ( $PG{$pg}{new} && $PG{$pg}{old}) {print "*------ $PG{$pg}{dname}: updated $bin_status\n" ; $PG{$pg}{status}=1;}
+ elsif (!$PG{$pg}{new} && $PG{$pg}{old} && !$PG{$pg}{update}){print "*------ $PG{$pg}{dname}: previous\n" ; $PG{$pg}{status}=1;}
+ elsif (!$PG{$pg}{new} && $PG{$pg}{old} && $PG{$pg}{update}){print "*------ $PG{$pg}{dname}: failed update (previous installation available)\n";$PG{$pg}{status}=0;}
+ else {print "*------ $PG{$pg}{dname}: failed installation\n";$PG{$pg}{status}=0;}
+ }
+ }
+my $failure;
+
+if ( !$PG{$target}){print "*------ SUMMARY mode Installation:\n";}
+foreach my $m (keys(%MODE))
+ {
+
+ if ( $target eq "all" || $target eq $m)
+ {
+ my $succesful=1;
+ foreach my $pg (keys(%PG))
+ {
+ if (($PG{$pg}{mode}=~/$m/) && $PG{$pg}{install} && $PG{$pg}{status}==0)
+ {
+ $succesful=0;
+ print "*!!!!!! $PG{$pg}{dname}: Missing\n";
+ }
+ }
+ if ( $succesful)
+ {
+ $MODE{$m}{status}=1;
+ print "*------ MODE $MODE{$m}{dname} SUCCESSFULLY installed\n";
+ }
+ else
+ {
+ $failure++;
+ $MODE{$m}{status}=0;
+ print "*!!!!!! MODE $MODE{$m}{dname} UNSUCCESSFULLY installed\n";
+ }
+ }
+ }
+
+
+
+if ($clean==1 && ($BASE=~/install4tcoffee/) ){print "*------ Clean Installation Directory: $BASE\n";`rm -rf $BASE`;}
+#failure if one program was not well installed
+foreach my $pg (keys(%PG)){if ($PG{$pg}{install} && $PG{$pg}{status}==0){exit ($EXIT_FAILURE);}}
+
+if ($failure)
+ {
+ print "*********************************************************************\n";
+ print "******** SOME PACKAGES FAILED TO INSTALL *****************\n";
+ print "*********************************************************************\n";
+ print "\nSome of the reported failures may be due to connectivity problems";
+ print "\nRerun the installation and the installer will specifically try to install the missing packages";
+ print "\nIf this Fails, go to the original website and install the package manually";
+ }
+
+print "*********************************************************************\n";
+print "******** FINALIZE YOUR INSTALLATION *****************\n";
+print "*********************************************************************\n";
+print "------- Your executables are in:\n";
+print "------- $PLUGINS_DIR:\n";
+print "------- Add this directory to your path with the following command:\n";
+print "------- export PATH=$PLUGINS_DIR:\$PATH\n";
+print "------- Make this permanent by adding this line to the file:\n";
+print "------- $HOME/.bashrc\n";
+exit ($EXIT_SUCCESS);
+
+#################################################################################
+# #
+# #
+# #
+# GENERIC INSTALLATION #
+# #
+# #
+# #
+#################################################################################
+sub get_CXX_compiler
+ {
+ my $c=@_[0];
+ my (@clist)=("g++");
+
+ return get_compil ($c, @clist);
+ }
+sub get_C_compiler
+ {
+ my $c=@_[0];
+ my (@clist)=("gcc", "cc", "icc");
+
+ return get_compil ($c, @clist);
+ }
+
+sub get_F_compiler
+ {
+ my ($c)=@_[0];
+ my @clist=("f77", "g77","g95", "gfortran", "ifort");
+ return get_compil ($c, @clist);
+ }
+
+sub get_compil
+ {
+ my ($fav,@clist)=(@_);
+
+ #return the first compiler found installed in the system. Check first the favorite
+ foreach my $c ($fav,@clist)
+ {
+ if (&pg_is_installed ($c)){return $c;}
+ }
+ return "";
+ }
+sub exit_if_pg_not_installed
+ {
+ my (@arg)=(@_);
+
+ foreach my $p (@arg)
+ {
+ if ( !&pg_is_installed ($p))
+ {
+ print "!!!!!!!! The $p utility must be installed for this installation to proceed [FATAL]\n";
+ die;
+ }
+ }
+ return 1;
+ }
+sub set_proxy
+ {
+ my ($proxy)=(@_);
+ my (@list,$p);
+
+ @list= ("HTTP_proxy", "http_proxy", "HTTP_PROXY", "ALL_proxy", "all_proxy","HTTP_proxy_4_TCOFFEE","http_proxy_4_TCOFFEE");
+
+ if (!$proxy)
+ {
+ foreach my $p (@list)
+ {
+ if ( ($ENV_SET{$p}) || $ENV{$p}){$proxy=$ENV{$p};}
+ }
+ }
+ foreach my $p(@list){$ENV{$p}=$proxy;}
+ }
+
+sub check_internet_connection
+ {
+ my $internet;
+
+ if ( -e "x"){unlink ("x");}
+ if (&pg_is_installed ("wget")){`wget www.google.com -Ox >/dev/null 2>/dev/null`;}
+ elsif (&pg_is_installed ("curl")){`curl www.google.com -ox >/dev/null 2>/dev/null`;}
+ else
+ {
+ printf stderr "\nERROR: No pg for remote file fetching [wget or curl][FATAL]\n";
+ exit ($EXIT_FAILURE);
+ }
+
+ if ( !-e "x" || -s "x" < 10){$internet=0;}
+ else {$internet=1;}
+ if (-e "x"){unlink "x";}
+ return $internet;
+ }
+sub url2file
+ {
+ my ($cmd, $file,$wget_arg, $curl_arg)=(@_);
+ my ($exit,$flag, $pg, $arg);
+
+ if ($INTERNET || check_internet_connection ()){$INTERNET=1;}
+ else
+ {
+ print STDERR "ERROR: No Internet Connection [FATAL:install.pl]\n";
+ exit ($EXIT_FAILURE);
+ }
+
+ if (&pg_is_installed ("wget")){$pg="wget"; $flag="-O";$arg="--tries=2 --connect-timeout=10 $wget_arg";}
+ elsif (&pg_is_installed ("curl")){$pg="curl"; $flag="-o";$arg=$curl_arg;}
+ else
+ {
+ printf stderr "\nERROR: No pg for remote file fetching [wget or curl][FATAL]\n";
+ exit ($EXIT_FAILURE);
+ }
+
+
+ if (-e $file){unlink($file);}
+ $exit=system "$pg $cmd $flag$file $arg";
+ return $exit;
+ }
+
+sub pg_is_installed
+ {
+ my ($p, $dir)=(@_);
+ my ($r,$m, $ret);
+ my ($supported, $language, $compil);
+
+
+ if ( $PG{$p})
+ {
+ $language=$PG{$p}{language2};
+ $compil=$PG{$language}{compiler};
+ }
+
+ if ( $compil eq "CPAN")
+ {
+ if ( system ("perl -M$p -e 1")==$EXIT_SUCCESS){$ret=1;}
+ else {$ret=0;}
+ }
+ elsif ($dir)
+ {
+ if (-e "$dir/$p" || -e "$dir/$p\.exe"){$ret=1;}
+ else {$ret=0;}
+ }
