Commit 87d5e99e authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 13.30.0.6a5203f

parent c1276b4a

bin/linux/t_coffee

0 → 100755
+4.33 MiB

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install

+145 −42
Original line number Diff line number Diff line
@@ -9,7 +9,11 @@ use strict; 


our (%MODE, %PG, %ENV_SET, %SUPPORTED_OS);





#DO NOT EDIT MANUALLY START

#To be populated with edit_version.pl

our $VERSION="0";

our $VERSION="Version_13.30.0.6a5203f";#POPULATED by edit_version.pl from #_#UPDATE_VERSION

#DO NOT EDIT MANUALLY END

our $EXIT_SUCCESS=0;

our $EXIT_FAILURE=1;

our $INTERNET=0;
@@ -37,6 +41,8 @@ our $TCMETHODS; 
our $TCPLUGINS;

our $PLUGINS_DIR="";

our $INSTALL_DIR="";

our $email;

our $recompile;



###########   DEFINITIONS ##############################

#
@@ -64,7 +70,6 @@ my @smode=("all", "clean", "install"); 


########################################################

&initialize_PG();



#Parse The Command Line

my $cl=join( " ", @ARGV);

if ($#ARGV==-1 || ($cl=~/-h/) ||($cl=~/-H/) )
@@ -88,6 +93,8 @@ if (($cl=~/-h/) ||($cl=~/-H/) ) 
    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] -recompile            [forces the recompilation of T-Coffee]\n";



    print "!!!!!!! ./install [optional:target] -force                [Forces recompilation over everything]\n";

    

    print "!!!!!!! ./install [optional:target] -root                 [You are running as root]\n";
@@ -96,8 +103,11 @@ if (($cl=~/-h/) ||($cl=~/-H/) ) 
    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] -tcdir=/foor/bar      [base path where T-Coffee will be installed - default ~/.t_coffee]\n";

    print "!!!!!!! ./install [optional:target] -repo=/path/to/repo   [binaries repository root directory]\n";

    print "!!!!!!! ./install [optional:target] -email=<your email>   [needed for remote BLAST]\n";

    print "!!!!!!! ./install [optional:target] -proxy=<proxy>   [may be needed to access remote services]\n";

    

    print "!!!!!!! mode:";

    foreach $m (keys(%MODE)){print "$m ";}

    print "\n";
@@ -128,7 +138,12 @@ our ($ROOT_INSTALL, $NO_QUESTION, $default_update_action,$BINARIES_ONLY,$force, 
if ( ($cl=~/-root/)){$ROOT_INSTALL=1;}

if ( ($cl=~/-no_question/)){$NO_QUESTION=1;}

if ( ($cl=~/-update/)){$default_update_action="update";}

if ( ($cl=~/-recompile/)){$recompile=1;}





#By defualt the program will attempt to install packages from binaries maintained on www.tcoffee.org

$BINARIES_ONLY=1;



if ( ($cl=~/-nobinaries/)){$BINARIES_ONLY=0;}

if ( ($cl=~/-force/)){$force=1;$default_update_action="update"}

if ( ($cl=~/-exec=\s*(\S+)/)){$INSTALL_DIR=$1;}
@@ -140,6 +155,10 @@ if ( ($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; }



if ( ($cl=~/-email=\s*(\S+)/)){$email=$1;}





#automated update

if ($tclinkdb){&update_tclinkdb ($tclinkdb);}
@@ -162,10 +181,10 @@ if(!$TCDIR) { $TCDIR="$HOME/.t_coffee"; } 
#Prepare the Installation Structure



our $BASE="$CD/bin";

our $BIN="$BASE/binaries/$OS";

our $DOWNLOAD_DIR="$BASE/download";

our $BIN="$BASE/cache/binaries/$OS";

our $DOWNLOAD_DIR="$BASE/cache/download";

our $DOWNLOAD_FILE="$DOWNLOAD_DIR/files";

our $TMP="$BASE/tmp";

our $TMP="$BASE/cache/tmp";



&add_dir($BASE);

