+++ /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