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JWS-112 Bumping version of T-Coffee to version 11.00.8cbe486.
[jabaws.git] / binaries / src / tcoffee / install
diff --git a/binaries/src/tcoffee/install b/binaries/src/tcoffee/install
index f3f5fc9..36bce79 100644 (file)
--- a/binaries/src/tcoffee/install
+++ b/binaries/src/tcoffee/install
@@ -48,7 +48,7 @@ our $CPP="g++";
 our $CPPFLAGS="";
 
 our $CC="gcc";
-our $CFLAGS="";
+our $CFLAGS=$ENV{'CFLAGS'};
 
 our $FC="f77";
 our $FFLAGS="";
@@ -245,7 +245,7 @@ $PG{C}{compiler}=get_C_compiler($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;}
+if ($CFLAGS ne "" ){$PG{C}{options}=$CFLAGS;}
 foreach my $c (keys(%PG))
   {
     my $arguments;
@@ -254,7 +254,7 @@ foreach my $c (keys(%PG))
        $arguments="$PG{$c}{compiler_flag}=$PG{$c}{compiler} ";
        if ($PG{$c}{options})
          {
-           $arguments.="$PG{$c}{options_flag}=$PG{$c}{options} ";
+           $arguments.="$PG{$c}{options_flag}='" . $PG{$c}{options} . "' ";
          }
        $PG{$c}{arguments}=$arguments;
       }
@@ -778,12 +778,6 @@ sub install_source_package
        if (-e "./configure")
          {
            #new sap distribution
-           if ($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");
@@ -811,6 +805,27 @@ sub install_source_package
        &check_cp ("./src/$pg", "$BIN");
        repo_store("./src/$pg");
       }
+
+    #
+    # CLUSTAL-OMEGA module
+    #
+    elsif ($pg eq "clustalo")
+      {
+       &flush_command("./configure");
+       &flush_command("make $arguments");
+       &check_cp ("./src/$pg", "$BIN");
+       repo_store("./src/$pg");
+      }
+
+    #
+    # STRIKE module
+    #
+    elsif ($pg eq "strike")
+      {
+       &flush_command("make $arguments");
+       &check_cp ("./bin/$pg", "$BIN");
+       repo_store("./bin/$pg");
+      }
     
     #
     # FSA module
@@ -1097,9 +1112,11 @@ sub install_t_coffee
     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");}
+    if ( $CC ne ""){
+      print "make -i $arguments t_coffee \n";
+      &flush_command ("make -i $arguments t_coffee");
+    }
     &check_cp ($pg, $BIN);
     
     chdir $CDIR;
@@ -1140,6 +1157,15 @@ sub install_binary_package
     my $isdir;
     &input_os();
     
+    #
+    # - paolodt - Check if the module exists in the repository cache 
+    #
+       if( repo_load($pg) ) {
+           $PG{$pg}{from_binary}=1;
+               return 1;
+       }
+    # - paolodt - end 
+    
     if (!&supported_os($OS)){return 0;}
     if ( $PG{$pg}{binary}){$name=$PG{$pg}{binary};}
     else 
@@ -1530,11 +1556,27 @@ sub initialize_PG
 $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"}{"language"}="C++";
+$PG{"t_coffee"}{"language2"}="CXX";
 $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{"clustalo"}{"4_TCOFFEE"}="CLUSTALO";
+$PG{"clustalo"}{"type"}="sequence_multiple_aligner";
+$PG{"clustalo"}{"ADDRESS"}="http://www.clustal.org/omega/";
+$PG{"clustalo"}{"language"}="C++";
+$PG{"clustalo"}{"language2"}="C++";
+$PG{"clustalo"}{"source"}="http://www.clustal.org/omega/clustal-omega-1.1.0.tar.gz";
+$PG{"clustalo"}{"mode"}="mcoffee";
+$PG{"clustalo"}{"version"}="1.1.0";
+$PG{"strike"}{"4_TCOFFEE"}="STRIKE";
+$PG{"strike"}{"type"}="sequence_alignment_scoring";
+$PG{"strike"}{"ADDRESS"}="http://www.tcoffee.org/Projects/strike/index.html";
+$PG{"strike"}{"language"}="C++";
+$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{"clustalw2"}{"4_TCOFFEE"}="CLUSTALW2";
 $PG{"clustalw2"}{"type"}="sequence_multiple_aligner";
 $PG{"clustalw2"}{"ADDRESS"}="http://www.clustal.org";
@@ -1664,7 +1706,7 @@ $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"}{"source"}="http://www.ebi.ac.uk/goldman-srv/prank/src/prank/prank.src.100802.tgz";
 $PG{"prank"}{"mode"}="mcoffee";
 $PG{"prank"}{"version"}="100303";
 $PG{"sap"}{"4_TCOFFEE"}="SAP";
@@ -1672,18 +1714,18 @@ $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"}{"source"}="http://mathbio.nimr.mrc.ac.uk/download/SAP/sap-1.1.3.tar.gz";
 $PG{"sap"}{"mode"}="expresso,3dcoffee";
-$PG{"sap"}{"version"}="1.1.1";
+$PG{"sap"}{"version"}="1.1.3";
 $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"}{"ADDRESS"}="http://zhanglab.ccmb.med.umich.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"}{"source"}="http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.f";
+$PG{"TMalign"}{"linux"}="http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign_32.gz";
 $PG{"TMalign"}{"mode"}="expresso,3dcoffee";
-$PG{"TMalign"}{"version"}="1.0";
+$PG{"TMalign"}{"version"}="2013.05.11";
 $PG{"mustang"}{"4_TCOFFEE"}="MUSTANG";
 $PG{"mustang"}{"type"}="structure_pairwise_aligner";
 $PG{"mustang"}{"ADDRESS"}="http://www.cs.mu.oz.au/~arun/mustang";
@@ -1763,8 +1805,10 @@ $PG{"hmmtop"}{"ADDRESS"}="www.enzim.hu/hmmtop/";
 $PG{"hmmtop"}{"language"}="C";
 $PG{"hmmtop"}{"language2"}="C";
 $PG{"hmmtop"}{"source"}="empty";
+$PG{"hmmtop"}{"binary"}="hmmtop";
 $PG{"hmmtop"}{"update_action"}="never";
 $PG{"hmmtop"}{"mode"}="tcoffee";
+$PG{"hmmtop"}{"version"}="2.1";
 $PG{"gorIV"}{"4_TCOFFEE"}="GOR4";
 $PG{"gorIV"}{"type"}="protein_secondarystructure_predictor";
 $PG{"gorIV"}{"ADDRESS"}="http://mig.jouy.inra.fr/logiciels/gorIV/";
@@ -1791,14 +1835,6 @@ $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";