&add_dir($BIN);
@@ -181,7 +200,7 @@ if (!$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);}

if    (!$INSTALL_DIR && !$ROOT_INSTALL){$INSTALL_DIR="$TCDIR/bin/$OS";mkpath ($INSTALL_DIR);}

elsif (!$INSTALL_DIR &&  $ROOT_INSTALL){$INSTALL_DIR="/usr/local/bin/";}



#prepare mcoffee files [Only if vanilla installation]
@@ -189,9 +208,15 @@ if (-d "mcoffee"){`cp mcoffee/* $TCM`;} 




#prepare the environement

our $ENV_FILE="$TCDIR/t_coffee_env";

our $ENV_FILE="$TCDIR/.t_coffee_env";

unlink ($ENV_FILE);

&add2env_file ($ENV_FILE,"EMAIL_4_TCOFFEE", $email);

&add2env_file ($ENV_FILE,"http_proxy_4_TCOFFEE", $proxy);

&env_file2putenv ($ENV_FILE);

&set_proxy($proxy);







my ($target, $p, $r);

$target=$p;
@@ -395,12 +420,21 @@ if ($failure) 
print "*********************************************************************\n";

print "********              FINALIZE YOUR INSTALLATION    *****************\n";

print "*********************************************************************\n";

print "------- Your executables are in:\n"; 

print "------- Your third party 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";

print "------- Your t_coffee exccutable is in\n";

print "-------       $INSTALL_DIR:\n";

print "------- In order to make your installation permanent add these two lines\n";

print "-------       export PATH=$INSTALL_DIR:\$PATH\n";

print "-------       export PLUGINS_4_TCOFFEE=$PLUGINS_DIR:\n";

if ($OS eq "linux")

  {

    print "-------       to the file: $HOME/.bashrc\n";

  }

else 

  {

    print "-------       to the file: $HOME/.profile\n";

  }

exit ($EXIT_SUCCESS);  

  

#################################################################################
@@ -506,7 +540,7 @@ sub url2file 
	exit ($EXIT_FAILURE);

      }

    

    if     (&pg_is_installed    ("wget")){$pg="wget"; $flag="-O";$arg="--tries=2 --connect-timeout=10 $wget_arg";}

    if     (&pg_is_installed    ("wget")){$pg="wget"; $flag="-O";$arg="--tries=2 --connect-timeout=10 --no-check-certificate $wget_arg";}

    elsif  (&pg_is_installed    ("curl")){$pg="curl"; $flag="-o";$arg=$curl_arg;}

    else

      {
@@ -561,14 +595,22 @@ sub install 
    

    if (!$ROOT_INSTALL)

      {

	

	if (-e "$BIN/t_coffee"){`$CP $BIN/t_coffee $INSTALL_DIR`};

	`cp $BIN/* $PLUGINS_DIR`;

	`$CP $BIN/* $PLUGINS_DIR`;

	if (-e "$BIN/t_coffee")

	  {

	    `$CP $BIN/t_coffee $INSTALL_DIR`;

	      unlink("$PLUGINS_DIR/t_coffee");

	  }

	$copied=1;

      }

    else

      {

	$copied=&root_run ("You must be root to finalize the installation", "$CP $BIN/* $INSTALL_DIR $SILENT");

	$copied=&root_run ("You must be root to finalize the installation", "$CP $BIN/* $PLUGINS_DIR $SILENT");

	if (-e "$BIN/t_coffee")

	  {

	    &root_run ("You must be root to finalize the installation", "$CP $BIN/t_coffee $INSTALL_DIR");

	    &root_run ("You must be root to finalize the installation", "rm  $PLUGINS_DIR/t_coffee");

	  }

      }
@@ -582,10 +624,18 @@ sub install 
    }

  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= "*!!!!!! T-Coffee has been installed in $INSTALL_DIR\n";

      $report= "*!!!!!! T-Coffee and associated packages have been copied in: $PLUGINS_DIR\n";

      $report.="*!!!!!! This T-Coffee location is NOT on your PATH sytem variable\n";

      if ( $OS eq "linux")

	{

	  $report.="*!!!!!! You can do so by adding the following line in your ~/.bashrc file:\n";

      $report.="*!!!!!! export PATH=$new_bin:\$PATH\n";

	}

      else

	{

	  $report.="*!!!!!! You can do so by adding the following line in your ~/.profile file:\n";