+ elsif (-e "$PLUGINS_DIR/$p" || -e "$PLUGINS_DIR/$p.exe"){$ret=1;}
+ else
+ {
+ $r=`which $p 2>/dev/null`;
+ if ($r eq ""){$ret=0;}
+ else {$ret=1;}
+ }
+
+ return $ret;
+ }
+sub install
+ {
+ my ($new_bin)=(@_);
+ my ($copied, $report);
+
+
+ if (!$ROOT_INSTALL)
+ {
+
+ if (-e "$BIN/t_coffee"){`$CP $BIN/t_coffee $INSTALL_DIR`};
+ `cp $BIN/* $PLUGINS_DIR`;
+ $copied=1;
+ }
+ else
+ {
+ $copied=&root_run ("You must be root to finalize the installation", "$CP $BIN/* $INSTALL_DIR $SILENT");
+ }
+
+
+ if ( !$copied)
+ {
+ $report="*!!!!!! Installation unsuccesful. The executables have been left in $BASE/bin\n";
+ }
+ elsif ( $copied && $ROOT)
+ {
+ $report="*------ Installation succesful. Your executables have been copied in $new_bin and are on your PATH\n";
+ }
+ elsif ( $copied && !$ROOT)
+ {
+ $report= "*!!!!!! T-Coffee and associated packages have been copied in: $new_bin\n";
+ $report.="*!!!!!! This address is NOT in your PATH sytem variable\n";
+ $report.="*!!!!!! You can do so by adding the following line in your ~/.bashrc file:\n";
+ $report.="*!!!!!! export PATH=$new_bin:\$PATH\n";
+ }
+ return $report;
+}
+
+sub sign_license_ni
+ {
+ my $F=new FileHandle;
+ open ($F, "license.txt");
+ while (<$F>)
+ {
+ print "$_";
+ }
+ close ($F);
+
+ return;
+ }
+#################################################################################
+# #
+# #
+# #
+# INDIVIDUAL MULTIPLE SEQUENCE ALIGNMNT PACKAGES INSTALLATION #
+# #
+# #
+# #
+#################################################################################
+
+sub install_pg
+ {
+ my ($pg)=(@_);
+ my ($report, $previous, $language, $compiler, $return);
+
+ if (!$PG{$pg}{install}){return 1;}
+
+ $previous=&pg_is_installed ($pg);
+
+ if ($PG{$pg}{update_action} eq "no_update" && $previous)
+ {
+ $PG{$pg}{old}=1;
+ $PG{$pg}{new}=0;
+ $return=1;
+ }
+ else
+ {
+ $PG{$pg}{old}=$previous;
+
+ if ($PG{$pg} {language2} eq "Perl"){&install_perl_package ($pg);}
+ elsif ($BINARIES_ONLY && &install_binary_package ($pg)){$PG{$pg}{from_binary}=1;}
+ elsif (&install_source_package ($pg)){;}
+ else
+ {
+
+ if (!&supported_os($OS))
+ {
+ print "!!!!!!!! $pg compilation failed, binary unsupported for $OS\n";
+ }
+ elsif (!($PG{$pg}{from_binary}=&install_binary_package ($pg)))
+ {
+ print "!!!!!!!! $pg compilation and binary installation failed\n";
+ }
+ }
+ $PG{$pg}{new}=$return=&pg_is_installed ($pg,$BIN);
+ }
+
+
+ return $return;
+ }
+sub install_perl_package
+ {
+ my ($pg)=(@_);
+ my ($report, $language, $compiler);
+
+ $language=$PG{$pg} {language2};
+ $compiler=$PG{$language}{compiler};
+
+ if (!&pg_is_installed ($pg))
+ {
+ if ( $OS eq "windows"){`perl -M$compiler -e 'install $pg'`;}
+ elsif ( $ROOT eq "sudo"){system ("sudo perl -M$compiler -e 'install $pg'");}
+ else {system ("su root -c perl -M$compiler -e 'install $pg'");}
+ }
+ return &pg_is_installed ($pg);
+ }
+
+
+
+sub install_source_package
+ {
+ my ($pg)=(@_);
+ my ($report, $download, $arguments, $language, $address, $name, $ext, $main_dir, $distrib);
+ my $wget_tmp="$TMP/wget.tmp";
+ my (@fl);
+ if ( -e "$BIN/$pg" || -e "$BIN/$pg.exe"){return 1;}
+
+ #
+ # check if the module exists in the repository cache
+ #
+ if( repo_load($pg) ) {
+ return 1;
+ }
+
+ if ($pg eq "t_coffee") {return &install_t_coffee ($pg);}
+ elsif ($pg eq "TMalign"){return &install_TMalign ($pg);}
+
+ chdir $DISTRIBUTIONS;
+
+ $download=$PG{$pg}{source};
+
+ if (($download =~/tgz/))
+ {
+ ($address,$name,$ext)=($download=~/(.+\/)([^\/]+)(\.tgz).*/);
+ }
+ elsif (($download=~/tar\.gz/))
+ {
+ ($address,$name,$ext)=($download=~/(.+\/)([^\/]+)(\.tar\.gz).*/);
+ }
+ elsif (($download=~/tar/))
+ {
+ ($address,$name,$ext)=($download=~/(.+\/)([^\/]+)(\.tar).*/);
+ }
+ else
+ {
+ ($address,$name)=($download=~/(.+\/)([^\/]+)/);
+ $ext="";
+ }
+ $distrib="$name$ext";
+
+ if ( !-d $pg){mkdir $pg;}
+ chdir $pg;
+
+ #get the distribution if available
+ if ( -e "$DOWNLOAD_DIR/$distrib")
+ {
+ `$CP $DOWNLOAD_DIR/$distrib .`;
+ }
+ #UNTAR and Prepare everything
+ if (!-e "$name.tar" && !-e "$name")
+ {
+ &check_rm ($wget_tmp);
+ print "\n------- Downloading/Installing $pg\n";
+
+ if (!-e $distrib && &url2file ("$download", "$wget_tmp")==$EXIT_SUCCESS)
+ {
+
+ `mv $wget_tmp $distrib`;
+ `$CP $distrib $DOWNLOAD_DIR/`;
+ }
+
+ if (!-e $distrib)
+ {
+ print "!!!!!!! Download of $pg distribution failed\n";
+ print "!!!!!!! Check Address: $PG{$pg}{source}\n";
+ return 0;
+ }
+ print "\n------- unzipping/untaring $name\n";
+ if (($ext =~/z/))
+ {
+ &flush_command ("gunzip $name$ext");
+
+ }
+ if (($ext =~/tar/) || ($ext =~/tgz/))
+ {
+ &flush_command("tar -xvf $name.tar");
+ }
+ }
+ #Guess and enter the distribution directory
+ @fl=ls($p);
+ foreach my $f (@fl)
+ {
+ if (-d $f)
+ {
+ $main_dir=$f;
+ }
+ }
+ if (-d $main_dir)
+
+ {
+ chdir $main_dir;}
+ else
+ {
+ print "Error: $main_dir does not exist";
+ }
+ print "\n------- Compiling/Installing $pg\n";
+ `make clean $SILENT`;
+
+
+ #
+ # SAP module
+ #
+ if ($pg eq "sap")
+ {
+ if (-e "./configure")
+ {
+ #new sap distribution
+ if ($OS eq "macosx")
+ {
+ &replace_line_in_file ("./src/galloc.h", "malloc.h", "");
+ &replace_line_in_file ("./src/pdbprot.h", "malloc.h", "");
+ &replace_line_in_file ("./src/pdbprot.c", "malloc.h", "");
+ }
+
+ &flush_command ("./configure");
+ &flush_command ("make clean");
+ &flush_command ("make");
+ &check_cp ("./src/$pg", "$BIN");
+ repo_store("./src/$pg");
+ }
+ else
+ {
+ #old style distribution
+ `rm *.o sap sap.exe ./util/aa/*.o ./util/wt/.o $SILENT`;
