JPRED-2 copy the portable branch into Git

[jpred.git] / jpred / lib / Paths.pm

diff --git a/jpred/lib/Paths.pm b/jpred/lib/Paths.pm
index 7ca2847..9a51953 100644 (file)
--- a/jpred/lib/Paths.pm
+++ b/jpred/lib/Paths.pm
@@ -11,34 +11,116 @@ Paths - Sets paths for executable programs
 
 =head1 DESCRIPTION
 
-This module gathers together all of the little pieces of information that would other wise be floating around in all of the other modules that run external programs. Namely, the path to the executable and nessecery environment variables. 
+This module gathers together all of the little pieces of information that would other wise be 
+floating around in all of the other modules that run external programs. Namely, the path to 
+the executable and nessecery environment variables. 
 
-Putting it all here should mean that this is the only file that needs updating when their location changes, or it's redeployed. Plus some degree of automagic can be used to try and detect changes.
+Putting it all here should mean that this is the only file that needs updating when their 
+location changes, or it's redeployed. Plus some degree of automagic can be used to try 
+and detect changes.
 
 =cut
 
-our @EXPORT_OK = qw($ff_bignet $analyze $batchman $sov $pairwise $oc $jnet $fastacmd $hmmbuild $hmmconvert $psiblastbin);
+our @EXPORT_OK = qw(
+  $ff_bignet
+  $analyze
+  $batchman
+  $sov
+  $pairwise
+  $oc
+  $jnet
+  $fastacmd
+  $hmmbuild
+  $hmmconvert
+  $psiblastbin
+  $alscript
+  $readseq
+  check_OS
+  setup_env
+);
 
 my $HOME = $ENV{HOME};
+#
 # main production path
-#my $BINDIR = '/homes/www-jpred/live/jpred/bin';
+#my $SOFTDIR = '/homes/www-jpred/live/jpred/bin';
+#my $platform_dir = "x86_64";
+#
 # development path
-my $BINDIR = '/homes/www-jpred/devel/jpred/bin';
-
-our $pairwise  = "$BINDIR/pairwise";  # CC modified for correct path
-our $oc        = "$BINDIR/oc";
-our $jnet      = "$BINDIR/jnet";
-our $fastacmd  = "$BINDIR/fastacmd";              # CC added to avoid failure on cluster
-our $hmmbuild  = "$BINDIR/hmmbuild";
-our $hmmconvert = "$BINDIR/hmmconvert";
-our $psiblastbin  = "$BINDIR/blastpgp";
+#my $SOFTDIR = '/homes/www-jpred/devel/jpred/bin';
+#my $platform_dir = "x86_64";
+#
+# my laptop test path
+my $SOFTDIR       = '/home/asherstnev/Projects/Jpred.project/jpred/branches/portable';
+my $platform_name = "x86_64";
+
+our $pairwise    = "$SOFTDIR/$platform_name/pairwise";
+our $oc          = "$SOFTDIR/$platform_name/oc";
+our $jnet        = "$SOFTDIR/$platform_name/jnet";
+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)
-our $analyze   = "$HOME/projects/Jnet/bin/snns/analyze";    # CC modified for new path (SNNS app)
-our $batchman  = "$HOME/projects/Jnet/bin/snns/batchman";   # CC modified for new path (SNNS app)
+our $ff_bignet = "$HOME/projects/Jnet/bin/snns/ff_bignet";    # CC modified for new path (SNNS app)
+our $analyze   = "$HOME/projects/Jnet/bin/snns/analyze";      # CC modified for new path (SNNS app)
+our $batchman  = "$HOME/projects/Jnet/bin/snns/batchman";     # CC modified for new path (SNNS app)
 our $sov       = "$HOME/projects/Jnet/bin/sov";
 
+sub setup_env {
+  my $newsoftdir       = shift;
+  my $newplatform_name = shift;
+
+  if ( defined $newsoftdir ) {
+    if ( -d $newsoftdir ) {
+      $SOFTDIR = $newsoftdir;
+    } else {
+      warn "setup_env: directory with Jpred software $newsoftdir does not exist. The default directory is used...\n";
+    }
+  }
+  if ( defined $newplatform_name ) {
+    $platform_name = $newplatform_name;
+  }
+
+  $oc          = "$SOFTDIR/$platform_name/oc";
+  $jnet        = "$SOFTDIR/$platform_name/jnet";
+  $fastacmd    = "$SOFTDIR/$platform_name/fastacmd";
+  $pairwise    = "$SOFTDIR/$platform_name/pairwise";
+  $hmmbuild    = "$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 {
+  if ( "linux" eq $^O or "Linux" eq $^O ) {
+    my $status = system "uname -m > .platform";
+    open my $PLH, "<", ".platform" or die "can't check platform information";
+    my $plt = <$PLH>;
+    close $PLH;
+    chop $plt;
+    $platform_name = "i686" if ( $plt =~ /i[3-6]86/ );
+  } elsif ( "MSWin32" eq $^O ) {
+    $platform_name = "win";
+  } else {
+    warn "check_OS: unknown platform, I'll try to use x86_64 binaries....";
+  }
+
+  $oc          = "$SOFTDIR/$platform_name/oc";
+  $jnet        = "$SOFTDIR/$platform_name/jnet";
+  $fastacmd    = "$SOFTDIR/$platform_name/fastacmd";
+  $pairwise    = "$SOFTDIR/$platform_name/pairwise";
+  $hmmbuild    = "$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;
+}
 
 =head1 AUTOMATED CHANGES
 
@@ -46,11 +128,4 @@ Currently the paths are altered on the basis of per host rules.
 
 =cut
 
-#my $host = Sys::Hostname::hostname();
-#if (grep { $host =~ $_ } qr/^(anshar|kinshar)/o, qr/^cluster-64-/o) {
-#      for my $temp (@EXPORT_OK) {
-#              eval "$temp =~ s#$HOME\/tmp#$HOME#g";
-#      }
-#}
-
 1;