	}

      $report.="*!!!!!! export PATH=$INSTALL_DIR:\$PATH\n";

    }

  return $report;

}
@@ -606,7 +656,7 @@ sub sign_license_ni 
#                                                                               #

#                                                                               #

#                                                                               #

#                   INDIVIDUAL MULTIPLE SEQUENCE ALIGNMNT PACKAGES INSTALLATION #

#                  INDIVIDUAL MULTIPLE SEQUENCE ALIGNMENT PACKAGES INSTALLATION #

#                                                                               #

#                                                                               #

#                                                                               #
@@ -632,7 +682,7 @@ sub install_pg 
	$PG{$pg}{old}=$previous;

	

	if ($PG{$pg} {language2} eq "Perl"){&install_perl_package ($pg);}

	elsif ($pg ne "t_coffee" && $BINARIES_ONLY && &install_binary_package ($pg)){$PG{$pg}{from_binary}=1;}

	elsif ($BINARIES_ONLY && &install_binary_package ($pg)){$PG{$pg}{from_binary}=1;}

	elsif (&install_source_package ($pg)){;}

	else 

	  {
@@ -677,7 +727,7 @@ sub install_source_package 
    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;}

    if ( $default_update_action ne "update" && (-e "$BIN/$pg" || -e "$BIN/$pg.exe" )  ){return 1;}

    

    #

    # check if the module exists in the repository cache
@@ -686,7 +736,7 @@ sub install_source_package 
		return 1;

	}

    

    if ($pg eq "t_coffee")  {return   &install_t_coffee ($pg);}

    if ($pg eq "t_coffee")  {return   &install_t_coffee_source ($pg);}

    elsif ($pg eq "TMalign"){return   &install_TMalign ($pg);}

    

    chdir $DISTRIBUTIONS;
@@ -742,7 +792,7 @@ sub install_source_package 
	print "\n------- unzipping/untaring $name\n";

	if (($ext =~/z/))

	  { 

	    &flush_command ("gunzip $name$ext");

	    &flush_command ("gunzip -f $name$ext");

	    

	  }

	if (($ext =~/tar/) || ($ext =~/tgz/))
@@ -1105,10 +1155,11 @@ sub install_source_package 
    return &pg_is_installed ($pg, $BIN);

  }



sub install_t_coffee

sub install_t_coffee_source

  {

    my ($pg)=(@_);

    my ($report,$cflags, $arguments, $language, $compiler) ;



    #1-Install T-Coffee

    chdir "t_coffee_source";

    &flush_command ("make clean");
@@ -1116,7 +1167,8 @@ sub install_t_coffee 
    $language=$PG{$pg} {language2};

    $arguments=$PG{$language}{arguments};

    

    if ( $CC ne ""){

    if ( $CC ne "")

      {

	print "make -i $arguments t_coffee \n";

	&flush_command ("make -i $arguments t_coffee");

      }
@@ -1150,6 +1202,8 @@ sub pg_has_binary_distrib 
    my ($pg)=(@_);

    if ($PG{$pg}{windows}){return 1;}

    elsif ($PG{$pg}{osx}){return 1;}

    elsif ($PG{$pg}{macosx}){return 1;}



    elsif ($PG{$pg}{linux}){return 1;}

    return 0;

  }
@@ -1172,8 +1226,26 @@ sub install_binary_package 
    if (!&supported_os($OS)){return 0;}

    if ( $PG{$pg}{binary}){$name=$PG{$pg}{binary};}

    else {$name=$pg;}

    

    $download="$WEB_BASE/Packages/Binaries/$OS/$name";

    if ($name eq "t_coffee")

      {

	#check if local bin is there

	if (-e "./bin/$OS/t_coffee")

	  {

	    print "\n------- Installing  T-Coffee from Pre-Compiled/Pre-Downloaded $OS binary\n";

	    print "\n------- If you want to trigger a fresh compilation use -recompile\n";

	    &check_cp ("./bin/$OS/t_coffee", $BIN);

	    return &pg_is_installed ($pg, $BIN);

	  }

	#try to get precompiled binary -- available from MAC is distribution from MAC

	else

	  {

	    $download="$WEB_BASE/Packages/Binaries/tcoffee/$OS/$name.$VERSION";