+ &flush_command ("make $arguments sap");
+ &check_cp ($pg, "$BIN");
+ repo_store($pg);
+ }
+ }
+
+ #
+ # CLUSTALW2 module
+ #
+ elsif ($pg eq "clustalw2")
+ {
+ &flush_command("./configure");
+ &flush_command("make $arguments");
+ &check_cp ("./src/$pg", "$BIN");
+ repo_store("./src/$pg");
+ }
+
+ #
+ # FSA module
+ #
+ elsif ($pg eq "fsa")
+ {
+ &flush_command("./configure --prefix=$BIN");
+ &flush_command("make $arguments");
+ &flush_command ("make install");
+
+ repo_store("fsa", "$BIN/bin");
+ `mv $BIN/bin/* $BIN`;
+ `rmdir $BIN/bin`;
+ }
+
+ #
+ # CLUSTALW module
+ #
+ elsif ($pg eq "clustalw")
+ {
+ &flush_command("make $arguments clustalw");
+ `$CP $pg $BIN $SILENT`;
+ repo_store($pg);
+ }
+
+ #
+ # MAFFT module
+ #
+ elsif ($pg eq "mafft")
+ {
+ my $base=cwd();
+ my $c;
+
+ #compile core
+ mkpath ("./mafft/bin");
+ mkpath ("./mafft/lib");
+ chdir "$base/core";
+ `make clean $SILENT`;
+ &flush_command ("make $arguments");
+ &flush_command ("make install LIBDIR=../mafft/lib BINDIR=../mafft/bin");
+
+ #compile extension
+ chdir "$base/extensions";
+ `make clean $SILENT`;
+ &flush_command ("make $arguments");
+ &flush_command ("make install LIBDIR=../mafft/lib BINDIR=../mafft/bin");
+
+ #put everything in mafft and copy the compiled stuff in bin
+ chdir "$base";
+ if ($ROOT_INSTALL)
+ {
+ &root_run ("You Must be Root to Install MAFFT\n", "mkdir /usr/local/mafft/;$CP mafft/lib/* /usr/local/mafft;$CP mafft/lib/mafft* /usr/local/bin ;$CP mafft/bin/mafft /usr/local/bin/; ");
+ }
+ else
+ {
+ `$CP mafft/lib/* $BIN`;
+ `$CP mafft/bin/mafft $BIN`;
+ }
+ `tar -cvf mafft.tar mafft`;
+ `gzip mafft.tar`;
+ `mv mafft.tar.gz $BIN`;
+
+ repo_store("mafft/bin/mafft", "mafft/lib/", "$BIN/mafft.tar.gz");
+ }
+
+ #
+ # DIALIGN-TX module
+ #
+ elsif ( $pg eq "dialign-tx" )
+ {
+ my $f;
+ my $base=cwd();
+
+ chdir "./source";
+ if ($OS eq "macosx"){&flush_command ("cp makefile.MAC_OS makefile");}
+
+ &flush_command (" make CPPFLAGS='-O3 -funroll-loops' all");
+
+ chdir "..";
+ &check_cp ("./source/$pg", "$BIN");
+ repo_store("./source/$pg");
+ }
+
+ #
+ # DIALIGN-T module
+ # (is the same as dialign-tx, but it is mantained for backward name compatibility with tcoffee)
+ #
+ elsif ( $pg eq "dialign-t" )
+ {
+ my $f;
+ my $base=cwd();
+
+ chdir "./source";
+ if ($OS eq "macosx"){&flush_command ("cp makefile.MAC_OS makefile");}
+
+ &flush_command (" make CPPFLAGS='-O3 -funroll-loops' all");
+
+ chdir "..";
+ &check_cp ("./source/dialign-tx", "$BIN/dialign-t");
+ repo_store("$BIN/dialign-t");
+ }
+
+ #
+ # POA module
+ #
+ elsif ($pg eq "poa")
+ {
+ &flush_command ("make $arguments poa");
+ &check_cp ("$pg", "$BIN");
+ repo_store("$pg");
+ }
+
+
+ #
+ # PROBCONS module
+ #
+ elsif ( $pg eq "probcons")
+ {
+ &add_C_libraries("./ProbabilisticModel.h", "list", "cstring");
+
+ `rm *.exe $SILENT`;
+ &flush_command ("make $arguments probcons");
+ &check_cp("$pg", "$BIN/$pg");
+ repo_store("$pg");
+ }
+
+ #
+ # PROBCONS RNA module
+ #
+ elsif ( $pg eq "probconsRNA")
+ {
+ &add_C_libraries("./ProbabilisticModel.h", "list", "cstring");
+ &add_C_libraries("./Main.cc", "iomanip", "cstring","climits");
+ `rm *.exe $SILENT`;
+ &flush_command ("make $arguments probcons");
+ &check_cp("probcons", "$BIN/$pg");
+ repo_store("$BIN/$pg");
+ }
+
+ #
+ # MUSCLE module
+ #
+ elsif ( $pg eq "muscle")
+ {
+ `rm *.o muscle muscle.exe $SILENT`;
+ if ($OS eq "macosx" || $OS eq "linux")
+ {
+ &replace_line_in_file ("./Makefile", "LDLIBS = -lm -static", "LDLIBS = -lm");
+ }
+ elsif ($OS eq "windows")
+ {
+ &replace_line_in_file ("./intmath.cpp", "double log2e", "double cedric_log");
+ &replace_line_in_file ("./intmath.cpp", "double log2", "double log_notuse");
+ &replace_line_in_file ("./intmath.cpp", "double cedric_log", "double log2e");
+ }
+ &flush_command ("make $arguments all");
+ &check_cp("$pg", "$BIN");
+ repo_store("$pg");
+ }
+
+ #
+ # MUS4 module
+ #
+ elsif ( $pg eq "mus4")
+ {
+ `rm *.o muscle muscle.exe $SILENT`;
+ &flush_command ("./mk");
+ &check_cp("$pg", "$BIN");
+ repo_store("$pg");
+ }
+
+ #
+ # PCMA module
+ #
+ elsif ( $pg eq "pcma")
+ {
+ if ($OS eq "macosx")
+ {
+ &replace_line_in_file ("./alcomp2.c", "malloc.h", "");
+ }
+ &flush_command ("make $arguments pcma");
+ &check_cp("$pg", "$BIN");
+ repo_store("$pg");
+ }
+
+ #
+ # KALIGN module
+ #
+ elsif ($pg eq "kalign")
+ {
+ &flush_command ("./configure");
+ &flush_command("make $arguments");
+ &check_cp ("$pg",$BIN);
+ repo_store("$pg");
+ }
+
+ #
+ # AMAP module
+ #
+ elsif ( $pg eq "amap")
+ {
+ &add_C_libraries("./Amap.cc", "iomanip", "cstring","climits");
+ `make clean $SILENT`;
+ &flush_command ("make $arguments all");
+ &check_cp ("$pg", $BIN);
+ repo_store("$pg");
+ }
+
+ #
+ # PRODA module
+ #
+ elsif ( $pg eq "proda")
+ {
+ &add_C_libraries("AlignedFragment.h", "vector", "iostream", "cstring","cstdlib");
+ &add_C_libraries("Main.cc", "vector", "climits");
+ &add_C_libraries("Sequence.cc", "stdlib.h", "cstdio");
+ &flush_command ("make $arguments all");
+ &check_cp ("$pg", $BIN);
+ repo_store("$pg");
+ }
+
+ #
+ # PRANK module
+ #
+ elsif ( $pg eq "prank")
+ {
+ &flush_command ("make $arguments all");
+ &check_cp ("$pg", $BIN);
+ repo_store("$pg");
+ }
+
+ #
+ # !!!! MUSTANG module
+ #
+ elsif ( $pg eq "mustang")
+ {
+ &flush_command ("rm ./bin/*");
+ &flush_command ("make $arguments all");
+
+ if ( $OS=~/windows/){&flush_command("cp ./bin/* $BIN/mustang.exe");}
+ else {&flush_command("cp ./bin/* $BIN/mustang");}
+
