Add SS prediction for multiple aligment into jpred.pl. Before this was a part of...

[jabaws.git] / binaries / src / jpred / lib / Paths.pm

diff --git a/binaries/src/jpred/lib/Paths.pm b/binaries/src/jpred/lib/Paths.pm
index 9fa5ca3..9a51953 100644 (file)
--- a/binaries/src/jpred/lib/Paths.pm
+++ b/binaries/src/jpred/lib/Paths.pm
@@ -33,6 +33,8 @@ our @EXPORT_OK = qw(
   $hmmbuild
   $hmmconvert
   $psiblastbin
+  $alscript
+  $readseq
   check_OS
   setup_env
 );
@@ -58,6 +60,8 @@ our $fastacmd    = "$SOFTDIR/$platform_name/fastacmd";
 our $hmmbuild    = "$SOFTDIR/$platform_name/hmmbuild";
 our $hmmconvert  = "$SOFTDIR/$platform_name/hmmconvert";
 our $psiblastbin = "$SOFTDIR/$platform_name/blastpgp";
+our $alscript    = "$SOFTDIR/$platform_name/alscript";
+our $readseq     = "$SOFTDIR/$platform_name/readseq";
 
 # required for training with SNNS, but unused currently
 our $ff_bignet = "$HOME/projects/Jnet/bin/snns/ff_bignet";    # CC modified for new path (SNNS app)
@@ -87,6 +91,8 @@ sub setup_env {
   $hmmbuild    = "$SOFTDIR/$platform_name/hmmbuild";
   $psiblastbin = "$SOFTDIR/$platform_name/blastpgp";
   $hmmconvert  = "$SOFTDIR/$platform_name/hmmconvert";
+  $alscript    = "$SOFTDIR/$platform_name/alscript";
+  $readseq     = "$SOFTDIR/$platform_name/readseq";
 }
 
 sub check_OS {
@@ -103,8 +109,6 @@ sub check_OS {
     warn "check_OS: unknown platform, I'll try to use x86_64 binaries....";
   }
 
-#  print "\n\ncheck_OS: SOFTDIR -> $SOFTDIR\n\n";
-
   $oc          = "$SOFTDIR/$platform_name/oc";
   $jnet        = "$SOFTDIR/$platform_name/jnet";
   $fastacmd    = "$SOFTDIR/$platform_name/fastacmd";
@@ -112,6 +116,8 @@ sub check_OS {
   $hmmbuild    = "$SOFTDIR/$platform_name/hmmbuild";
   $psiblastbin = "$SOFTDIR/$platform_name/blastpgp";
   $hmmconvert  = "$SOFTDIR/$platform_name/hmmconvert";
+  $alscript    = "$SOFTDIR/$platform_name/alscript";
+  $readseq     = "$SOFTDIR/$platform_name/readseq";
 
   return $platform_name;
 }