	  }

      }

    else

      {

	$download="$WEB_BASE/Packages/Binaries/plugins/$OS/$name";

      }

    

    $base=cwd();

    chdir $TMP;
@@ -1191,13 +1263,14 @@ sub install_binary_package 
      {

	print "!!!!!!! $PG{$pg}{dname}: Download of $pg binary failed\n";

	print "!!!!!!! $PG{$pg}{dname}: Check Address: $download\n";

	chdir $base;

	return 0;

      }

    print "\n------- Installing $pg\n";

    

    if ($name =~/tar\.gz/)

      {

	`gunzip  $name`;

	`gunzip  -f $name`;

	`tar -xvf $pg.tar`;

	chdir $pg;

	`chmod u+x *`;
@@ -1212,9 +1285,11 @@ sub install_binary_package 
      }

    chdir $base;

    $PG{$pg}{from_binary}=1;



    return &pg_is_installed ($pg, $BIN);

  }



	

################################################################################

#                                                                               #

#                                                                               #
@@ -1478,6 +1553,29 @@ sub supported_os 
    return $SUPPORTED_OS{$os};

  }



sub add2env_file

  {

    my ($env, $var, $value)=(@_);

    my $F = new FileHandle;

    my $t;

    if (!$value){return;}

    #make sure new variables do not get duplicated

    if ( -e $env)

      {

	open ($F, "$env");

	while (<$F>)

	  {

	    my $line=$_;

	    if (!($line=~/$var/)){$t.=$line;}

	  }

	close ($F);

      }

    $t.="$var=$value\n";

    open ($F, ">$env");

    print $F "$t";

    $ENV{$var}=$value;

    close ($F);

  }    

    

################################################################################

#                                                                               #
@@ -1545,8 +1643,9 @@ $PG{"t_coffee"}{"type"}="sequence_multiple_aligner"; 
$PG{"t_coffee"}{"ADDRESS"}="http://www.tcoffee.org";

$PG{"t_coffee"}{"language"}="C++";

$PG{"t_coffee"}{"language2"}="CXX";

$PG{"t_coffee"}{"source"}="http://www.tcoffee.org/Packages/Stable/Latest/T-COFFEE_distribution.tar.gz";

$PG{"t_coffee"}{"source"}="http://www.tcoffee.org/Packages/sources/tcoffee/stable/T-COFFEE_distribution.tar.gz";

$PG{"t_coffee"}{"update_action"}="always";

$PG{"t_coffee"}{"binary"}="t_coffee";

$PG{"t_coffee"}{"mode"}="tcoffee,mcoffee,rcoffee,expresso,3dcoffee";

$PG{"clustalo"}{"4_TCOFFEE"}="CLUSTALO";

$PG{"clustalo"}{"type"}="sequence_multiple_aligner";
@@ -1565,6 +1664,7 @@ $PG{"strike"}{"language2"}="CXX"; 
$PG{"strike"}{"source"}="http://www.tcoffee.org/Projects/strike/strike_v1.2.tar.bz2";

$PG{"strike"}{"mode"}="tcoffee,expresso";

$PG{"strike"}{"version"}="1.2";

$PG{"strike"}{"binary"}="strike";

$PG{"clustalw2"}{"4_TCOFFEE"}="CLUSTALW2";

$PG{"clustalw2"}{"type"}="sequence_multiple_aligner";

$PG{"clustalw2"}{"ADDRESS"}="http://www.clustal.org";
@@ -1572,6 +1672,7 @@ $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"}{"binary"}="clustalw2";

$PG{"clustalw2"}{"version"}="2.0.10";

$PG{"clustalw"}{"4_TCOFFEE"}="CLUSTALW";

$PG{"clustalw"}{"type"}="sequence_multiple_aligner";
@@ -1581,6 +1682,7 @@ $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{"clustalw"}{"binary"}="clustalw";

$PG{"dialign-t"}{"4_TCOFFEE"}="DIALIGNT";

$PG{"dialign-t"}{"type"}="sequence_multiple_aligner";