+ repo_store("$BIN/mustang");
+ }
+
+ #
+ # RNAplfold module
+ #
+ elsif ( $pg eq "RNAplfold")
+ {
+ &flush_command("./configure");
+ &flush_command ("make $arguments all");
+ &check_cp("./Progs/RNAplfold", "$BIN");
+ &check_cp("./Progs/RNAalifold", "$BIN");
+ &check_cp("./Progs/RNAfold", "$BIN");
+
+ repo_store("./Progs/RNAplfold", "./Progs/RNAalifold", "./Progs/RNAfold");
+ }
+
+ #
+ # !!! RETREE module
+ #
+ elsif ( $pg eq "retree")
+ {
+ chdir "src";
+ &flush_command ("make $arguments all");
+ &flush_command ("make put");
+ system "cp ../exe/* $BIN";
+
+ repo_store("retree", "../exe");
+ }
+
+ chdir $CDIR;
+ return &pg_is_installed ($pg, $BIN);
+ }
+
+sub install_t_coffee
+ {
+ my ($pg)=(@_);
+ my ($report,$cflags, $arguments, $language, $compiler) ;
+ #1-Install T-Coffee
+ chdir "t_coffee_source";
+ &flush_command ("make clean");
+ print "\n------- Compiling T-Coffee\n";
+ $language=$PG{$pg} {language2};
+ $arguments=$PG{$language}{arguments};
+ if (!($arguments =~/CFLAGS/)){$arguments .= " CFLAGS=-O2 ";}
+
+ if ( $CC ne ""){&flush_command ("make -i $arguments t_coffee");}
+ &check_cp ($pg, $BIN);
+
+ chdir $CDIR;
+ return &pg_is_installed ($pg, $BIN);
+ }
+sub install_TMalign
+ {
+ my ($pg)=(@_);
+ my $report;
+ chdir "t_coffee_source";
+ print "\n------- Compiling TMalign\n";
+ `rm TMalign TMalign.exe $SILENT`;
+ if ( $FC ne ""){&flush_command ("make -i $PG{Fortran}{arguments} TMalign");}
+ &check_cp ($pg, $BIN);
+ repo_store($pg);
+
+ if ( !-e "$BIN/$pg" && pg_has_binary_distrib ($pg))
+ {
+ print "!!!!!!! Compilation of $pg impossible. Will try to install from binary\n";
+ return &install_binary_package ($pg);
+ }
+ chdir $CDIR;
+ return &pg_is_installed ($pg, $BIN);
+ }
+
+sub pg_has_binary_distrib
+ {
+ my ($pg)=(@_);
+ if ($PG{$pg}{windows}){return 1;}
+ elsif ($PG{$pg}{osx}){return 1;}
+ elsif ($PG{$pg}{linux}){return 1;}
+ return 0;
+ }
+sub install_binary_package
+ {
+ my ($pg)=(@_);
+ my ($base,$report,$name, $download, $arguments, $language, $dir);
+ my $isdir;
+ &input_os();
+
+ if (!&supported_os($OS)){return 0;}
+ if ( $PG{$pg}{binary}){$name=$PG{$pg}{binary};}
+ else
+ {
+ $name=$pg;
+ if ( $OS eq "windows"){$name.=".exe";}
+ }
+
+ $download="$WEB_BASE/Packages/Binaries/$OS/$name";
+
+ $base=cwd();
+ chdir $TMP;
+
+ if (!-e $name)
+ {
+ `rm x $SILENT`;
+ if ( url2file("$download","x")==$EXIT_SUCCESS)
+ {
+ `mv x $name`;
+ }
+ }
+
+ if (!-e $name)
+ {
+ print "!!!!!!! $PG{$pg}{dname}: Download of $pg binary failed\n";
+ print "!!!!!!! $PG{$pg}{dname}: Check Address: $download\n";
+ return 0;
+ }
+ print "\n------- Installing $pg\n";
+
+ if ($name =~/tar\.gz/)
+ {
+ `gunzip $name`;
+ `tar -xvf $pg.tar`;
+ chdir $pg;
+ if ( $pg eq "mafft")
+ {
+ if ($ROOT_INSTALL)
+ {
+ &root_run ("You Must be Roor to Install MAFFT\n", "$CP mafft/bin/* /usr/local/mafft;mkdir /usr/local/mafft/; $CP mafft/lib/* /usr/local/bin/");
+ }
+ else
+ {
+ `$CP $TMP/$pg/bin/* $BIN $SILENT`;
+ `$CP $TMP/$pg/lib/* $BIN $SILENT`;
+ }
+ }
+ else
+ {
+ if (-e "$TMP/$pg/data"){`$CP $TMP/$pg/data/* $TCM $SILENT`;}
+ if (!($pg=~/\*/)){`rm -rf $pg`;}
+ }
+ }
+ else
+ {
+ &check_cp ("$pg", "$BIN");
+ `chmod u+x $BIN/$pg`;
+ unlink ($pg);
+ }
+ chdir $base;
+ $PG{$pg}{from_binary}=1;
+ return &pg_is_installed ($pg, $BIN);
+ }
+
+################################################################################
+# #
+# #
+# #
+# Simple Utilities #
+# #
+# #
+# #
+#################################################################################
+sub add_dir
+ {
+ my $dir=@_[0];
+
+ if (!-e $dir && !-d $dir)
+ {
+ my @l;
+ umask (0000);
+ @l=mkpath ($dir,{mode => 0777});
+
+ }
+ else
+ {
+ return 0;
+ }
+ }
+sub check_rm
+ {
+ my ($file)=(@_);
+
+ if ( -e $file)
+ {
+ return unlink($file);
+ }
+ return 0;
+ }
+sub check_cp
+ {
+ my ($from, $to)=(@_);
+ if ( !-e $from && -e "$from\.exe"){$from="$from\.exe";}
+ if ( !-e $from){return 0;}
+
+ `$CP $from $to`;
+ return 1;
+ }
+
+#
+# Cache the specified package
+#
+# - path (mandatory): the source path to be cached
+# - pg (optional): the package name
+#
+sub repo_store
+{
+ # check that all required data are available
+ if( $REPO_ROOT eq "" ) { return; }
+
+
+ # extract the package name from the specified path
+ my $pg =`basename $_[0]`;
+ chomp($pg);
+
+ my $VER = $PG{$pg}{version};
+ my $CACHE = "$REPO_ROOT/$pg/$VER/$OSNAME-$OSARCH";
+
+ print "-------- Storing package: \"$pg\" to path: $CACHE\n";
+
+ # clean the cache path if exists and create it again
+ `rm -rf $CACHE`;
+ `mkdir -p $CACHE`;
+
+ for my $path (@_) {
+
+ # check if it is a single file
+ if( -f $path ) {
+ `cp $path $CACHE`;
+ }
+ # .. or a directory, in this case copy all the content
+ elsif( -d $path ) {
+ opendir(IMD, $path);
+ my @thefiles= readdir(IMD);
+ closedir(IMD);
+
+ for my $_file (@thefiles) {
+ if( $_file ne "." && $_file ne "..") {
+ `cp $path/$_file $CACHE`;
+ }
+ }
+ }
+ }
+
+
+}
+
+#
+# Retrieve a target object from the build binary repository
+# - pg (mandatory): a know target package name, it will be used to access to the $PG packages map
+#
+sub repo_load
+{
+ my ($pg)=(@_);
+
+ # check that all required data are available
+ if( $REPO_ROOT eq "" ) { return 0; }
+
+ my $VER = $PG{$pg}{version};
+ my $CACHE = "$REPO_ROOT/$pg/$VER/$OSNAME-$OSARCH";
+ if( !-e "$CACHE/$pg" ) {
+ print "-------- Module \"$pg\" NOT found on repository cache.\n";
+ return 0;
+ }
+
+ print "-------- Module \"$pg\" found on repository cache. Using copy on path: $CACHE\n";
+ `cp $CACHE/* $BIN`;
+ return 1;
+}
+
+sub check_file_list_exists
+ {
+ my ($base, @flist)=(@_);
+ my $f;
+
+ foreach $f (@flist)
+ {
+ if ( !-e "$base/$f"){return 0;}
+ }
+ return 1;
+ }
+sub ls
+ {
+ my $f=@_[0];
+ my @fl;
+ chomp(@fl=`ls -1 $f`);
+ return @fl;
+ }
+sub flush_command
+ {
+ my $command=@_[0];
+ my $F=new FileHandle;
+ open ($F, "$command|");
+ while (<$F>){print " --- $_";}
+ close ($F);
+ }
+
+sub input_installation_directory
+ {
+ my $dir=@_[0];
+ my $new;
+
+ print "------- The current installation directory is: [$dir]\n";
+ print "??????? Return to keep the default or new value:";
+
+ if ($NO_QUESTION==0)
+ {
+ chomp ($new=<stdin>);
+ while ( $new ne "" && !input_yes ("You have entered $new. Is this correct? ([y]/n):"))
+ {
+ print "???????New installation directory:";
+ chomp ($new=<stdin>);
+ }
+ $dir=($new eq "")?$dir:$new;
+ $dir=~s/\/$//;
+ }
+
+ if ( -d $dir){return $dir;}
+ elsif (&root_run ("You must be root to create $dir","mkdir $dir")==$EXIT_SUCCESS){return $dir;}
+ else
+ {
+ print "!!!!!!! $dir could not be created\n";
+ if ( $NO_QUESTION)
+ {
+ return "";
+ }
+ elsif ( &input_yes ("??????? Do you want to provide a new directory([y]/n)?:"))
+ {
+ return input_installation_directory ($dir);
+ }
+ else
+ {
+ return "";
+ }
+ }
+
+ }
+sub input_yes
+ {
+ my $question =@_[0];
+ my $answer;
+
+ if ($NO_QUESTION==1){return 1;}
+
+ if ($question eq ""){$question="??????? Do you wish to proceed ([y]/n)?:";}
+ print $question;
+ chomp($answer=lc(<STDIN>));
+ if (($answer=~/^y/) || $answer eq ""){return 1;}
+ elsif ( ($answer=~/^n/)){return 0;}
+ else
+ {
+ return input_yes($question);
+ }
+ }
+sub root_run
+ {
+ my ($txt, $cmd)=(@_);
+
+ if ( system ($cmd)==$EXIT_SUCCESS){return $EXIT_SUCCESS;}
+ else
+ {
+ print "------- $txt\n";
+ if ( $ROOT eq "sudo"){return system ("sudo $cmd");}
+ else {return system ("su root -c \"$cmd\"");}
+ }
+ }
+#analyze environement
+sub get_root
+ {
+ if (&pg_is_installed ("sudo")){return "sudo";}
+ else {return "su";}
+ }
+
+sub get_os
+ {
+ my $raw_os=`uname`;
+ my $os;
+
+ $raw_os=lc ($raw_os);
+
+ if ($raw_os =~/cygwin/){$os="windows";}
+ elsif ($raw_os =~/linux/){$os="linux";}
+ elsif ($raw_os =~/osx/){$os="macosx";}
+ elsif ($raw_os =~/darwin/){$os="macosx";}
+ else
+ {
+ $os=$raw_os;
+ }
+ return $os;
+ }
+sub input_os
+ {
+ my $answer;
+ if ($OS) {return $OS;}
+
+ print "??????? which os do you use: [w]indows, [l]inux, [m]acosx:?";
+ $answer=lc(<STDIN>);
+
+ if (($answer=~/^m/)){$OS="macosx";}
+ elsif ( ($answer=~/^w/)){$OS="windows";}
+ elsif ( ($answer=~/^linux/)){$OS="linux";}
+
+ else
+ {
+ return &input_os();
+ }
+ return $OS;
+ }
+
+sub supported_os
+ {
+ my ($os)=(@_[0]);
+ return $SUPPORTED_OS{$os};
+ }
+
+
+################################################################################
+# #
+# #
+# #
+# update/initialize links #
+# #
+# #
+# #
+#################################################################################
+
+
+sub update_tclinkdb
+ {
+ my $file =@_[0];
+ my $name;
+ my $F=new FileHandle;
+ my ($download, $address, $name, $l, $db);
+
+ if ( $file eq "update"){$file=$TCLINKDB_ADDRESS;}
+
+ if ( $file =~/http:\/\// || $file =~/ftp:\/\//)
+ {
+ ($address, $name)=($download=~/(.*)\/([^\/]+)$/);
+ `rm x $SILENT`;
+ if (&url2file ($file,"x")==$EXIT_SUCCESS)
+ {
+ print "------- Susscessful upload of $name";
+ `mv x $name`;
+ $file=$name;
+ }
+ }
+ open ($F, "$file");
+ while (<$F>)
+ {
+ my $l=$_;
+ if (($l =~/^\/\//) || ($db=~/^#/)){;}
+ elsif ( !($l =~/\w/)){;}
+ else
+ {
+ my @v=split (/\s+/, $l);
+ if ( $l=~/^MODE/)
+ {
+ $MODE{$v[1]}{$v[2]}=$v[3];
+ }
+ elsif ($l=~/^PG/)
+ {
+ $PG{$v[1]}{$v[2]}=$v[3];
+ }
+ }
+ }
+ close ($F);
+ &post_process_PG();
+ return;
+ }
+
+
+
+sub initialize_PG
+ {
+#TclinkdbStart End tag for the list updating
+
+$PG{"t_coffee"}{"4_TCOFFEE"}="TCOFFEE";
+$PG{"t_coffee"}{"type"}="sequence_multiple_aligner";
+$PG{"t_coffee"}{"ADDRESS"}="http://www.tcoffee.org";
+$PG{"t_coffee"}{"language"}="C";
+$PG{"t_coffee"}{"language2"}="C";
+$PG{"t_coffee"}{"source"}="http://www.tcoffee.org/Packages/T-COFFEE_distribution.tar.gz";
+$PG{"t_coffee"}{"update_action"}="always";
+$PG{"t_coffee"}{"mode"}="tcoffee,mcoffee,rcoffee,expresso,3dcoffee";
+$PG{"clustalw2"}{"4_TCOFFEE"}="CLUSTALW2";
+$PG{"clustalw2"}{"type"}="sequence_multiple_aligner";
+$PG{"clustalw2"}{"ADDRESS"}="http://www.clustal.org";
+$PG{"clustalw2"}{"language"}="C++";
+$PG{"clustalw2"}{"language2"}="CXX";
+$PG{"clustalw2"}{"source"}="http://www.clustal.org/download/2.0.10/clustalw-2.0.10-src.tar.gz";
+$PG{"clustalw2"}{"mode"}="mcoffee,rcoffee";
+$PG{"clustalw2"}{"version"}="2.0.10";
+$PG{"clustalw"}{"4_TCOFFEE"}="CLUSTALW";
+$PG{"clustalw"}{"type"}="sequence_multiple_aligner";
+$PG{"clustalw"}{"ADDRESS"}="http://www.clustal.org";
+$PG{"clustalw"}{"language"}="C";
+$PG{"clustalw"}{"language2"}="C";
+$PG{"clustalw"}{"source"}="http://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/ClustalW/clustalw1.82.UNIX.tar.gz";
+$PG{"clustalw"}{"mode"}="mcoffee,rcoffee";
+$PG{"clustalw"}{"version"}="1.82";
+$PG{"dialign-t"}{"4_TCOFFEE"}="DIALIGNT";
+$PG{"dialign-t"}{"type"}="sequence_multiple_aligner";
+$PG{"dialign-t"}{"ADDRESS"}="http://dialign-tx.gobics.de/";
+$PG{"dialign-t"}{"DIR"}="/usr/share/dialign-tx/";
+$PG{"dialign-t"}{"language"}="C";
+$PG{"dialign-t"}{"language2"}="C";
+$PG{"dialign-t"}{"source"}="http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz";
+$PG{"dialign-t"}{"mode"}="mcoffee";