$PG{"dialign-t"}{"ADDRESS"}="http://dialign-tx.gobics.de/";
@@ -1729,6 +1831,7 @@ $PG{"sap"}{"language2"}="C"; 
$PG{"sap"}{"source"}="https://github.com/jkleinj/SAP/archive/v.1.1.3.tar.gz";

$PG{"sap"}{"mode"}="expresso,3dcoffee";

$PG{"sap"}{"version"}="1.1.3";

$PG{"sap"}{"binary"}="sap";

$PG{"TMalign"}{"4_TCOFFEE"}="TMALIGN";

$PG{"TMalign"}{"type"}="structure_pairwise_aligner";

$PG{"TMalign"}{"ADDRESS"}="http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.f";
@@ -1821,7 +1924,7 @@ $PG{"hmmtop"}{"language2"}="C"; 
$PG{"hmmtop"}{"source"}="http://www.tcoffee.org/Packages/mirrors/hmmtop2.1.tgz";

$PG{"hmmtop"}{"binary"}="hmmtop";

$PG{"hmmtop"}{"update_action"}="never";

$PG{"hmmtop"}{"mode"}="tcoffee";

$PG{"hmmtop"}{"mode"}="psicoffee";

$PG{"hmmtop"}{"version"}="2.1";

$PG{"gorIV"}{"4_TCOFFEE"}="GOR4";

$PG{"gorIV"}{"type"}="protein_secondarystructure_predictor";
@@ -1880,7 +1983,7 @@ $PG{"XML::Simple"}{"language"}="Perl"; 
$PG{"XML::Simple"}{"language2"}="Perl";

$PG{"XML::Simple"}{"source"}="empty";

$PG{"XML::Simple"}{"mode"}="psicoffee,expresso,accurate";

$PG{"x3dna"}{"4_TCOFFEE"}="x3dna-ssr";

$PG{"x3dna"}{"4_TCOFFEE"}="x3dna";

$PG{"x3dna"}{"type"}="RNA_secondarystructure_predictor";

$PG{"x3dna"}{"ADDRESS"}="http://x3dna.bio.columbia.edu/";

$PG{"x3dna"}{"source"}="http://www.tcoffee.org/Packages/mirrors/source/x3dna-v2.3-linux-64bit.tar.gz";
@@ -1949,7 +2052,7 @@ $PG{Fortran}{type}="compiler"; 
$PG{Perl}{compiler}="CPAN";

$PG{Perl}{type}="compiler";



$SUPPORTED_OS{macox}="Macintosh";

$SUPPORTED_OS{macosx}="Macintosh";

$SUPPORTED_OS{linux}="Linux";

$SUPPORTED_OS{windows}="Cygwin";

license.txt

+1 −1
Original line number Diff line number Diff line 
-------------------------------COPYRIGHT NOTICE------------------------------/

  ACADEMIC LICENCE AGREEMENT



  © Centro de Regulacio Genomica and Cedric Notredame  ( 11 Dec 2018 - 09:27). 

  © Centro de Regulacio Genomica and Cedric Notredame  ( 30 Jul 2019 - 01:49). 

		    GNU GENERAL PUBLIC LICENSE

		       Version 2, June 1991

t_coffee_source/coffee_defines.h

+1 −1
Original line number Diff line number Diff line
@@ -2,7 +2,7 @@ 
/*  (c) Centro de Regulacio Genomica                                                        */

/*  and                                                                                     */

/*  Cedric Notredame                                                                        */

/*  11 Dec 2018 - 09:27.                                                                    */

/*  30 Jul 2019 - 01:49.                                                                    */

/*All rights reserved.                                                                      */

/*This file is part of T-COFFEE.                                                            */

/*                                                                                          */

t_coffee_source/data_headers/perl_header_lib.h

+1 −1
Original line number Diff line number Diff line
@@ -2,7 +2,7 @@ 
/*  (c) Centro de Regulacio Genomica                                                        */

/*  and                                                                                     */

/*  Cedric Notredame                                                                        */

/*  11 Dec 2018 - 09:27.                                                                    */

/*  30 Jul 2019 - 01:49.                                                                    */

/*All rights reserved.                                                                      */

/*This file is part of T-COFFEE.                                                            */

/*                                                                                          */