+$PG{"dialign-t"}{"binary"}="dialign-t";
+$PG{"dialign-t"}{"version"}="1.0.2";
+$PG{"dialign-tx"}{"4_TCOFFEE"}="DIALIGNTX";
+$PG{"dialign-tx"}{"type"}="sequence_multiple_aligner";
+$PG{"dialign-tx"}{"ADDRESS"}="http://dialign-tx.gobics.de/";
+$PG{"dialign-tx"}{"DIR"}="/usr/share/dialign-tx/";
+$PG{"dialign-tx"}{"language"}="C";
+$PG{"dialign-tx"}{"language2"}="C";
+$PG{"dialign-tx"}{"source"}="http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz";
+$PG{"dialign-tx"}{"mode"}="mcoffee";
+$PG{"dialign-tx"}{"binary"}="dialign-tx";
+$PG{"dialign-tx"}{"version"}="1.0.2";
+$PG{"poa"}{"4_TCOFFEE"}="POA";
+$PG{"poa"}{"type"}="sequence_multiple_aligner";
+$PG{"poa"}{"ADDRESS"}="http://www.bioinformatics.ucla.edu/poa/";
+$PG{"poa"}{"language"}="C";
+$PG{"poa"}{"language2"}="C";
+$PG{"poa"}{"source"}="http://downloads.sourceforge.net/poamsa/poaV2.tar.gz";
+$PG{"poa"}{"DIR"}="/usr/share/";
+$PG{"poa"}{"FILE1"}="blosum80.mat";
+$PG{"poa"}{"mode"}="mcoffee";
+$PG{"poa"}{"binary"}="poa";
+$PG{"poa"}{"version"}="2.0";
+$PG{"probcons"}{"4_TCOFFEE"}="PROBCONS";
+$PG{"probcons"}{"type"}="sequence_multiple_aligner";
+$PG{"probcons"}{"ADDRESS"}="http://probcons.stanford.edu/";
+$PG{"probcons"}{"language2"}="CXX";
+$PG{"probcons"}{"language"}="C++";
+$PG{"probcons"}{"source"}="http://probcons.stanford.edu/probcons_v1_12.tar.gz";
+$PG{"probcons"}{"mode"}="mcoffee";
+$PG{"probcons"}{"binary"}="probcons";
+$PG{"probcons"}{"version"}="1.12";
+$PG{"mafft"}{"4_TCOFFEE"}="MAFFT";
+$PG{"mafft"}{"type"}="sequence_multiple_aligner";
+$PG{"mafft"}{"ADDRESS"}="http://align.bmr.kyushu-u.ac.jp/mafft/online/server/";
+$PG{"mafft"}{"language"}="C";
+$PG{"mafft"}{"language"}="C";
+$PG{"mafft"}{"source"}="http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-with-extensions-src.tgz";
+$PG{"mafft"}{"windows"}="http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-mingw.tar";
+$PG{"mafft"}{"mode"}="mcoffee,rcoffee";
+$PG{"mafft"}{"binary"}="mafft.tar.gz";
+$PG{"mafft"}{"version"}="6.603";
+$PG{"muscle"}{"4_TCOFFEE"}="MUSCLE";
+$PG{"muscle"}{"type"}="sequence_multiple_aligner";
+$PG{"muscle"}{"ADDRESS"}="http://www.drive5.com/muscle/";
+$PG{"muscle"}{"language"}="C++";
+$PG{"muscle"}{"language2"}="GPP";
+$PG{"muscle"}{"source"}="http://www.drive5.com/muscle/downloads3.7/muscle3.7_src.tar.gz";
+$PG{"muscle"}{"windows"}="http://www.drive5.com/muscle/downloads3.7/muscle3.7_win32.zip";
+$PG{"muscle"}{"linux"}="http://www.drive5.com/muscle/downloads3.7/muscle3.7_linux_ia32.tar.gz";
+$PG{"muscle"}{"mode"}="mcoffee,rcoffee";
+$PG{"muscle"}{"version"}="3.7";
+$PG{"mus4"}{"4_TCOFFEE"}="MUS4";
+$PG{"mus4"}{"type"}="sequence_multiple_aligner";
+$PG{"mus4"}{"ADDRESS"}="http://www.drive5.com/muscle/";
+$PG{"mus4"}{"language"}="C++";
+$PG{"mus4"}{"language2"}="GPP";
+$PG{"mus4"}{"source"}="http://www.drive5.com/muscle/muscle4.0_src.tar.gz";
+$PG{"mus4"}{"mode"}="mcoffee,rcoffee";
+$PG{"mus4"}{"version"}="4.0";
+$PG{"pcma"}{"4_TCOFFEE"}="PCMA";
+$PG{"pcma"}{"type"}="sequence_multiple_aligner";
+$PG{"pcma"}{"ADDRESS"}="ftp://iole.swmed.edu/pub/PCMA/";
+$PG{"pcma"}{"language"}="C";
+$PG{"pcma"}{"language2"}="C";
+$PG{"pcma"}{"source"}="ftp://iole.swmed.edu/pub/PCMA/pcma.tar.gz";
+$PG{"pcma"}{"mode"}="mcoffee";
+$PG{"pcma"}{"version"}="1.0";
+$PG{"kalign"}{"4_TCOFFEE"}="KALIGN";
+$PG{"kalign"}{"type"}="sequence_multiple_aligner";
+$PG{"kalign"}{"ADDRESS"}="http://msa.cgb.ki.se";
+$PG{"kalign"}{"language"}="C";
+$PG{"kalign"}{"language2"}="C";
+$PG{"kalign"}{"source"}="http://msa.cgb.ki.se/downloads/kalign/current.tar.gz";
+$PG{"kalign"}{"mode"}="mcoffee";
+$PG{"kalign"}{"version"}="1.0";
+$PG{"amap"}{"4_TCOFFEE"}="AMAP";
+$PG{"amap"}{"type"}="sequence_multiple_aligner";
+$PG{"amap"}{"ADDRESS"}="http://bio.math.berkeley.edu/amap/";
+$PG{"amap"}{"language"}="C++";
+$PG{"amap"}{"language2"}="CXX";
+$PG{"amap"}{"source"}="http://amap-align.googlecode.com/files/amap.2.0.tar.gz";
+$PG{"amap"}{"mode"}="mcoffee";
+$PG{"amap"}{"version"}="2.0";
+$PG{"proda"}{"4_TCOFFEE"}="PRODA";
+$PG{"proda"}{"type"}="sequence_multiple_aligner";
+$PG{"proda"}{"ADDRESS"}="http://proda.stanford.edu";
+$PG{"proda"}{"language"}="C++";
+$PG{"proda"}{"language2"}="CXX";
+$PG{"proda"}{"source"}="http://proda.stanford.edu/proda_1_0.tar.gz";
+$PG{"proda"}{"mode"}="mcoffee";
+$PG{"proda"}{"version"}="1.0";
+$PG{"fsa"}{"4_TCOFFEE"}="FSA";
+$PG{"fsa"}{"type"}="sequence_multiple_aligner";
+$PG{"fsa"}{"ADDRESS"}="http://fsa.sourceforge.net/";
+$PG{"fsa"}{"language"}="C++";
+$PG{"fsa"}{"language2"}="CXX";
+$PG{"fsa"}{"source"}="http://sourceforge.net/projects/fsa/files/fsa-1.15.3.tar.gz/download/";
+$PG{"fsa"}{"mode"}="mcoffee";
+$PG{"fsa"}{"version"}="1.15.3";
+$PG{"prank"}{"4_TCOFFEE"}="PRANK";
+$PG{"prank"}{"type"}="sequence_multiple_aligner";
+$PG{"prank"}{"ADDRESS"}="http://www.ebi.ac.uk/goldman-srv/prank/";
+$PG{"prank"}{"language"}="C++";
+$PG{"prank"}{"language2"}="CXX";
+$PG{"prank"}{"source"}="http://www.ebi.ac.uk/goldman-srv/prank/src/prank/prank.src.100303.tgz";
+$PG{"prank"}{"mode"}="mcoffee";
+$PG{"prank"}{"version"}="100303";
+$PG{"sap"}{"4_TCOFFEE"}="SAP";
+$PG{"sap"}{"type"}="structure_pairwise_aligner";
+$PG{"sap"}{"ADDRESS"}="http://mathbio.nimr.mrc.ac.uk/wiki/Software";
+$PG{"sap"}{"language"}="C";
+$PG{"sap"}{"language2"}="C";
+$PG{"sap"}{"source"}="http://mathbio.nimr.mrc.ac.uk/download/sap-1.1.1.tar.gz";
+$PG{"sap"}{"mode"}="expresso,3dcoffee";
+$PG{"sap"}{"version"}="1.1.1";
+$PG{"TMalign"}{"4_TCOFFEE"}="TMALIGN";
+$PG{"TMalign"}{"type"}="structure_pairwise_aligner";
+$PG{"TMalign"}{"ADDRESS"}="http://zhang.bioinformatics.ku.edu/TM-align/TMalign.f";
+$PG{"TMalign"}{"language"}="Fortran";
+$PG{"TMalign"}{"language2"}="Fortran";
+$PG{"TMalign"}{"source"}="http://zhang.bioinformatics.ku.edu/TM-align/TMalign.f";
+$PG{"TMalign"}{"linux"}="http://zhang.bioinformatics.ku.edu/TM-align/TMalign_32.gz";
+$PG{"TMalign"}{"mode"}="expresso,3dcoffee";
+$PG{"TMalign"}{"version"}="1.0";
+$PG{"mustang"}{"4_TCOFFEE"}="MUSTANG";
+$PG{"mustang"}{"type"}="structure_pairwise_aligner";
+$PG{"mustang"}{"ADDRESS"}="http://www.cs.mu.oz.au/~arun/mustang";
+$PG{"mustang"}{"language"}="C++";
+$PG{"mustang"}{"language2"}="CXX";
+$PG{"mustang"}{"source"}="http://ww2.cs.mu.oz.au/~arun/mustang/mustang_v3.2.1.tgz";
+$PG{"mustang"}{"mode"}="expresso,3dcoffee";
+$PG{"mustang"}{"version"}="3.2.1";
+$PG{"lsqman"}{"4_TCOFFEE"}="LSQMAN";
+$PG{"lsqman"}{"type"}="structure_pairwise_aligner";
+$PG{"lsqman"}{"ADDRESS"}="empty";
+$PG{"lsqman"}{"language"}="empty";
+$PG{"lsqman"}{"language2"}="empty";
+$PG{"lsqman"}{"source"}="empty";
+$PG{"lsqman"}{"update_action"}="never";
+$PG{"lsqman"}{"mode"}="expresso,3dcoffee";
+$PG{"align_pdb"}{"4_TCOFFEE"}="ALIGN_PDB";
+$PG{"align_pdb"}{"type"}="structure_pairwise_aligner";
+$PG{"align_pdb"}{"ADDRESS"}="empty";
+$PG{"align_pdb"}{"language"}="empty";
+$PG{"align_pdb"}{"language2"}="empty";
+$PG{"align_pdb"}{"source"}="empty";
+$PG{"align_pdb"}{"update_action"}="never";
+$PG{"align_pdb"}{"mode"}="expresso,3dcoffee";
+$PG{"fugueali"}{"4_TCOFFEE"}="FUGUE";
+$PG{"fugueali"}{"type"}="structure_pairwise_aligner";
+$PG{"fugueali"}{"ADDRESS"}="http://www-cryst.bioc.cam.ac.uk/fugue/download.html";
+$PG{"fugueali"}{"language"}="empty";
+$PG{"fugueali"}{"language2"}="empty";
+$PG{"fugueali"}{"source"}="empty";
+$PG{"fugueali"}{"update_action"}="never";
+$PG{"fugueali"}{"mode"}="expresso,3dcoffee";
+$PG{"dalilite.pl"}{"4_TCOFFEE"}="DALILITEc";
+$PG{"dalilite.pl"}{"type"}="structure_pairwise_aligner";
+$PG{"dalilite.pl"}{"ADDRESS"}="built_in";
+$PG{"dalilite.pl"}{"ADDRESS2"}="http://www.ebi.ac.uk/Tools/webservices/services/dalilite";
+$PG{"dalilite.pl"}{"language"}="Perl";
+$PG{"dalilite.pl"}{"language2"}="Perl";
+$PG{"dalilite.pl"}{"source"}="empty";
+$PG{"dalilite.pl"}{"update_action"}="never";
+$PG{"dalilite.pl"}{"mode"}="expresso,3dcoffee";
+$PG{"probconsRNA"}{"4_TCOFFEE"}="PROBCONSRNA";
+$PG{"probconsRNA"}{"type"}="RNA_multiple_aligner";
+$PG{"probconsRNA"}{"ADDRESS"}="http://probcons.stanford.edu/";
+$PG{"probconsRNA"}{"language"}="C++";
+$PG{"probconsRNA"}{"language2"}="CXX";
+$PG{"probconsRNA"}{"source"}="http://probcons.stanford.edu/probconsRNA.tar.gz";
+$PG{"probconsRNA"}{"mode"}="mcoffee,rcoffee";
+$PG{"probconsRNA"}{"version"}="1.0";
+$PG{"sfold"}{"4_TCOFFEE"}="CONSAN";
+$PG{"sfold"}{"type"}="RNA_pairwise_aligner";
+$PG{"sfold"}{"ADDRESS"}="http://selab.janelia.org/software/consan/";
+$PG{"sfold"}{"language"}="empty";
+$PG{"sfold"}{"language2"}="empty";
+$PG{"sfold"}{"source"}="empty";
+$PG{"sfold"}{"update_action"}="never";
+$PG{"sfold"}{"mode"}="rcoffee";
+$PG{"RNAplfold"}{"4_TCOFFEE"}="RNAPLFOLD";
+$PG{"RNAplfold"}{"type"}="RNA_secondarystructure_predictor";
+$PG{"RNAplfold"}{"ADDRESS"}="http://www.tbi.univie.ac.at/~ivo/RNA/";
+$PG{"RNAplfold"}{"language"}="C";
+$PG{"RNAplfold"}{"language2"}="C";
+$PG{"RNAplfold"}{"source"}="http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-1.7.2.tar.gz";
+$PG{"RNAplfold"}{"mode"}="rcoffee,";
+$PG{"RNAplfold"}{"version"}="1.7.2";
+$PG{"retree"}{"4_TCOFFEE"}="PHYLIP";
+$PG{"retree"}{"type"}="RNA_secondarystructure_predictor";
+$PG{"retree"}{"ADDRESS"}="http://evolution.gs.washington.edu/phylip/";
+$PG{"retree"}{"language"}="C";
+$PG{"retree"}{"language2"}="C";
+$PG{"retree"}{"source"}="http://evolution.gs.washington.edu/phylip/download/phylip-3.69.tar.gz";
+$PG{"retree"}{"mode"}="trmsd,";
+$PG{"retree"}{"version"}="3.69";
+$PG{"hmmtop"}{"4_TCOFFEE"}="HMMTOP";
+$PG{"hmmtop"}{"type"}="protein_secondarystructure_predictor";
+$PG{"hmmtop"}{"ADDRESS"}="www.enzim.hu/hmmtop/";
+$PG{"hmmtop"}{"language"}="C";
+$PG{"hmmtop"}{"language2"}="C";
+$PG{"hmmtop"}{"source"}="empty";
+$PG{"hmmtop"}{"update_action"}="never";
+$PG{"hmmtop"}{"mode"}="tcoffee";
+$PG{"gorIV"}{"4_TCOFFEE"}="GOR4";
+$PG{"gorIV"}{"type"}="protein_secondarystructure_predictor";
+$PG{"gorIV"}{"ADDRESS"}="http://mig.jouy.inra.fr/logiciels/gorIV/";
+$PG{"gorIV"}{"language"}="C";
+$PG{"gorIV"}{"language2"}="C";
+$PG{"gorIV"}{"source"}="http://mig.jouy.inra.fr/logiciels/gorIV/GOR_IV.tar.gz";
+$PG{"gorIV"}{"update_action"}="never";
+$PG{"gorIV"}{"mode"}="tcoffee";
+$PG{"wublast.pl"}{"4_TCOFFEE"}="EBIWUBLASTc";
+$PG{"wublast.pl"}{"type"}="protein_homology_predictor";
+$PG{"wublast.pl"}{"ADDRESS"}="built_in";
+$PG{"wublast.pl"}{"ADDRESS2"}="http://www.ebi.ac.uk/Tools/webservices/services/wublast";
+$PG{"wublast.pl"}{"language"}="Perl";
+$PG{"wublast.pl"}{"language2"}="Perl";
+$PG{"wublast.pl"}{"source"}="empty";
+$PG{"wublast.pl"}{"update_action"}="never";
+$PG{"wublast.pl"}{"mode"}="psicoffee,expresso,accurate";
+$PG{"blastpgp.pl"}{"4_TCOFFEE"}="EBIBLASTPGPc";
+$PG{"blastpgp.pl"}{"type"}="protein_homology_predictor";
+$PG{"blastpgp.pl"}{"ADDRESS"}="built_in";
+$PG{"blastpgp.pl"}{"ADDRESS2"}="http://www.ebi.ac.uk/Tools/webservices/services/blastpgp";
+$PG{"blastpgp.pl"}{"language"}="Perl";
+$PG{"blastpgp.pl"}{"language2"}="Perl";
+$PG{"blastpgp.pl"}{"source"}="empty";
+$PG{"blastpgp.pl"}{"update_action"}="never";
+$PG{"blastpgp.pl"}{"mode"}="psicoffee,expresso,accurate";
+$PG{"blastcl3"}{"4_TCOFFEE"}="NCBIWEBBLAST";
+$PG{"blastcl3"}{"type"}="protein_homology_predictor";
+$PG{"blastcl3"}{"ADDRESS"}="ftp://ftp.ncbi.nih.gov/blast/executables/LATEST";
+$PG{"blastcl3"}{"language"}="C";
+$PG{"blastcl3"}{"language2"}="C";
+$PG{"blastcl3"}{"source"}="empty";
+$PG{"blastcl3"}{"update_action"}="never";
+$PG{"blastcl3"}{"mode"}="psicoffee,expresso,3dcoffee";
+$PG{"blastall"}{"4_TCOFFEE"}="blastall";
+$PG{"blastall"}{"type"}="protein_homology_predictor";
+$PG{"blastall"}{"ADDRESS"}="ftp://ftp.ncbi.nih.gov/blast/executables/LATEST";
+$PG{"blastall"}{"language"}="C";
+$PG{"blastall"}{"language2"}="C";
+$PG{"blastall"}{"source"}="empty";
+$PG{"blastall"}{"update_action"}="never";
+$PG{"blastall"}{"mode"}="psicoffee,expresso,3dcoffee";
+$PG{"legacy_blast.pl"}{"4_TCOFFEE"}="NCBIBLAST";
+$PG{"legacy_blast.pl"}{"type"}="protein_homology_predictor";
+$PG{"legacy_blast.pl"}{"ADDRESS"}="ftp://ftp.ncbi.nih.gov/blast/executables/LATEST";
+$PG{"legacy_blast.pl"}{"language"}="C";
+$PG{"legacy_blast.pl"}{"language2"}="C";
+$PG{"legacy_blast.pl"}{"source"}="empty";
+$PG{"legacy_blast.pl"}{"update_action"}="never";
+$PG{"legacy_blast.pl"}{"mode"}="psicoffee,expresso,3dcoffee";
+$PG{"SOAP::Lite"}{"4_TCOFFEE"}="SOAPLITE";
+$PG{"SOAP::Lite"}{"type"}="library";
+$PG{"SOAP::Lite"}{"ADDRESS"}="http://cpansearch.perl.org/src/MKUTTER/SOAP-Lite-0.710.08/Makefile.PL";
+$PG{"SOAP::Lite"}{"language"}="Perl";
+$PG{"SOAP::Lite"}{"language2"}="Perl";
+$PG{"SOAP::Lite"}{"source"}="empty";
+$PG{"blastpgp"}{"update_action"}="never";
+$PG{"SOAP::Lite"}{"mode"}="none";
+$PG{"XML::Simple"}{"4_TCOFFEE"}="XMLSIMPLE";
+$PG{"XML::Simple"}{"type"}="library";
+$PG{"XML::Simple"}{"ADDRESS"}="http://search.cpan.org/~grantm/XML-Simple-2.18/lib/XML/Simple.pm";
+$PG{"XML::Simple"}{"language"}="Perl";
+$PG{"XML::Simple"}{"language2"}="Perl";
+$PG{"XML::Simple"}{"source"}="empty";
+$PG{"XML::Simple"}{"mode"}="psicoffee,expresso,accurate";
+$MODE{"tcoffee"}{"name"}="tcoffee";
+$MODE{"rcoffee"}{"name"}="rcoffee";
+$MODE{"3dcoffee"}{"name"}="3dcoffee";
+$MODE{"mcoffee"}{"name"}="mcoffee";
+$MODE{"expresso"}{"name"}="expresso";
+$MODE{"trmsd"}{"name"}="trmsd";
+$MODE{"accurate"}{"name"}="accurate";
+$MODE{"seq_reformat"}{"name"}="seq_reformat";
+#TclinkdbEnd End tag for the list updating
+
+########### Compilers ##############################
+#
+#
+
+$PG{C}{compiler}="gcc";
+$PG{C}{compiler_flag}="CC";
+$PG{C}{options}="";
+$PG{C}{options_flag}="CFLAGS";
+$PG{C}{type}="compiler";
+
+$PG{"CXX"}{compiler}="g++";
+$PG{"CXX"}{compiler_flag}="CXX";
+$PG{"CXX"}{options}="";
+$PG{"CXX"}{options_flag}="CXXFLAGS";
+$PG{CXX}{type}="compiler";
+
+$PG{"CPP"}{compiler}="g++";
+$PG{"CPP"}{compiler_flag}="CPP";
+$PG{"CPP"}{options}="";
+$PG{"CPP"}{options_flag}="CPPFLAGS";
+$PG{CPP}{type}="compiler";
+
+$PG{"GPP"}{compiler}="g++";
+$PG{"GPP"}{compiler_flag}="GPP";
+$PG{"GPP"}{options}="";
+$PG{"GPP"}{options_flag}="CFLAGS";
+$PG{GPP}{type}="compiler";
+
+$PG{Fortran}{compiler}="g77";
+$PG{Fortran}{compiler_flag}="FCC";
+$PG{Fortran}{type}="compiler";
+
+$PG{Perl}{compiler}="CPAN";
+$PG{Perl}{type}="compiler";
+
+$SUPPORTED_OS{macox}="Macintosh";
+$SUPPORTED_OS{linux}="Linux";
+$SUPPORTED_OS{windows}="Cygwin";
+
+
+
+$MODE{t_coffee}{description}=" for regular multiple sequence alignments";
+$MODE{rcoffee} {description}=" for RNA multiple sequence alignments";
+
+$MODE{psicoffee} {description}=" for Homology Extended multiple sequence alignments";
+$MODE{expresso}{description}=" for very accurate structure based multiple sequence alignments";
+$MODE{"3dcoffee"}{description}=" for multiple structure alignments";
+$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
+";
+
+
+&post_process_PG();
+return;
+}
+
+sub post_process_PG
+ {
+ my $p;
+
+ %PG=&name2dname (%PG);
+ %MODE=&name2dname(%MODE);
+ foreach $p (keys(%PG)){if ( $PG{$p}{type} eq "compiler"){$PG{$p}{update_action}="never";}}
+
+ }
+
+sub name2dname
+ {
+ my (%L)=(@_);
+ my ($l, $ml);
+
+ foreach my $pg (keys(%L))
+ {
+ $l=length ($pg);
+ if ( $l>$ml){$ml=$l;}
+ }
+ $ml+=1;
+ foreach my $pg (keys(%L))
+ {
+ my $name;
+ $l=$ml-length ($pg);
+ $name=$pg;
+ for ( $b=0; $b<$l; $b++)
+ {
+ $name .=" ";
+ }
+ $L{$pg}{dname}=$name;
+ }
+ return %L;
+ }
+
+sub env_file2putenv
+ {
+ my $f=@_[0];
+ my $F=new FileHandle;
+ my $n;
+
+ open ($F, "$f");
+ while (<$F>)
+ {
+ my $line=$_;
+ my($var, $value)=($_=~/(\S+)\=(\S*)/);
+ $ENV{$var}=$value;
+ $ENV_SET{$var}=1;
+ $n++;
+ }
+ close ($F);
+ return $n;
+ }
+
+sub replace_line_in_file
+ {
+ my ($file, $wordin, $wordout)=@_;
+ my $O=new FileHandle;
+ my $I=new FileHandle;
+ my $l;
+ if (!-e $file){return;}
+
+ system ("mv $file $file.old");
+ open ($O, ">$file");
+ open ($I, "$file.old");
+ while (<$I>)
+ {
+ $l=$_;
+ if (!($l=~/$wordin/)){print $O "$l";}
+ elsif ( $wordout ne ""){$l=~s/$wordin/$wordout/g;print $O "$l";}
+ }
+ close ($O);
+ close ($I);
+ return;
+ }
+
+sub add_C_libraries
+ {
+ my ($file,$first,@list)=@_;
+
+ my $O=new FileHandle;
+ my $I=new FileHandle;
+ my ($l,$anchor);
+ if (!-e $file){return;}
+
+ $anchor="#include <$first>";
+
+ system ("mv $file $file.old");
+ open ($O, ">$file");
+ open ($I, "$file.old");
+ while (<$I>)
+ {
+ $l=$_;
+ print $O "$l";
+ if (!($l=~/$anchor/))
+ {
+
+ foreach my $lib (@list)
+ {
+ print $O "#include <$lib>\n";
+ }
+ }
+ }
+ close ($O);
+ close ($I);
+ return;
+ }
git://source.jalview.org / jabaws.git / blobdiff